http://journals.iucr.org/f/journalhomepage.html Acta Crystallographica Section F Structural Biology and Crystallization Communications aims to provide a home for communications on the crystallization and structure determination of biological macromolecules. It will commence publication in January 2005 and will include three categories of publication: Structural genomics communications, Protein structure communications, Crystallization communications. Articles will be available online when ready, making publication as fast as possible, and will include unlimited free colour illustrations, movies and other enhancements. The editorial process will be completely electronic with respect to deposition, submission, refereeing and publication. en-gb Copyright (c) 2008 International Union of Crystallography International Union of Crystallography International Union of Crystallography http://journals.iucr.org urn:issn:1744-3091 Acta Crystallographica Section F Structural Biology and Crystallization Communications aims to provide a home for communications on the crystallization and structure determination of biological macromolecules. It will commence publication in January 2005 and will include three categories of publication: Structural genomics communications, Protein structure communications, Crystallization communications. Articles will be available online when ready, making publication as fast as possible, and will include unlimited free colour illustrations, movies and other enhancements. The editorial process will be completely electronic with respect to deposition, submission, refereeing and publication. text/html Open access article in Acta Crystallographica Section F Structural Biology and Crystallization Communications text monthly 1 2002-01-01T00:00+00:00 med@iucr.org Acta Crystallographica Section F Structural Biology and Crystallization Communications Copyright (c) 2008 International Union of Crystallography urn:issn:1744-3091 http://journals.iucr.org/logos/rss10f.gif http://journals.iucr.org/f/journalhomepage.html Still image http://scripts.iucr.org/cgi-bin/paper?rp9017 A correction is made to the list of authors for Ito et al. [Acta Cryst. (2008). F64, 531–532]. Copyright (c) 2008 International Union of Crystallography urn:issn:1744-3091 Ito, L. Hidaka, Y. Okumura, M. Konishi, H. Adermann, K. Yamaguchi, H. 2008-08-01 doi:10.1107/S1744309108021477 International Union of Crystallography A corrigendum to the article by Ito et al. [Acta Cryst. (2008). F64, 531–532]. en PROUROGUANYLIN; PRECURSOR PROTEINS; PEPTIDE HORMONES; CORRIGENDUM A correction is made to the list of authors for Ito et al. [Acta Cryst. (2008). F64, 531–532]. text/html Crystallization and preliminary X-ray structural studies of human prouroguanylin. Corrigendum text 8 64 2008-08-01 Acta Crystallographica Section F: Structural Biology and Crystallization Communications Copyright (c) 2008 International Union of Crystallography addenda and errata 771 771 http://scripts.iucr.org/cgi-bin/paper?bw9226 A correction is made to the name one of the authors of Lafaye et al. [Acta Cryst. (2008). F64, 111–114]. Copyright (c) 2008 International Union of Crystallography urn:issn:1744-3091 Lafaye, C. Iwema, T. Ferrer, J.-L. Kroll, J.S. Griat, M. Serre, L. 2008-08-01 doi:10.1107/S1744309108020307 International Union of Crystallography A corrigendum to the paper by Lafaye et al. [Acta Cryst. (2008). F64, 111–114]. en NEISSERIA; VIRULENCE; OXIDOREDUCTASES; CORRIGENDUM A correction is made to the name one of the authors of Lafaye et al. [Acta Cryst. (2008). F64, 111–114]. text/html Preliminary crystallographic data of the three homologues of the thiol–disulfide oxidoreductase DsbA in Neisseria meningitidis. Corrigendum text 8 64 2008-08-01 Acta Crystallographica Section F: Structural Biology and Crystallization Communications Copyright (c) 2008 International Union of Crystallography addenda and errata 770 770 http://scripts.iucr.org/cgi-bin/paper?en5301 MotB is an essential component of the proton motive force-driven bacterial flagellar motor. It binds to the stress-bearing layer of peptidoglycan in the periplasm, anchoring the MotA/MotB stator unit to the cell wall. Proton flow through the channel formed by the transmembrane helices of MotA and MotB generates the turning force (torque) applied to the rotor. Crystals of recombinant Helicobacter pylori MotB have been obtained by the sitting-drop vapour-diffusion method using ammonium sulfate as a precipitant. These crystals belong to space group P41212 or its enantiomorph P43212, with unit-cell parameters a = 75.2, b = 75.2, c = 124.7 Å. The asymmetric unit appears to contain one subunit, corresponding to a packing density of 3.4 Å3 Da−1. The crystals diffract X-rays to at least 1.8 Å resolution on a synchrotron-radiation source. Copyright (c) 2008 International Union of Crystallography urn:issn:1744-3091 O'Neill, J. Roujeinikova, A. 2008-06-01 doi:10.1107/S1744309108012219 International Union of Crystallography The cloning, overexpression, purification, crystallization and preliminary X-ray diffraction analysis of H. pylori MotB, a peptidoglycan-binding component of the stator of the bacterial flagellar motor, are reported. en HELICOBACTER PYLORI; BACTERIAL FLAGELLAR MOTOR; PEPTIDOGLYCAN BINDING MotB is an essential component of the proton motive force-driven bacterial flagellar motor. It binds to the stress-bearing layer of peptidoglycan in the periplasm, anchoring the MotA/MotB stator unit to the cell wall. Proton flow through the channel formed by the transmembrane helices of MotA and MotB generates the turning force (torque) applied to the rotor. Crystals of recombinant Helicobacter pylori MotB have been obtained by the sitting-drop vapour-diffusion method using ammonium sulfate as a precipitant. These crystals belong to space group P41212 or its enantiomorph P43212, with unit-cell parameters a = 75.2, b = 75.2, c = 124.7 Å. The asymmetric unit appears to contain one subunit, corresponding to a packing density of 3.4 Å3 Da−1. The crystals diffract X-rays to at least 1.8 Å resolution on a synchrotron-radiation source. text/html Cloning, purification and crystallization of MotB, a stator component of the proton-driven bacterial flagellar motor text 6 64 2008-06-01 Acta Crystallographica Section F: Structural Biology and Crystallization Communications Copyright (c) 2008 International Union of Crystallography crystallization communications 561 563 http://scripts.iucr.org/cgi-bin/paper?hc5048 Hepatocyte nuclear factor 4α (HNF4α) is a member of the nuclear receptor superfamily that plays a central role in organ development and metabolic functions. Mutations on HNF4α cause maturity-onset diabetes of the young (MODY), a dominant monogenic cause of diabetes. In order to understand the molecular mechanism of promoter recognition and the molecular basis of disease-causing mutations, the recombinant HNF4α DNA-binding domain was prepared and used in a study of its binding properties and in crystallization with a 21-mer DNA fragment that contains the promoter element of another MODY gene, HNF1α. The HNF4α protein displays a cooperative and specific DNA-binding activity towards its target gene-recognition elements. Crystals of the complex diffract to 2.0 Å using a synchrotron-radiation source under cryogenic (100 K) conditions and belong to space group C2, with unit-cell parameters a = 121.63, b = 35.43, c = 70.99 Å, β = 119.36°. A molecular-replacement solution has been obtained and structure refinement is in progress. This structure and the binding studies will provide the groundwork for detailed functional and biochemical studies of the MODY mutants. Copyright (c) 2008 International Union of Crystallography urn:issn:1744-3091 Lu, P. Liu, J. Melikishvili, M. Fried, M.G. Chi, Y.-I. 2008-04-01 doi:10.1107/S1744309108007136 International Union of Crystallography Sample preparation, characterization, crystallization and preliminary X-ray analysis are reported for the HNF4α–DNA binary complex. en PROTEIN-DNA COMPLEX; GEL-SHIFT ASSAY; DIABETES; NUCLEAR RECEPTORS; ZINC-FINGER PROTEINS Hepatocyte nuclear factor 4α (HNF4α) is a member of the nuclear receptor superfamily that plays a central role in organ development and metabolic functions. Mutations on HNF4α cause maturity-onset diabetes of the young (MODY), a dominant monogenic cause of diabetes. In order to understand the molecular mechanism of promoter recognition and the molecular basis of disease-causing mutations, the recombinant HNF4α DNA-binding domain was prepared and used in a study of its binding properties and in crystallization with a 21-mer DNA fragment that contains the promoter element of another MODY gene, HNF1α. The HNF4α protein displays a cooperative and specific DNA-binding activity towards its target gene-recognition elements. Crystals of the complex diffract to 2.0 Å using a synchrotron-radiation source under cryogenic (100 K) conditions and belong to space group C2, with unit-cell parameters a = 121.63, b = 35.43, c = 70.99 Å, β = 119.36°. A molecular-replacement solution has been obtained and structure refinement is in progress. This structure and the binding studies will provide the groundwork for detailed functional and biochemical studies of the MODY mutants. text/html Crystallization of hepatocyte nuclear factor 4α (HNF4α) in complex with the HNF1α promoter element text 4 64 2008-04-01 Acta Crystallographica Section F: Structural Biology and Crystallization Communications Copyright (c) 2008 International Union of Crystallography crystallization communications 313 317 http://scripts.iucr.org/cgi-bin/paper?pu5213 The C-terminal domain of MotB (MotB-C) contains a putative peptidoglycan-binding motif and is believed to anchor the MotA/MotB stator unit of the bacterial flagellar motor to the cell wall. Crystals of Helicobacter pylori MotB-C (138 amino-acid residues) were obtained by the hanging-drop vapour-diffusion method using polyethylene glycol as a precipitant. These crystals belong to space group P21, with unit-cell parameters a = 50.8, b = 89.5, c = 66.3 Å, β = 112.5°. The crystals diffract X-rays to at least 1.6 Å resolution using a synchrotron-radiation source. Self-rotation function and Matthews