http://journals.iucr.org/d/issues/2010/02/00/isscontsbdy.html Acta Crystallographica Section D: Biological Crystallography welcomes the submission of papers covering any aspect of structural biology with a particular emphasis on the structures of biological macromolecules and the methods used to determine them. Reports on new protein structures are particularly encouraged, as are papers on crystallographic binding studies, structural analysis of mutants and other structure-function studies. Refinements of previously known structures may be published if sufficient new information is presented. Papers on crystallographic methods should be oriented towards biological crystallography, and may include new approaches to any aspect of structure determination or analysis. Papers on the crystallization of biological molecules will be accepted providing that these focus on new methods or other features that are of general importance or applicability. en Copyright (c) 2010 International Union of Crystallography 2010-02-01 International Union of Crystallography International Union of Crystallography http://journals.iucr.org urn:issn:0907-4449 Acta Crystallographica Section D: Biological Crystallography welcomes the submission of papers covering any aspect of structural biology with a particular emphasis on the structures of biological macromolecules and the methods used to determine them. Reports on new protein structures are particularly encouraged, as are papers on crystallographic binding studies, structural analysis of mutants and other structure-function studies. Refinements of previously known structures may be published if sufficient new information is presented. Papers on crystallographic methods should be oriented towards biological crystallography, and may include new approaches to any aspect of structure determination or analysis. Papers on the crystallization of biological molecules will be accepted providing that these focus on new methods or other features that are of general importance or applicability. text/html Acta Crystallographica Section D: Biological Crystallography, Volume 66, Part 2, 2010 text monthly 1 2002-01-01T00:00+00:00 2 66 2010-02-01 Copyright (c) 2010 International Union of Crystallography Acta Crystallographica Section D: Biological Crystallography 115 urn:issn:0907-4449 med@iucr.org February 2010 2010-02-01 http://journals.iucr.org/logos/rss10d.gif http://journals.iucr.org/d/issues/2010/02/00/isscontsbdy.html Still image http://scripts.iucr.org/cgi-bin/paper?me0415 Copyright (c) 2010 International Union of Crystallography urn:issn:0907-4449 Baker, E.N. Dauter, Z. Einspahr, H. Weiss, M.S. 2010-01-22 doi:10.1107/S0907444910001332 International Union of Crystallography en Editorial text/html In defence of our science – validation now! text 2 66 2010-01-22 Copyright (c) 2010 International Union of Crystallography Acta Crystallographica Section D: Biological Crystallography editorial 115 115 http://scripts.iucr.org/cgi-bin/paper?be5133 Asymmetric diadenosine tetraphosphate (Ap4A) hydrolases degrade the metabolite Ap4A back into ATP and AMP. The three-dimensional crystal structure of Ap4A hydrolase (16 kDa) from Aquifex aeolicus has been determined in free and ATP-bound forms at 1.8 and 1.95 Å resolution, respectively. The overall three-dimensional crystal structure of the enzyme shows an αβα-sandwich architecture with a characteristic loop adjacent to the catalytic site of the protein molecule. The ATP molecule is bound in the primary active site and the adenine moiety of the nucleotide binds in a ring-stacking arrangement equivalent to that observed in the X-ray structure of Ap4A hydrolase from Caenorhabditis elegans. Binding of ATP in the active site induces local conformational changes which may have important implications in the mechanism of substrate recognition in this class of enzymes. Furthermore, two invariant water molecules have been identified and their possible structural and/or functional roles are discussed. In addition, modelling of the substrate molecule at the primary active site of the enzyme suggests a possible path for entry and/or exit of the substrate and/or product molecule. Copyright (c) 2010 International Union of Crystallography urn:issn:0907-4449 Jeyakanthan, J. Kanaujia, S.P. Nishida, Y. Nakagawa, N. Praveen, S. Shinkai, A. Kuramitsu, S. Yokoyama, S. Sekar, K. 2010-01-22 doi:10.1107/S0907444909047064 International Union of Crystallography Crystal structures of free and ATP-bound forms of Ap4A hydrolase from A. aeolicus have been determined at 1.8 and 1.95 Å resolution, respectively. The ATP-bound crystal structure shows binding of the product molecule at the primary active site and of the substrate molecule at a noncatalytic site near the N-terminal region of the enzyme. en Ap4A hydrolase ATP binding Aquifex aeolicus V5 Asymmetric diadenosine tetraphosphate (Ap4A) hydrolases degrade the metabolite Ap4A back into ATP and AMP. The three-dimensional crystal structure of Ap4A hydrolase (16 kDa) from Aquifex aeolicus has been determined in free and ATP-bound forms at 1.8 and 1.95 Å resolution, respectively. The overall three-dimensional crystal structure of the enzyme shows an αβα-sandwich architecture with a characteristic loop adjacent to the catalytic site of the protein molecule. The ATP molecule is bound in the primary active site and the adenine moiety of the nucleotide binds in a ring-stacking arrangement equivalent to that observed in the X-ray structure of Ap4A hydrolase from Caenorhabditis elegans. Binding of ATP in the active site induces local conformational changes which may have important implications in the mechanism of substrate recognition in this class of enzymes. Furthermore, two invariant water molecules have been identified and their possible structural and/or functional roles are discussed. In addition, modelling of the substrate molecule at the primary active site of the enzyme suggests a possible path for entry and/or exit of the substrate and/or product molecule. text/html Free and ATP-bound structures of Ap4A hydrolase from Aquifex aeolicus V5 text 2 66 2010-01-22 Copyright (c) 2010 International Union of Crystallography Acta Crystallographica Section D: Biological Crystallography research papers