coefficient calculations suggest that the asymmetric unit contains one tetramer with 222 point-group symmetry. The anomalous difference Patterson maps calculated for an ytterbium-derivative crystal using diffraction data at a wavelength of 1.38 Å showed significant peaks on the v = 1/2 Harker section, suggesting that ab initio phase information could be derived from the MAD data. Copyright (c) 2008 International Union of Crystallography urn:issn:1744-3091 Roujeinikova, A. 2008-04-01 doi:10.1107/S1744309108005277 International Union of Crystallography The cloning, overexpression, purification, crystallization and preliminary X-ray diffraction analysis of a putative peptidoglycan-binding domain of H. pylori MotB, a stator component of the bacterial flagellar motor, are reported. en HELICOBACTER PYLORI; BACTERIAL FLAGELLAR MOTOR; PEPTIDOGLYCAN BINDING The C-terminal domain of MotB (MotB-C) contains a putative peptidoglycan-binding motif and is believed to anchor the MotA/MotB stator unit of the bacterial flagellar motor to the cell wall. Crystals of Helicobacter pylori MotB-C (138 amino-acid residues) were obtained by the hanging-drop vapour-diffusion method using polyethylene glycol as a precipitant. These crystals belong to space group P21, with unit-cell parameters a = 50.8, b = 89.5, c = 66.3 Å, β = 112.5°. The crystals diffract X-rays to at least 1.6 Å resolution using a synchrotron-radiation source. Self-rotation function and Matthews coefficient calculations suggest that the asymmetric unit contains one tetramer with 222 point-group symmetry. The anomalous difference Patterson maps calculated for an ytterbium-derivative crystal using diffraction data at a wavelength of 1.38 Å showed significant peaks on the v = 1/2 Harker section, suggesting that ab initio phase information could be derived from the MAD data. text/html Cloning, purification and preliminary X-ray analysis of the C-terminal domain of Helicobacter pylori MotB text 4 64 2008-04-01 Acta Crystallographica Section F: Structural Biology and Crystallization Communications Copyright (c) 2008 International Union of Crystallography crystallization communications 277 280 http://scripts.iucr.org/cgi-bin/paper?fw5161 ADP-ribosylation is a reversible and covalent post-translational modification in which the attachment of ADP-ribose is catalyzed by ADP-ribosyltransferases and the removal of ADP-ribose is catalyzed by ADP-ribosylhydrolases. ADP-ribosylhydrolase 3 from mouse, consisting of 347 amino-acid residues, has been cloned, purified and crystallized. The three-dimensional structure has been resolved at a resolution of 1.8 Å. The structure constitutes a compact all-α-­helical protein with two Mg2+ ions located in the active-site crevice. A structural comparison of mouse ADP-ribosylhydrolase 3 with its human orthologue shows a high degree of structural similarity. Furthermore, four prokaryotic proteins deposited in the PDB could be identified as being structurally related. Copyright (c) 2008 International Union of Crystallography urn:issn:1744-3091 Mueller-Dieckmann, C. Kernstock, S. Mueller-Dieckmann, J. Weiss, M.S. Koch-Nolte, F. 2008-03-01 doi:10.1107/S1744309108001413 International Union of Crystallography The crystal structure of ADP-ribosylhydrolase 3 from M. musculus has been determined and refined to a resolution of 1.8 Å. A detailed comparison with the human orthologue at the protein-sequence level as well as of the three-dimensional architecture is presented. en ADP-RIBOSYLHYDROLASE 3 ADP-ribosylation is a reversible and covalent post-translational modification in which the attachment of ADP-ribose is catalyzed by ADP-ribosyltransferases and the removal of ADP-ribose is catalyzed by ADP-ribosylhydrolases. ADP-ribosylhydrolase 3 from mouse, consisting of 347 amino-acid residues, has been cloned, purified and crystallized. The three-dimensional structure has been resolved at a resolution of 1.8 Å. The structure constitutes a compact all-α-­helical protein with two Mg2+ ions located in the active-site crevice. A structural comparison of mouse ADP-ribosylhydrolase 3 with its human orthologue shows a high degree of structural similarity. Furthermore, four prokaryotic proteins deposited in the PDB could be identified as being structurally related. text/html Structure of mouse ADP-ribosylhydrolase 3 (mARH3) text 3 64 2008-03-01 Acta Crystallographica Section F: Structural Biology and Crystallization Communications Copyright (c) 2008 International Union of Crystallography protein structure communications 156 162 http://scripts.iucr.org/cgi-bin/paper?en5276 Tuberculosis is a major cause of death worldwide. Understanding of the pathogenicity of Mycobacterium tuberculosis has been advanced by gene analysis and has led to the identification of genes that are important for intracellular survival in macrophages. One of these genes encodes HsaD, a meta-cleavage product (MCP) hydrolase that catalyzes the hydrolytic cleavage of a carbon–carbon bond in cholesterol metabolism. This paper describes the production of HsaD as a recombinant protein and, following crystallization, the determination of its three-dimensional structure to 2.35 Å resolution by X-ray crystallography at the Diamond Light Source in Oxfordshire, England. To the authors' knowledge, this study constitutes the first report of a structure determined at the new synchrotron facility. The volume of the active-site cleft of the HsaD enzyme is more than double the corresponding active-site volumes of related MCP hydrolases involved in the catabolism of aromatic compounds, consistent with the specificity of HsaD for steroids such as cholesterol. Knowledge of the structure of the enzyme facilitates the design of inhibitors. Copyright (c) 2008 International Union of Crystallography urn:issn:1744-3091 Lack, N. Lowe, E.D. Liu, J. Eltis, L.D. Noble, M.E.M. Sim, E. Westwood, I.M. 2008-01-01 doi:10.1107/S1744309107065931 International Union of Crystallography The structure of HsaD, a carbon–carbon bond serine hydrolase involved in steroid catabolism that is critical for the survival of M. tuberculosis inside human macrophages, has been solved by X-ray crystallography. Data were collected at the Diamond Light Source in Oxfordshire, England: this paper describes one of the first structures determined at the new synchrotron. en HSAD; MCP HYDROLASES; C-C BOND HYDROLASES; CHOLESTEROL; TUBERCULOSIS; DIAMOND Tuberculosis is a major cause of death worldwide. Understanding of the pathogenicity of Mycobacterium tuberculosis has been advanced by gene analysis and has led to the identification of genes that are important for intracellular survival in macrophages. One of these genes encodes HsaD, a meta-cleavage product (MCP) hydrolase that catalyzes the hydrolytic cleavage of a carbon–carbon bond in cholesterol metabolism. This paper describes the production of HsaD as a recombinant protein and, following crystallization, the determination of its three-dimensional structure to 2.35 Å resolution by X-ray crystallography at the Diamond Light Source in Oxfordshire, England. To the authors' knowledge, this study constitutes the first report of a structure determined at the new synchrotron facility. The volume of the active-site cleft of the HsaD enzyme is more than double the corresponding active-site volumes of related MCP hydrolases involved in the catabolism of aromatic compounds, consistent with the specificity of HsaD for steroids such as cholesterol. Knowledge of the structure of the enzyme facilitates the design of inhibitors. text/html Structure of HsaD, a steroid-degrading hydrolase, from Mycobacterium tuberculosis text 1 64 2008-01-01 Acta Crystallographica Section F: Structural Biology and Crystallization Communications Copyright (c) 2008 International Union of Crystallography protein structure communications 2 7 http://scripts.iucr.org/cgi-bin/paper?hc9013 A correction is made to the Experimental methods section of the article by Kefala & Weiss [(2006), Acta Cryst. F62, 1116–1119]. Copyright (c) 2008 International Union of Crystallography urn:issn:1744-3091 Kefala, G. Weiss, M.S. 2008-01-01 doi:10.1107/S1744309107065566 International Union of Crystallography A correction is made to the article by Kefala & Weiss [(2006), Acta Cryst. F62, 1116–1119]. en DIHYDRODIPICOLINATE SYNTHASE; MYCOBACTERIUM TUBERCULOSIS; RV2753C A correction is made to the Experimental methods section of the article by Kefala & Weiss [(2006), Acta Cryst. F62, 1116–1119]. text/html Cloning, expression, purification, crystallization and preliminary X-ray diffraction analysis of DapA (Rv2753c) from Mycobacterium tuberculosis. Corrigendum text 1 64 2008-01-01 Acta Crystallographica Section F: Structural Biology and Crystallization Communications Copyright (c) 2008 International Union of Crystallography addenda and errata 62 62 http://scripts.iucr.org/cgi-bin/paper?pu9193 A correction is made to one of the affiliations of the authors and also to a table heading in Miyakawa et al. (2007), Acta Cryst. F63, 737–739. Copyright (c) 2007 International Union of Crystallography urn:issn:1744-3091 Miyakawa, T. Sawano, Y. Miyazono, K. Hatano, K. Tanokura, M. 2007-10-01 doi:10.1107/S1744309107044119 International Union of Crystallography An erratum to the paper by Miyakawa et al. [(2007), Acta Cryst. F63, 737–739]. en GINKBILOBIN-2; ANTIFUNGAL PROTEINS; GINKGO BILOBA; ERRATUM A correction is made to one of the affiliations of the authors and also to a table heading in Miyakawa et al. (2007), Acta Cryst. F63, 737–739. text/html Crystallization and preliminary X-ray analysis of ginkbilobin-2 from Ginkgo biloba seeds: a novel antifungal protein with homology to the extracellular domain of plant cysteine-rich receptor-like kinases. Erratum text 10 63 2007-10-01 Acta Crystallographica Section F: Structural Biology and Crystallization Communications Copyright (c) 2007 International Union of Crystallography addenda and errata 899 899 http://scripts.iucr.org/cgi-bin/paper?gj5024 Sialyltransferases transfer sialic acid from cytidine-5-monophospho-N-acetylneuraminic acid (CMP-NeuAc) to the nonreducing termini of the oligosaccharyl structures of various glycoproteins and glycolipids. The newly cloned α2,6-sialyltransferase from Photobacterium sp. JT-ISH-224 (from the Vibrionaceae family) is composed of two domains: an unknown N-terminal domain and a catalytic C-terminal domain which shares significant homology with the Pasteurella multocida multifunctional sialyltransferase. The putative mature form of JT-ISH-224 α2,6-sialyltransferase was overproduced in Escherichia coli, purified and crystallized using the hanging-drop vapour-diffusion method at 293 K. The crystal belonged to space group P3121 or P3221, with unit-cell parameters a = b = 90.29, c = 204.33 Å. X-ray diffraction data were collected to 2.5 Å resolution. Copyright (c) 2007 International Union of Crystallography urn:issn:1744-3091 Okino, N. Kakuta, Y. Kajiwara, H. Ichikawa, M. Takakura, Y. Ito, M. Yamamoto, T. 2007-08-01 doi:10.1107/S1744309107031363 International Union of Crystallography Crystallization of the α2,6-sialyltransferase from Photobacterium. en [ALPHA]2,6-SIALYLTRANSFERASE; PHOTOBACTERIUM SP. JT-ISH-224 Sialyltransferases transfer sialic acid from cytidine-5-monophospho-N-acetylneuraminic acid (CMP-NeuAc) to the nonreducing termini of the oligosaccharyl structures of various glycoproteins and glycolipids. The newly cloned α2,6-sialyltransferase from Photobacterium sp. JT-ISH-224 (from the Vibrionaceae family) is composed of two domains: an unknown N-terminal domain and a catalytic C-terminal domain which shares significant homology with the Pasteurella multocida multifunctional sialyltransferase. The putative mature form of JT-ISH-224 α2,6-sialyltransferase was overproduced in Escherichia coli, purified and crystallized using the hanging-drop vapour-diffusion method at 293 K. The crystal belonged to space group P3121 or P3221, with unit-cell parameters a = b = 90.29, c = 204.33 Å. X-ray diffraction data were collected to 2.5 Å resolution. text/html Purification, crystallization and preliminary crystallographic characterization of the α2,6-sialyltransferase from Photobacterium sp. JT-ISH-224 text 8 63 2007-08-01 Acta Crystallographica Section F: Structural Biology and Crystallization Communications Copyright (c) 2007 International Union of Crystallography crystallization communications 662 664 http://scripts.iucr.org/cgi-bin/paper?pu5183 The deoxyuridine triphosphate nucleotidohydrolase gene from Arabidopsis thaliana was expressed and the gene product was purified. Crystallization was performed by the hanging-drop vapour-diffusion method at 298 K using 2 M ammonium sulfate as the precipitant. X-ray diffraction data were collected to 2.2 Å resolution using Cu Kα radiation. The crystal belongs to the orthorhombic space group P212121, with unit-cell parameters a = 69.90, b = 70.86 Å, c = 75.55 Å. Assuming the presence of a trimer in the asymmetric unit, the solvent content was 30%, with a VM of 1.8 Å3 Da−1. Copyright (c) 2007 International Union of Crystallography urn:issn:1744-3091 Bajaj, M. Moriyama, H. 2007-05-01 doi:10.1107/S1744309107016004 International Union of Crystallography The first crystallization of deoxyuridine triphosphate nucleotidohydrolase from plant, Arabidopsis thaliana, has been performed. An additive, taurine, was effective in producing the single crystal. en DEOXYURIDINE TRIPHOSPHATE NUCLEOTIDOHYDROLASE; ARABIDOPSIS THALIANA The deoxyuridine triphosphate nucleotidohydrolase gene from Arabidopsis thaliana was expressed and the gene product was purified. Crystallization was performed by the hanging-drop vapour-diffusion method at 298 K using 2 M ammonium sulfate as the precipitant. X-ray diffraction data were collected to 2.2 Å resolution using Cu Kα radiation. The crystal belongs to the orthorhombic space group P212121, with unit-cell parameters a = 69.90, b = 70.86 Å, c = 75.55 Å. Assuming the presence of a trimer in the asymmetric unit, the solvent content was 30%, with a VM of 1.8 Å3 Da−1. text/html Purification, crystallization and preliminary crystallographic analysis of deoxyuridine triphosphate nucleotidohydrolase from Arabidopsis thaliana text 5 63 2007-05-01 Acta Crystallographica Section F: Structural Biology and Crystallization Communications Copyright (c) 2007 International Union of Crystallography crystallization communications 409 411 http://scripts.iucr.org/cgi-bin/paper?en5228 l-2-Keto-3-deoxyarabonate (l-KDA) dehydratase is a novel member of the dihydrodipicolinate synthase (DHDPS)/N-acetylneuraminate lyase (NAL) protein family and catalyzes the hydration of l-KDA to α-ketoglutaric semialdehyde. l-KDA dehydratase was overexpressed, purified and crystallized at 291 K using the hanging-drop vapour-diffusion method. The crystal diffracts to 2.0 Å resolution using synchrotron radiation and belongs to the trigonal space group P3121 or its enantiomorph P3221, with unit-cell parameters a = b = 78.91, c = 207.71 Å. Copyright (c) 2007 International Union of Crystallography urn:issn:1744-3091 Shimada, N. Mikami, B. Watanabe, S. Makino, K. 2007-05-01 doi:10.1107/S1744309107015102 International Union of Crystallography l-2-Keto-3-deoxyarabonate dehydratase was overexpressed, purified and crystallized at 291 K using the hanging-drop vapour-diffusion method. en L-2-KETO-3-DEOXYARABONATE DEHYDRATASE; DIHYDRODIPICOLINATE SYNTHASE/N-ACETYLNEURAMINATE LYASE PROTEIN FAMILY l-2-Keto-3-deoxyarabonate (l-KDA) dehydratase is a novel member of the dihydrodipicolinate synthase (DHDPS)/N-acetylneuraminate lyase (NAL) protein family and catalyzes the hydration of l-KDA to α-ketoglutaric semialdehyde. l-KDA dehydratase was overexpressed, purified and crystallized at 291 K using the hanging-drop vapour-diffusion method. The crystal diffracts to 2.0 Å resolution using synchrotron radiation and belongs to the trigonal space group P3121 or its enantiomorph P3221, with unit-cell parameters a = b = 78.91, c = 207.71 Å. text/html Preliminary crystallographic analysis of l-2-keto-3-deoxyarabonate dehydratase, an enzyme involved in an alternative bacterial pathway of l-­arabinose metabolism text 5 63 2007-05-01 Acta Crystallographica Section F: Structural Biology and Crystallization Communications Copyright (c) 2007 International Union of Crystallography crystallization communications 393 395 http://scripts.iucr.org/cgi-bin/paper?hc5021 1,3-Propanediol dehydrogenase (1,3-PD-DH), encoded by the dhaT gene, is a key enzyme in the dissimilation process for converting glycerol to 1,3-propanediol in the human pathogen Klebsiella pneumoniae. Single colourless crystals were obtained from a recombinant preparation of 1,3-propanediol dehydrogenase overexpressed in Escherichia coli. The crystals belong to space group P21, with unit-cell parameters a = 91.9, b = 226.6, c = 232.6 Å, β = 92.9°. The crystals probably contain two decamers in the asymmetric unit, with a VM value of 3.07 Å3 Da−1 and an estimated solvent content of 59%. Diffraction data were collected to 2.7 Å resolution using synchrotron radiation at the ID14-4 beamline of the European Synchrotron Radiation Facility. Copyright (c) 2007 International Union of Crystallography urn:issn:1744-3091 Marçal, D. Rego, A.T. Fogg, M.J. Wilson, K.S. Carrondo, M.A. Enguita, F.J. 2007-03-01 doi:10.1107/S1744309107008834 International Union of Crystallography 1,3-Propanediol dehydrogenase from K. pneumoniae has been overexpressed in E. coli, purified and crystallized. Diffraction data have been collected to 2.7 Å resolution. en 1,3-PROPANEDIOL DEHYDROGENASE; KLEBSIELLA PNEUMONIAE; GLYCEROL METABOLISM; KES; OPPORTUNISTIC PATHOGENS 1,3-Propanediol dehydrogenase (1,3-PD-DH), encoded by the dhaT gene, is a key enzyme in the dissimilation process for converting glycerol to 1,3-propanediol in the human pathogen Klebsiella pneumoniae. Single colourless crystals were obtained from a recombinant preparation of 1,3-propanediol dehydrogenase overexpressed in Escherichia coli. The crystals belong to space group P21, with unit-cell parameters a = 91.9, b = 226.6, c = 232.6 Å, β = 92.9°. The crystals probably contain two decamers in the asymmetric unit, with a VM value of 3.07 Å3 Da−1 and an estimated solvent content of 59%. Diffraction data were collected to 2.7 Å resolution using synchrotron radiation at the ID14-4 beamline of the European Synchrotron Radiation Facility. text/html Crystallization and preliminary X-ray characterization of 1,3-propanediol dehydrogenase from the human pathogen Klebsiella pneumoniae text 3 63 2007-03-01 Acta Crystallographica Section F: Structural Biology and Crystallization Communications Copyright (c) 2007 International Union of Crystallography crystallization communications 249 251 http://scripts.iucr.org/cgi-bin/paper?pu5181 Crystals of recombinant NovP (subunit MW = 29 967 Da; 262 amino acids), an S-adenosyl-l-methionine-dependent O-methyltransferase from Streptomyces spheroides, were grown by vapour diffusion. The protein crystallized in space group P2, with unit-cell parameters a = 51.81, b = 46.04, c = 61.22 Å, β = 104.97°. Native data to a maximum resolution of 1.4 Å were collected from a single crystal at the synchrotron. NovP is involved in the biosynthesis of the aminocoumarin antibiotic novobiocin that targets the essential bacterial enzyme DNA gyrase. Copyright (c) 2007 International Union of Crystallography urn:issn:1744-3091 Stevenson, C.E.M. Freel Meyers, C.L. Walsh, C.T. Lawson, D.M. 2007-03-01 doi:10.1107/S1744309107008287 International Union of Crystallography Monoclinic crystals of NovP, an O-methyltransferase from S. spheroides, were obtained and native X-ray data to 1.4 Å resolution were recorded. en NOVP; O-METHYLTRANSFERASE; STREPTOMYCES; NOVOBIOCIN; ANTIBIOTIC BIOSYNTHESIS Crystals of recombinant NovP (subunit MW = 29 967 Da; 262 amino acids), an S-adenosyl-l-methionine-dependent O-methyltransferase from Streptomyces spheroides, were grown by vapour diffusion. The protein crystallized in space group P2, with unit-cell parameters a = 51.81, b = 46.04, c = 61.22 Å, β = 104.97°. Native data to a maximum resolution of 1.4 Å were collected from a single crystal at the synchrotron. NovP is involved in the biosynthesis of the aminocoumarin antibiotic novobiocin that targets the essential bacterial enzyme DNA gyrase. text/html Crystallization and preliminary X-ray analysis of the O-methyltransferase NovP from the novobiocin-biosynthetic cluster of Streptomyces spheroides text 3 63 2007-03-01 Acta Crystallographica Section F: Structural Biology and Crystallization Communications Copyright (c) 2007 International Union of Crystallography crystallization communications 236 238 http://scripts.iucr.org/cgi-bin/paper?bw5192 Crystals of recombinant AbsC (subunit MW = 18 313 Da; 158 amino acids), a novel regulator of antibiotic production from Streptomyces coelicolor, were grown by vapour diffusion. The protein crystallizes in space group P212121, with unit-cell parameters a = 43.53, b = 121.30, c = 143.75 Å. Native data to a resolution of 2.25 Å were recorded at station PX 14.1 (Daresbury) from a single crystal. Preliminary analysis of these data suggests that the asymmetric unit contains four copies of the AbsC monomer, giving an estimated solvent content of 47.0%. AbsC belongs to the MarR family of proteins that mediate ligand-responsive transcriptional control. Copyright (c) 2007 International Union of Crystallography urn:issn:1744-3091 Stevenson, C.E.M. Kock, H. Mootien, S. Davies, S.C. Bibb, M.J. Lawson, D.M. 2007-03-01 doi:10.1107/S1744309107007944 International Union of Crystallography A novel regulator of antibiotic production in S. coelicolor, AbsC, has been crystallized in space group P212121. X-ray data to 2.25 Å resolution were collected on station PX 14.1 at Daresbury. en ABSC; STREPTOMYCES; ANTIBIOTIC PRODUCTION; MARR HOMOLOGUE; TRANSCRIPTIONAL REGULATION Crystals of recombinant AbsC (subunit MW = 18 313 Da; 158 amino acids), a novel regulator of antibiotic production from Streptomyces coelicolor, were grown by vapour diffusion. The protein crystallizes in space group P212121, with unit-cell parameters a = 43.53, b = 121.30, c = 143.75 Å. Native data to a resolution of 2.25 Å were recorded at station PX 14.1 (Daresbury) from a single crystal. Preliminary analysis of these data suggests that the asymmetric unit contains four copies of the AbsC monomer, giving an estimated solvent content of 47.0%. AbsC belongs to the MarR family of proteins that mediate ligand-responsive transcriptional control. text/html Crystallization and preliminary X-ray analysis of AbsC, a novel regulator of antibiotic production in Streptomyces coelicolor text 3 63 2007-03-01 Acta Crystallographica Section F: Structural Biology and Crystallization Communications Copyright (c) 2007 International Union of Crystallography crystallization communications 233 235 http://scripts.iucr.org/cgi-bin/paper?gx5109 Bacillus anthracis is a spore-forming bacterium and the causative agent of the disease anthrax. The Oxford Protein Production Facility has been targeting proteins from B. anthracis in order to develop high-throughput technologies within the Structural Proteomics in Europe project. As part of this work, the structure of 5-formyltetrahydrofolate cyclo-ligase (BA4489) has been determined by X-ray crystallography to 1.6 Å resolution. The structure, solved in complex with magnesium-ion-bound ADP and phosphate, gives a detailed picture of the proposed catalytic mechanism of the enzyme. Chemical differences from other cyclo-ligase structures close to the active site that could be exploited to design specific inhibitors are also highlighted. Copyright (c) 2007 International Union of Crystallography urn:issn:1744-3091 Meier, C. Carter, L.G. Winter, G. Owens, R.J. Stuart, D.I. Esnouf, R.M. 2007-03-01 doi:10.1107/S1744309107007221 International Union of Crystallography The structure of 5-formyltetrahydrofolate cyclo-ligase from B. anthracis determined by X-ray crystallography at a resolution of 1.6 Å is described. en 5,10-METHENYLTETRAHYDROFOLATE SYNTHETASE; MTHFS Bacillus anthracis is a spore-forming bacterium and the causative agent of the disease anthrax. The Oxford Protein Production Facility has been targeting proteins from B. anthracis in order to develop high-throughput technologies within the Structural Proteomics in Europe project. As part of this work, the structure of 5-formyltetrahydrofolate cyclo-ligase (BA4489) has been determined by X-ray crystallography to 1.6 Å resolution. The structure, solved in complex with magnesium-ion-bound ADP and phosphate, gives a detailed picture of the proposed catalytic mechanism of the enzyme. Chemical differences from other cyclo-ligase structures close to the active site that could be exploited to design specific inhibitors are also highlighted. text/html Structure of 5-formyltetrahydrofolate cyclo-ligase from Bacillus anthracis (BA4489) text 3 63 2007-03-01 Acta Crystallographica Section F: Structural Biology and Crystallization Communications Copyright (c) 2007 International Union of Crystallography protein structure communications 168 172 http://scripts.iucr.org/cgi-bin/paper?hv5079 The X-ray crystal structure of a single-chain monellin protein (MNEI) has been determined at 1.15 Å resolution. The model was refined to convergence employing anisotropic displacement parameters and riding H atoms to produce a final model with Rwork and Rfree values of 0.132 and 0.162, respectively. The crystal contains a single MNEI protein in the asymmetric unit and unusually lacks the dimer interface observed in all previous crystal structures of monellin and its single-chain derivatives. The high resolution allowed a more detailed view of MNEI than previously possible, with 38 of the 96 residues modelled with alternative side-chain conformations, including four core residues Thr12, Cys41, Leu62 and Ile75. Four stably bound negative ions were also located, providing new insight into potential electrostatic interactions of MNEI with the largely negatively charged surface of the sweet taste receptor T1R2–T1R3. Copyright (c) 2007 International Union of Crystallography urn:issn:1744-3091 Hobbs, J.R. Munger, S.D. Conn, G.L. 2007-03-01 doi:10.1107/S1744309107005271 International Union of Crystallography The crystal structure of the sweet protein MNEI at 1.15 Å resolution reveals networks of alternate conformations and stably bound negative ions. en MONELLIN; SWEET PROTEIN; SWEET TASTE; T1R2-T1R3 RECEPTOR The X-ray crystal structure of a single-chain monellin protein (MNEI) has been determined at 1.15 Å resolution. The model was refined to convergence employing anisotropic displacement parameters and riding H atoms to produce a final model with Rwork and Rfree values of 0.132 and 0.162, respectively. The crystal contains a single MNEI protein in the asymmetric unit and unusually lacks the dimer interface observed in all previous crystal structures of monellin and its single-chain derivatives. The high resolution allowed a more detailed view of MNEI than previously possible, with 38 of the 96 residues modelled with alternative side-chain conformations, including four core residues Thr12, Cys41, Leu62 and Ile75. Four stably bound negative ions were also located, providing new insight into potential electrostatic interactions of MNEI with the largely negatively charged surface of the sweet taste receptor T1R2–T1R3. text/html Monellin (MNEI) at 1.15 Å resolution text 3 63 2007-03-01 Acta Crystallographica Section F: Structural Biology and Crystallization Communications Copyright (c) 2007 International Union of Crystallography protein structure communications 162 167 http://scripts.iucr.org/cgi-bin/paper?be5077 Crystals of a single-point mutant (T109S) of Escherichia coli dihydroorotase (DHOase) with diminished activity grown in the presence of l-dihydroorotate (l-DHO) are tetragonal, with a monomer in the asymmetric unit. These crystals are extremely unstable and disintegrate shortly after formation, which is followed by the growth of orthorhombic crystals from the remnants of the tetragonal crystals or at new nucleation sites. Orthorhombic crystals, for which a structure has previously been reported [Thoden et al. (2001), Biochemistry, 40, 6989–6997; Lee et al. (2005), J. Mol. Biol. 348, 523–533], contain a dimer of DHOase in the asymmetric unit; the active site of one monomer contains the substrate N-carbamyl-l-aspartate (l-CA-asp) and the active site of the other monomer contains the product of the reaction, l-DHO. In the subunit with l-­DHO in the active site, a surface loop (residues 105–115) is `open'. In the other subunit, with l-CA-asp in the active site, the loop folds inwards, forming specific hydrogen bonds from the loop to the l-CA-asp. The tetragonal crystal form can be stabilized by crystallization in the presence of the inhibitor 5-fluoroorotate (FOA), a product (l-DHO) mimic. Crystals of the complex of T109S DHOase with FOA are tetragonal, space group P41212, with unit-cell parameters a = b = 72.6, c = 176.1 Å. The structure has been refined to R and Rfree values of 0.218 and 0.257, despite severe anisotropy of the diffraction. In this structure, the flexible loops are both in the `open' conformation, which is consistent with FOA, like l-­DHO, binding at both sites. The behaviour of the T109S mutant crystals of DHOase in the presence of l-DHO is explained by initial binding of l-DHO to both subunits, followed by slow conversion to l-CA-asp, with consequent movement of the flexible loop and dissolution of the crystals. Orthorhombic crystals are then able to grow in the presence of l-DHO and l-CA-asp. Copyright (c) 2007 International Union of Crystallography urn:issn:1744-3091 Lee, M. Maher, M.J. Guss, J.M. 2007-03-01 doi:10.1107/S1744309107004009 International Union of Crystallography A single-point mutant (T109S) of E. coli dihydroorotase initially crystallizes so that the two monomers of the dimer are related by a crystallographic twofold axis. In the presence of substrate, conversion to the previously observed asymmetric dimer with substrate bound in one subunit and product in the other is observed. en DIHYDROOROTASE; CONFORMATIONAL CHANGE; LOOP MOVEMENT; CATALYTIC STATE; CRYSTAL CONTACTS; CRYSTAL INSTABILITY Crystals of a single-point mutant (T109S) of Escherichia coli dihydroorotase (DHOase) with diminished activity grown in the presence of l-dihydroorotate (l-DHO) are tetragonal, with a monomer in the asymmetric unit. These crystals are extremely unstable and disintegrate shortly after formation, which is followed by the growth of orthorhombic crystals from the remnants of the tetragonal crystals or at new nucleation sites. Orthorhombic crystals, for which a structure has previously been reported [Thoden et al. (2001), Biochemistry, 40, 6989–6997; Lee et al. (2005), J. Mol. Biol. 348, 523–533], contain a dimer of DHOase in the asymmetric unit; the active site of one monomer contains the substrate N-carbamyl-l-aspartate (l-CA-asp) and the active site of the other monomer contains the product of the reaction, l-DHO. In the subunit with l-­DHO in the active site, a surface loop (residues 105–115) is `open'. In the other subunit, with l-CA-asp in the active site, the loop folds inwards, forming specific hydrogen bonds from the loop to the l-CA-asp. The tetragonal crystal form can be stabilized by crystallization in the presence of the inhibitor 5-fluoroorotate (FOA), a product (l-DHO) mimic. Crystals of the complex of T109S DHOase with FOA are tetragonal, space group P41212, with unit-cell parameters a = b = 72.6, c = 176.1 Å. The structure has been refined to R and Rfree values of 0.218 and 0.257, despite severe anisotropy of the diffraction. In this structure, the flexible loops are both in the `open' conformation, which is consistent with FOA, like l-­DHO, binding at both sites. The behaviour of the T109S mutant crystals of DHOase in the presence of l-DHO is explained by initial binding of l-DHO to both subunits, followed by slow conversion to l-CA-asp, with consequent movement of the flexible loop and dissolution of the crystals. Orthorhombic crystals are then able to grow in the presence of l-DHO and l-CA-asp. text/html Structure of the T109S mutant of Escherichia coli dihydroorotase complexed with the inhibitor 5-­fluoroorotate: catalytic activity is reflected by the crystal form text 3 63 2007-03-01 Acta Crystallographica Section F: Structural Biology and Crystallization Communications Copyright (c) 2007 International Union of Crystallography protein structure communications 154 161 http://scripts.iucr.org/cgi-bin/paper?bo9002 A correction is made to the names of two of the authors in Mastrangelo et al. (2006), Acta Cryst. F62, 768–770. Copyright (c) 2007 International Union of Crystallography urn:issn:1744-3091 Mastrangelo, E. Bollati, M. Milani, M. De Lamballerie, X. Brisbarre, N. Dalle, K. Lantez, V. Egloff, M.-P. Coutard, B. Canard, B. Gould, E. Forrester, N. Bolognesi, M. 2007-03-01 doi:10.1107/S1744309107009098 International Union of Crystallography A corrigendum to the paper by Mastrangelo et al. (2006), Acta Cryst. F62, 768–770. en (NUCLEOSIDE-2'-O-)-METHYLTRANSFERASES; FLAVIVIRUSES; MEABAN VIRUS; YOKOSE VIRUS; CORRIGENDUM A correction is made to the names of two of the authors in Mastrangelo et al. (2006), Acta Cryst. F62, 768–770. text/html Preliminary characterization of (nucleoside-2′-O-)-methyltransferase crystals from Meaban and Yokose flaviviruses. Corrigendum text 3 63 2007-03-01 Acta Crystallographica Section F: Structural Biology and Crystallization Communications Copyright (c) 2007 International Union of Crystallography addenda and errata 252 252 http://scripts.iucr.org/cgi-bin/paper?hc5020 The enzyme ω-transaminase catalyses the conversion of chiral ω-amines to ketones. The recombinant enzyme from Chromobacterium violaceum has been purified to homogeneity. The enzyme was crystallized from PEG 4000 using the microbatch method. Data were collected to 1.7 Å resolution from a crystal belonging to the triclinic space group P1, with unit-cell parameters a = 58.9, b = 61.9, c = 63.9 Å, α = 71.9, β = 87.0, γ = 74.6°. Data were also collected to 1.95 Å from a second triclinic crystal form. The structure has been solved using the molecular-replacement method. Copyright (c) 2007 International Union of Crystallography urn:issn:1744-3091 Sayer, C. Isupov, M.N. Littlechild, J.A. 2007-02-01 doi:10.1107/S1744309107000863 International Union of Crystallography An ω-amino acid:pyruvate transaminase from C. violaceum has been purified and crystallized in two crystal forms. The structure has been solved using molecular replacement. en [OMEGA]-TRANSAMINASE; PYRIDOXAL 5'-PHOSPHATE The enzyme ω-transaminase catalyses the conversion of chiral ω-amines to ketones. The recombinant enzyme from Chromobacterium violaceum has been purified to homogeneity. The enzyme was crystallized from PEG 4000 using the microbatch method. Data were collected to 1.7 Å resolution from a crystal belonging to the triclinic space group P1, with unit-cell parameters a = 58.9, b = 61.9, c = 63.9 Å, α = 71.9, β = 87.0, γ = 74.6°. Data were also collected to 1.95 Å from a second triclinic crystal form. The structure has been solved using the molecular-replacement method. text/html Crystallization and preliminary X-ray diffraction analysis of ω-amino acid:pyruvate transaminase from Chromobacterium violaceum text 2 63 2007-02-01 Acta Crystallographica Section F: Structural Biology and Crystallization Communications Copyright (c) 2007 International Union of Crystallography crystallization communications 117 119 http://scripts.iucr.org/cgi-bin/paper?hc5023 The DnaD protein is an essential component of the chromosome-replication machinery of the Gram-positive bacterium Bacillus subtilis and is part of the primosomal cascade that ultimately loads the replicative ring helicase DnaC onto DNA. Moreover, DnaD is a global regulator of DNA architecture, as it forms higher order nucleoprotein structures in order to open supercoiled DNA. Here, the crystallization and preliminary X-ray diffraction analysis of the two domains of DnaD from B. subtilis are reported. Crystals of the N-terminal domain are trigonal, with either P3121 or P3221 space-group symmetry, and diffracted X-­rays to 2.0 Å resolution; crystals of the C-terminal domain are hexagonal, with space group P61 or P65, and diffracted X-rays to 2.9 Å resolution in-house. Determination of the structure of the DnaD domains will provide insight into how remodelling of the nucleoid is associated with priming of replication in the model Gram-positive organism B. subtilis. Copyright (c) 2007 International Union of Crystallography urn:issn:1744-3091 Schneider, S. Carneiro, M.J.V.M. Ioannou, C. Soultanas, P. Paoli, M. 2007-02-01 doi:10.1107/S1744309107000474 International Union of Crystallography Crystallization and preliminary X-ray diffraction analysis of the two domains of DnaD from B. subtilis is reported. en DNA REPLICATION; DNAD; BACILLUS SUBTILIS; PRIMOSOMAL CASCADE The DnaD protein is an essential component of the chromosome-replication machinery of the Gram-positive bacterium Bacillus subtilis and is part of the primosomal cascade that ultimately loads the replicative ring helicase DnaC onto DNA. Moreover, DnaD is a global regulator of DNA architecture, as it forms higher order nucleoprotein structures in order to open supercoiled DNA. Here, the crystallization and preliminary X-ray diffraction analysis of the two domains of DnaD from B. subtilis are reported. Crystals of the N-terminal domain are trigonal, with either P3121 or P3221 space-group symmetry, and diffracted X-­rays to 2.0 Å resolution; crystals of the C-terminal domain are hexagonal, with space group P61 or P65, and diffracted X-rays to 2.9 Å resolution in-house. Determination of the structure of the DnaD domains will provide insight into how remodelling of the nucleoid is associated with priming of replication in the model Gram-positive organism B. subtilis. text/html Crystallization and X-ray diffraction analysis of the DNA-remodelling protein DnaD from Bacillus subtilis text 2 63 2007-02-01 Acta Crystallographica Section F: Structural Biology and Crystallization Communications Copyright (c) 2007 International Union of Crystallography crystallization communications 110 113 http://scripts.iucr.org/cgi-bin/paper?bw9180 A correction is made to a statement in the article by Carr et al. (2006), Acta Cryst. F62, 1164–1167. Copyright (c) 2007 International Union of Crystallography urn:issn:1744-3091 Carr, S.B. Makris, G. Phillips, S.E.V. Thomas, C.D. 2007-01-01 doi:10.1107/S1744309106054650 International Union of Crystallography A corrigendum to the paper by Carr et al. (2006), Acta Cryst. F62, 1164–1167. en TOPOISOMERASE IV; DNA CLEAVAGE; QUINOLONE BINDING; TRANSLATIONAL NCS A correction is made to a statement in the article by Carr et al. (2006), Acta Cryst. F62, 1164–1167. text/html Crystallization and preliminary X-ray diffraction analysis of two N-terminal fragments of the DNA-cleavage domain of topoisomerase IV from Staphylococcus aureus. Corrigendum text 1 63 2007-01-01 Acta Crystallographica Section F: Structural Biology and Crystallization Communications Copyright (c) 2007 International Union of Crystallography addenda and errata 59 59 http://scripts.iucr.org/cgi-bin/paper?fw5110 YcdB is a periplasmic haem-containing protein from Escherichia coli that has a potential role in iron transport. It is currently the only reported haem-containing Tat-secreted substrate. Here, the overexpression, purification, crystallization and structure determination at 2.0 Å resolution are reported for the apo form of the protein. The apo-YcdB structure resembles those of members of the haem-dependent peroxidase family and thus confirms that YcdB is also a member of this family. Haem-soaking experiments with preformed apo-YcdB crystals have been optimized to successfully generate haem-containing YcdB crystals that diffract to 2.9 Å. Completion of model building and structure refinement are under way. Copyright (c) 2007 International Union of Crystallography urn:issn:1744-3091 Cartron, M.L. Mitchell, S.A. Woodhall, M.R. Andrews, S.C. Watson, K.A. 2007-01-01 doi:10.1107/S174430910604509X International Union of Crystallography The crystallization and structure determination of the apo form of a novel haem-containing Tat substrate, YcdB from E. coli, has been solved to 2.0 Å resolution. The preliminary structure shows similarity to other haem-dependent peroxidases, despite low sequence homology. en YCDN; YCDO; YCDB; FTR1P; TAT; IRON TRANSPORT; PEROXIDASES; DYP; ESCHERICHIA COLI YcdB is a periplasmic haem-containing protein from Escherichia coli that has a potential role in iron transport. It is currently the only reported haem-containing Tat-secreted substrate. Here, the overexpression, purification, crystallization and structure determination at 2.0 Å resolution are reported for the apo form of the protein. The apo-YcdB structure resembles those of members of the haem-dependent peroxidase family and thus confirms that YcdB is also a member of this family. Haem-soaking experiments with preformed apo-YcdB crystals have been optimized to successfully generate haem-containing YcdB crystals that diffract to 2.9 Å. Completion of model building and structure refinement are under way. text/html Preliminary X-ray diffraction analysis of YcdB from Escherichia coli: a novel haem-containing and Tat-­secreted periplasmic protein with a potential role in iron transport text 1 63 2007-01-01 Acta Crystallographica Section F: Structural Biology and Crystallization Communications Copyright (c) 2007 International Union of Crystallography crystallization communications 37 41 http://scripts.iucr.org/cgi-bin/paper?bw5180 DNA topoisomerase IV removes undesirable topological features from DNA molecules in order to help maintain chromosome stability. Two constructs of 56 and 59 kDa spanning the DNA-cleavage domain of the A subunit of topoisomerase IV from Staphylococcus aureus (termed GrlA56 and GrlA59) have been crystallized. Crystals were grown at 291 K using the sitting-drop vapour-diffusion technique with PEG 3350 as a precipitant. Preliminary X-­ray analysis revealed that GrlA56 crystals belong to space group P21, diffract to a resolution of 2.9 Å and possess unit-cell parameters a = 83.6, b = 171.5, c = 87.8 Å, β = 90.1°, while crystals of GrlA59 belong to space group P21212, with unit-cell parameters a = 41.5, b = 171.89, c = 87.9 Å. These crystals diffract to a resolution of 2.8 Å. This is the first report of the crystallization and preliminary X-ray analysis of the DNA-cleavage domain of a topoisomerase IV from a Gram-positive organism. Copyright (c) 2006 International Union of Crystallography urn:issn:1744-3091 Carr, S.B. Makris, G. Phillips, S.E.V. Thomas, C.D. 2006-11-01 doi:10.1107/S1744309106044150 International Union of Crystallography The crystallization and data collection of topoisomerase IV from S. aureus is described. Phasing by molecular replacement proved difficult owing to the presence of translational NCS and strategies used to overcome this are discussed. en TOPOISOMERASE IV; DNA CLEAVAGE; QUINOLONE BINDING; TRANSLATIONAL NCS DNA topoisomerase IV removes undesirable topological features from DNA molecules in order to help maintain chromosome stability. Two constructs of 56 and 59 kDa spanning the DNA-cleavage domain of the A subunit of topoisomerase IV from Staphylococcus aureus (termed GrlA56 and GrlA59) have been crystallized. Crystals were grown at 291 K using the sitting-drop vapour-diffusion technique with PEG 3350 as a precipitant. Preliminary X-­ray analysis revealed that GrlA56 crystals belong to space group P21, diffract to a resolution of 2.9 Å and possess unit-cell parameters a = 83.6, b = 171.5, c = 87.8 Å, β = 90.1°, while crystals of GrlA59 belong to space group P21212, with unit-cell parameters a = 41.5, b = 171.89, c = 87.9 Å. These crystals diffract to a resolution of 2.8 Å. This is the first report of the crystallization and preliminary X-ray analysis of the DNA-cleavage domain of a topoisomerase IV from a Gram-positive organism. text/html Crystallization and preliminary X-ray diffraction analysis of two N-terminal fragments of the DNA-cleavage domain of topoisomerase IV from Staphylococcus aureus text 11 62 2006-11-01 Acta Crystallographica Section F: Structural Biology and Crystallization Communications Copyright (c) 2006 International Union of Crystallography crystallization communications 1164 1167 http://scripts.iucr.org/cgi-bin/paper?bw5178 Crystals of recombinant CloQ (subunit MW = 35 626 Da; 324 amino acids), an aromatic prenyltransferase from Streptomyces roseochromogenes, were grown by vapour diffusion. The protein crystallizes in space group I4122, with unit-cell parameters a = b = 135.19, c = 98.13 Å. Native data from a single crystal were recorded to a resolution of 2.2 Å in-house. Preliminary analysis of these data indicated that the asymmetric unit corresponds to a monomer, giving an estimated solvent content of 60.6%. CloQ is involved in the biosynthesis of the aminocoumarin antibiotic clorobiocin, which targets the essential bacterial enzyme DNA gyrase. Copyright (c) 2006 International Union of Crystallography urn:issn:1744-3091 Keller, S. Pojer, F. Heide, L. Lawson, D.M. 2006-11-01 doi:10.1107/S1744309106042527 International Union of Crystallography An aromatic prenyltransferase (CloQ) from S. roseochromogenes that is implicated in clorobiocin biosynthesis has been crystallized in space group I4122. X-ray data to 2.2 Å resolution were collected in-house. en CLOQ; PRENYLTRANSFERASES; STREPTOMYCES; CLOROBIOCIN; ANTIBIOTIC BIOSYNTHESIS Crystals of recombinant CloQ (subunit MW = 35 626 Da; 324 amino acids), an aromatic prenyltransferase from Streptomyces roseochromogenes, were grown by vapour diffusion. The protein crystallizes in space group I4122, with unit-cell parameters a = b = 135.19, c = 98.13 Å. Native data from a single crystal were recorded to a resolution of 2.2 Å in-house. Preliminary analysis of these data indicated that the asymmetric unit corresponds to a monomer, giving an estimated solvent content of 60.6%. CloQ is involved in the biosynthesis of the aminocoumarin antibiotic clorobiocin, which targets the essential bacterial enzyme DNA gyrase. text/html Crystallization and preliminary X-ray analysis of the aromatic prenyltransferase CloQ from the clorobiocin biosynthetic cluster of Streptomyces roseochromogenes text 11 62 2006-11-01 Acta Crystallographica Section F: Structural Biology and Crystallization Communications Copyright (c) 2006 International Union of Crystallography crystallization communications 1153 1155 http://scripts.iucr.org/cgi-bin/paper?sw5016 The structure of recombinant Aquifex aeolicus UDP-3-O-acyl-N-acetylglucosamine deacetylase (LpxC) in complex with UDP has been determined to a resolution of 2.2 Å. Previous studies have characterized the binding sites of the fatty-acid and sugar moieties of the substrate, UDP-(3-O-hydroxymyristoyl)-N-­acetylglucosamine, but not that of the nucleotide. The uracil-binding site is constructed from amino acids that are highly conserved across species. Hydrophobic associations with the Phe155 and Arg250 side chains in combination with hydrogen-bonding interactions with the main chain of Glu154 and the side chains of Tyr151 and Lys227 position the base. The phosphate and ribose groups are directed away from the active site and interact with Arg137, Lys156, Glu186 and Arg250. The orientation of the phosphate-ribose tail is not conducive to catalysis, perhaps owing to the position of an inhibitory Zn2+. However, based on the position of uracil revealed in this study and on the previously reported complex of LpxC with an inhibitor, a model is proposed for substrate binding. Copyright (c) 2006 International Union of Crystallography urn:issn:1744-3091 Buetow, L. Dawson, A. Hunter, W.N. 2006-11-01 doi:10.1107/S1744309106041893 International Union of Crystallography The structure of UDP-3-O-acyl-N-acetylglucosamine deacetylase (LpxC) in complex with UDP is reported. The complex allows for a description of how the enzyme recognizes and binds a nucleotide moiety and enables the construction of an LpxC-substrate model. en LIPID A; AQUIFEX AEOLICUS; LPXC The structure of recombinant Aquifex aeolicus UDP-3-O-acyl-N-acetylglucosamine deacetylase (LpxC) in complex with UDP has been determined to a resolution of 2.2 Å. Previous studies have characterized the binding sites of the fatty-acid and sugar moieties of the substrate, UDP-(3-O-hydroxymyristoyl)-N-­acetylglucosamine, but not that of the nucleotide. The uracil-binding site is constructed from amino acids that are highly conserved across species. Hydrophobic associations with the Phe155 and Arg250 side chains in combination with hydrogen-bonding interactions with the main chain of Glu154 and the side chains of Tyr151 and Lys227 position the base. The phosphate and ribose groups are directed away from the active site and interact with Arg137, Lys156, Glu186 and Arg250. The orientation of the phosphate-ribose tail is not conducive to catalysis, perhaps owing to the position of an inhibitory Zn2+. However, based on the position of uracil revealed in this study and on the previously reported complex of LpxC with an inhibitor, a model is proposed for substrate binding. text/html The nucleotide-binding site of Aquifex aeolicus LpxC text 11 62 2006-11-01 Acta Crystallographica Section F: Structural Biology and Crystallization Communications Copyright (c) 2006 International Union of Crystallography protein structure communications 1082 1086 http://scripts.iucr.org/cgi-bin/paper?en5202 Pyrrolnitrin is the active ingredient of drugs for the treatment of superficial fungal infections and was used as a lead structure for the development of fludioxonil. It is an effective agent for plant diseases caused by the fungal pathogen Rhizoctonia solani. Pyrrolnitrin is made in four steps, the second of which, catalyzed by PrnB, is a novel chemical rearrangement of 7-chlorotryptophan. PrnB was overproduced in Pseudomonas fluorescens (BL915) and well diffracting crystals were obtained of a triple cysteine-to-serine mutant by sitting-drop vapour diffusion. Crystals grown in the presence of l-7-chlorotryptophan, d-­tryptophan and l-tryptophan are reported. Data sets for each are reported with high-resolution limits of 2.0, 1.75 and 1.75 Å, respectively. Two crystals (PrnB in the presence of d-tryptophan and l-7-chlorotryptophan) belong to space group C2 with similar unit-cell parameters (a = 68.6, b = 79.5, c = 92.7 Å, α = γ = 90.0, β = 103.8°). Crystals grown in the presence of l-­tryptophan belong to space group C2221 and have unit-cell parameters a = 67.7, b = 80.1, c = 129.5 Å. All crystals contain a monomer in the asymmetric unit. Copyright (c) 2006 International Union of Crystallography urn:issn:1744-3091 De Laurentis, W. Leang, K. Hahn, K. Podemski, B. Adam, A. Kroschwald, S. Carter, L.G. van Pee, K.-H. Naismith, J.H. 2006-11-01 doi:10.1107/S1744309106041649 International Union of Crystallography Crystals of PrnB, the second enzyme in pyrrolnitrin biosynthesis are reported. en PRNB; PYRROLNITRIN BIOSYNTHESIS Pyrrolnitrin is the active ingredient of drugs for the treatment of superficial fungal infections and was used as a lead structure for the development of fludioxonil. It is an effective agent for plant diseases caused by the fungal pathogen Rhizoctonia solani. Pyrrolnitrin is made in four steps, the second of which, catalyzed by PrnB, is a novel chemical rearrangement of 7-chlorotryptophan. PrnB was overproduced in Pseudomonas fluorescens (BL915) and well diffracting crystals were obtained of a triple cysteine-to-serine mutant by sitting-drop vapour diffusion. Crystals grown in the presence of l-7-chlorotryptophan, d-­tryptophan and l-tryptophan are reported. Data sets for each are reported with high-resolution limits of 2.0, 1.75 and 1.75 Å, respectively. Two crystals (PrnB in the presence of d-tryptophan and l-7-chlorotryptophan) belong to space group C2 with similar unit-cell parameters (a = 68.6, b = 79.5, c = 92.7 Å, α = γ = 90.0, β = 103.8°). Crystals grown in the presence of l-­tryptophan belong to space group C2221 and have unit-cell parameters a = 67.7, b = 80.1, c = 129.5 Å. All crystals contain a monomer in the asymmetric unit. text/html Preliminary crystallographic characterization of PrnB, the second enzyme in the pyrrolnitrin biosynthetic pathway text 11 62 2006-11-01 Acta Crystallographica Section F: Structural Biology and Crystallization Communications Copyright (c) 2006 International Union of Crystallography crystallization communications 1134 1137 http://scripts.iucr.org/cgi-bin/paper?hc5016 Ranasmurfin, a previously uncharacterized ∼13 kDa blue protein found in the nests of the frog Polypedates leucomystax, has been purified and crystallized. The crystals are an intense blue colour and diffract to 1.51 Å with P21 symmetry and unit-cell parameters a = 40.9, b = 59.9, c = 45.0 Å, β = 93.3°. Self-rotation function analysis indicates the presence of a dimer in the asymmetric unit. Biochemical data suggest that the blue colour of the protein is related to dimer formation. Sequence data for the protein are incomplete, but thus far have identified no model for molecular replacement. A fluorescence scan shows a peak at 9.676 keV, indicating that the protein binds zinc and suggesting a route for structure solution. Copyright (c) 2006 International Union of Crystallography urn:issn:1744-3091 McMahon, S.A. Walsh, M.A. Ching, R.T.Y. Carter, L.G. Dorward, M. Johnson, K.A. Liu, H. Oke, M. Bloch, C. Kennedy, M.W. Latiff, A.A. Cooper, A. Taylor, G.L. White, M.F. Naismith, J.H. 2006-11-01 doi:10.1107/S1744309106040036 International Union of Crystallography A novel blue protein from frog nests has been crystallized. en RANASMURFIN Ranasmurfin, a previously uncharacterized ∼13 kDa blue protein found in the nests of the frog Polypedates leucomystax, has been purified and crystallized. The crystals are an intense blue colour and diffract to 1.51 Å with P21 symmetry and unit-cell parameters a = 40.9, b = 59.9, c = 45.0 Å, β = 93.3°. Self-rotation function analysis indicates the presence of a dimer in the asymmetric unit. Biochemical data suggest that the blue colour of the protein is related to dimer formation. Sequence data for the protein are incomplete, but thus far have identified no model for molecular replacement. A fluorescence scan shows a peak at 9.676 keV, indicating that the protein binds zinc and suggesting a route for structure solution. text/html Crystallization of Ranasmurfin, a blue-coloured protein from Polypedates leucomystax text 11 62 2006-11-01 Acta Crystallographica Section F: Structural Biology and Crystallization Communications Copyright (c) 2006 International Union of Crystallography crystallization communications 1124 1126 http://scripts.iucr.org/cgi-bin/paper?fw5102 Escherichia coli bacterioferritin was serendipitously crystallized in a novel cubic crystal form and its structure could be determined to 2.5 Å resolution despite a high degree of merohedral twinning. This is the first report of crystallographic data on `as-isolated' E. coli bacterioferritin. The ferroxidase active site contains positive difference density consistent with two metal ions that had co-purified with the protein. X-ray fluorescence studies suggest that the metal composition is different from that of previous structures and is a mix of zinc and native iron ions. The ferroxidase-centre configuration displays a similar flexibility as previously noted for other bacterioferritins. Copyright (c) 2006 International Union of Crystallography urn:issn:1744-3091 van Eerde, A. Wolterink-van Loo, S. van der Oost, J. Dijkstra, B.W. 2006-11-01 doi:10.1107/S1744309106039583 International Union of Crystallography E. coli bacterioferritin was crystallized in a novel crystal form from different conditions and the structure was solved. The crystals belonged to space group P213 and diffracted to a resolution of 2.5 Å. en ESCHERICHIA COLI BACTERIOFERRITIN; IRON STORAGE AND HOMEOSTASIS; FERROXIDASE; MEROHEDRAL TWINNING Escherichia coli bacterioferritin was serendipitously crystallized in a novel cubic crystal form and its structure could be determined to 2.5 Å resolution despite a high degree of merohedral twinning. This is the first report of crystallographic data on `as-isolated' E. coli bacterioferritin. The ferroxidase active site contains positive difference density consistent with two metal ions that had co-purified with the protein. X-ray fluorescence studies suggest that the metal composition is different from that of previous structures and is a mix of zinc and native iron ions. The ferroxidase-centre configuration displays a similar flexibility as previously noted for other bacterioferritins. text/html Fortuitous structure determination of `as-isolated' Escherichia coli bacterioferritin in a novel crystal form text 11 62 2006-11-01 Acta Crystallographica Section F: Structural Biology and Crystallization Communications Copyright (c) 2006 International Union of Crystallography protein structure communications 1061 1066 http://scripts.iucr.org/cgi-bin/paper?pu5149 Laccases are members of the blue multi-copper oxidase family that oxidize substrate molecules by accepting electrons at a mononuclear copper centre and transferring them to a trinuclear centre. Dioxygen binds to the trinuclear centre and, following the transfer of four electrons, is reduced to two molecules of water. Crystals of the laccase from Cerrena maxima have been obtained and X-­ray data were collected to 1.9 Å resolution using synchrotron radiation. A preliminary analysis shows that the enzyme has the typical laccase structure and several carbohydrate sites have been identified. The carbohydrate chains appear to be involved in stabilization of the intermolecular contacts in the crystal structure, thus promoting the formation of well ordered crystals of the enzyme. Here, the results of an X-ray crystallographic study on the laccase from the fungus Cerrena maxima are reported. Crystals that diffract well to a resolution of at least 1.9 Å (R factor = 18.953%; Rfree = 23.835; r.m.s.d. bond lengths, 0.06 Å; r.m.s.d. bond angles, 1.07°) have been obtained despite the presence of glycan moieties. The overall spatial organization of C. maxima laccase and the structure of its copper-containing active centre have been determined by the molecular-replacement method using the laccase from Trametes versicolor (Piontek et al., 2002) as a structural template. In addition, four glycan-binding sites were identified and the 1.9 Å X-ray data were used to determine the previously unknown primary structure of this protein. The identity (calculated from sequence alignment) between the C. maxima laccase and the T. versicolor laccase is about 87%. Tyr196 and Tyr372 show significant extra density at the ortho positions and this has been interpreted in terms of NO2 substituents. Copyright (c) 2006 International Union of Crystallography urn:issn:1744-3091 Lyashenko, A.V. Zhukhlistova, N.E. Gabdoulkhakov, A.G. Zhukova, Y.N. Voelter, W. Zaitsev, V.N. Bento, I. Stepanova, E.V. Kachalova, G.S. Koroleva, O.V. Cherkashyn, E.A. Tishkov, V.I. Lamzin, V.S. Schirwitz, K. Morgunova, E.Y. Betzel, C. Lindley, P.F. Mikhailov, A.M. 2006-10-01 doi:10.1107/S1744309106036578 International Union of Crystallography The crystallization and preliminary X-ray structure at 1.9 Å resolution of the fungal laccase from C. maxima are presented. en BLUE MULTI-COPPER ENZYMES; LACCASES; CERRENA MAXIMA Laccases are members of the blue multi-copper oxidase family that oxidize substrate molecules by accepting electrons at a mononuclear copper centre and transferring them to a trinuclear centre. Dioxygen binds to the trinuclear centre and, following the transfer of four electrons, is reduced to two molecules of water. Crystals of the laccase from Cerrena maxima have been obtained and X-­ray data were collected to 1.9 Å resolution using synchrotron radiation. A preliminary analysis shows that the enzyme has the typical laccase structure and several carbohydrate sites have been identified. The carbohydrate chains appear to be involved in stabilization of the intermolecular contacts in the crystal structure, thus promoting the formation of well ordered crystals of the enzyme. Here, the results of an X-ray crystallographic study on the laccase from the fungus Cerrena maxima are reported. Crystals that diffract well to a resolution of at least 1.9 Å (R factor = 18.953%; Rfree = 23.835; r.m.s.d. bond lengths, 0.06 Å; r.m.s.d. bond angles, 1.07°) have been obtained despite the presence of glycan moieties. The overall spatial organization of C. maxima laccase and the structure of its copper-containing active centre have been determined by the molecular-replacement method using the laccase from Trametes versicolor (Piontek et al., 2002) as a structural template. In addition, four glycan-binding sites were identified and the 1.9 Å X-ray data were used to determine the previously unknown primary structure of this protein. The identity (calculated from sequence alignment) between the C. maxima laccase and the T. versicolor laccase is about 87%. Tyr196 and Tyr372 show significant extra density at the ortho positions and this has been interpreted in terms of NO2 substituents. text/html Purification, crystallization and preliminary X-ray study of the fungal laccase from Cerrena maxima text 10 62 2006-10-01 Acta Crystallographica Section F: Structural Biology and Crystallization Communications Copyright (c) 2006 International Union of Crystallography protein structure communications 954 957 http://scripts.iucr.org/cgi-bin/paper?hv5065 Nucleotide monophosphate kinases (NMPKs) are potential antimicrobial drug targets owing to their role in supplying DNA and RNA precursors. The present work reports the crystal structure of Staphylococcus aureus guanylate monophosphate kinase (SaGMK) at 1.9 Å resolution. The structure shows that unlike most GMKs SaGMK is dimeric, confirming the role of the extended C-­terminus in dimer formation as first observed for Escherichia coli GMK (EcGMK). One of the two SaGMK dimers within the crystal asymmetric unit has two monomers in different conformations: an open form with a bound sulfate ion (mimicking the β-phosphate of ATP) and a closed form with bound GMP and sulfate ion. GMP-induced domain movements in SaGMK can thus be defined by comparison of these conformational states. Like other GMKs, the binding of GMP firstly triggers a partial closure of the enzyme, diminishing the distance between the GMP-binding and ATP-binding sites. In addition, the closed structure shows the presence of a potassium ion in contact with the guanine ring of GMP. The potassium ion appears to form an integral part of the GMP-binding site, as the Tyr36 side chain has significantly moved to form a metal ion–ligand coordination involving the lone pair of the side-chain O atom. The potassium-binding site might also be exploited in the design of novel inhibitors. Copyright (c) 2006 International Union of Crystallography urn:issn:1744-3091 El Omari, K. Dhaliwal, B. Lockyer, M. Charles, I. Hawkins, A.R. Stammers, D.K. 2006-10-01 doi:10.1107/S174430910603613X International Union of Crystallography The crystal structure of S. aureus guanylate monophosphate kinase has been determined to 1.9 Å resolution, revealing both open and closed forms within the asymmetric unit. These structures may be of use in anti-bacterial drug design. en GUANYLATE MONOPHOSPHATE KINASE; NUCLEOTIDE MONOPHOSPHATE KINASES; ANTIMICROBIALS Nucleotide monophosphate kinases (NMPKs) are potential antimicrobial drug targets owing to their role in supplying DNA and RNA precursors. The present work reports the crystal structure of Staphylococcus aureus guanylate monophosphate kinase (SaGMK) at 1.9 Å resolution. The structure shows that unlike most GMKs SaGMK is dimeric, confirming the role of the extended C-­terminus in dimer formation as first observed for Escherichia coli GMK (EcGMK). One of the two SaGMK dimers within the crystal asymmetric unit has two monomers in different conformations: an open form with a bound sulfate ion (mimicking the β-phosphate of ATP) and a closed form with bound GMP and sulfate ion. GMP-induced domain movements in SaGMK can thus be defined by comparison of these conformational states. Like other GMKs, the binding of GMP firstly triggers a partial closure of the enzyme, diminishing the distance between the GMP-binding and ATP-binding sites. In addition, the closed structure shows the presence of a potassium ion in contact with the guanine ring of GMP. The potassium ion appears to form an integral part of the GMP-binding site, as the Tyr36 side chain has significantly moved to form a metal ion–ligand coordination involving the lone pair of the side-chain O atom. The potassium-binding site might also be exploited in the design of novel inhibitors. text/html Structure of Staphylococcus aureus guanylate monophosphate kinase text 10 62 2006-10-01 Acta Crystallographica Section F: Structural Biology and Crystallization Communications Copyright (c) 2006 International Union of Crystallography protein structure communications 949 953 http://scripts.iucr.org/cgi-bin/paper?bw5160 The gene encoding 2-oxo-hept-3-ene-1,7-dioic acid (OHED) hydratase (HpcG) was cloned into the high-expression plasmid pET26b and overexpressed in Escherichia coli BL21(DE3). The enzyme was purified in three steps to greater than 95% purity prior to crystallization. Crystals were obtained by the hanging-drop vapour-diffusion method at 277 K in a number of screening conditions. Crystals measuring up to 1.5 mm in their longest dimension were grown from solutions containing polyethylene glycol 20 000. The crystals belonged to space group P41212 or P43212, with unit-cell parameters a = 136, b = 136, c = 192 Å. A complete data set was collected to 2.1 Å from a single cryocooled crystal at 100 K using synchrotron radiation. Copyright (c) 2006 International Union of Crystallography urn:issn:1744-3091 Adachi, T. Izumi, A. Rea, D. Park, S.-Y. Tame, J.R.H. Roper, D.I. 2006-10-01 doi:10.1107/S1744309106035901 International Union of Crystallography The gene encoding HpcG from the homoprotocatechuate (4-hydroxyphenylacetic acid) degradative pathway of E. coli C has been cloned and expressed and the protein has been purified. Crystals obtained from the purified recombinant enzyme, belonging to a tetragonal space group, diffracted to a resolution of 2.1 Å. en HOMOPROTOCATECHUATE; 4-HYDROXYPHENYLACETIC ACID; HYDRATASES The gene encoding 2-oxo-hept-3-ene-1,7-dioic acid (OHED) hydratase (HpcG) was cloned into the high-expression plasmid pET26b and overexpressed in Escherichia coli BL21(DE3). The enzyme was purified in three steps to greater than 95% purity prior to crystallization. Crystals were obtained by the hanging-drop vapour-diffusion method at 277 K in a number of screening conditions. Crystals measuring up to 1.5 mm in their longest dimension were grown from solutions containing polyethylene glycol 20 000. The crystals belonged to space group P41212 or P43212, with unit-cell parameters a = 136, b = 136, c = 192 Å. A complete data set was collected to 2.1 Å from a single cryocooled crystal at 100 K using synchrotron radiation. text/html Expression, purification and crystallization of 2-­oxo-hept-4-ene-1,7-dioate hydratase (HpcG) from Escherichia coli C text 10 62 2006-10-01 Acta Crystallographica Section F: Structural Biology and Crystallization Communications Copyright (c) 2006 International Union of Crystallography crystallization communications 1010 1012 http://scripts.iucr.org/cgi-bin/paper?pu5150 Pyridoxal kinases (PdxK) are able to catalyse the phosphorylation of three vitamin B6 precursors, pyridoxal, pyridoxine and pyridoxamine, to their 5′-­phosphates and play an important role in the vitamin B6 salvage pathway. Recently, the thiD gene of Bacillus subtilis was found to encode an enzyme which has the activity expected of a pyridoxal kinase despite its previous assignment as an HMPP kinase owing to higher sequence similarity. As such, this enzyme would appear to represent a new class of `HMPP kinase-like' pyridoxal kinases. B. subtilis thiD has been cloned and the protein has been overexpressed in Escherichia coli, purified and subsequently crystallized in a binary complex with ADP and Mg2+. X-ray diffraction data have been collected from crystals to 2.8 Å resolution at 100 K. The crystals belong to a primitive tetragonal system, point group 422, and analysis of the systematic absences suggest that they belong to one of the enantiomorphic pair of space groups P41212 or P43212. Consideration of the space-group symmetry and unit-cell parameters (a = b = 102.9, c = 252.6 Å, α = β = γ = 90°) suggest that the crystals contain between three and six molecules in the asymmetric unit. A full structure determination is under way to provide insights into aspects of the enzyme mechanism and substrate specificity. Copyright (c) 2006 International Union of Crystallography urn:issn:1744-3091 Newman, J.A. Das, S.K. Sedelnikova, S.E. Rice, D.W. 2006-10-01 doi:10.1107/S1744309106035779 International Union of Crystallography A putative pyridoxal kinase from B. subtilis has been cloned, overexpressed, purified and crystallized and data have been collected to 2.8 Å resolution. en THID; PDXK; HMPP KINASE; PYRIDOXAL KINASE; RIBOKINASE SUPERFAMILY Pyridoxal kinases (PdxK) are able to catalyse the phosphorylation of three vitamin B6 precursors, pyridoxal, pyridoxine and pyridoxamine, to their 5′-­phosphates and play an important role in the vitamin B6 salvage pathway. Recently, the thiD gene of Bacillus subtilis was found to encode an enzyme which has the activity expected of a pyridoxal kinase despite its previous assignment as an HMPP kinase owing to higher sequence similarity. As such, this enzyme would appear to represent a new class of `HMPP kinase-like' pyridoxal kinases. B. subtilis thiD has been cloned and the protein has been overexpressed in Escherichia coli, purified and subsequently crystallized in a binary complex with ADP and Mg2+. X-ray diffraction data have been collected from crystals to 2.8 Å resolution at 100 K. The crystals belong to a primitive tetragonal system, point group 422, and analysis of the systematic absences suggest that they belong to one of the enantiomorphic pair of space groups P41212 or P43212. Consideration of the space-group symmetry and unit-cell parameters (a = b = 102.9, c = 252.6 Å, α = β = γ = 90°) suggest that the crystals contain between three and six molecules in the asymmetric unit. A full structure determination is under way to provide insights into aspects of the enzyme mechanism and substrate specificity. text/html Cloning, purification and preliminary crystallographic analysis of a putative pyridoxal kinase from Bacillus subtilis text 10 62 2006-10-01 Acta Crystallographica Section F: Structural Biology and Crystallization Communications Copyright (c) 2006 International Union of Crystallography crystallization communications 1006 1009 http://scripts.iucr.org/cgi-bin/paper?en5189 PCNA is a ring-shaped protein that encircles DNA, providing a platform for the association of a wide variety of DNA-processing enzymes that utilize the PCNA sliding clamp to maintain proximity to their DNA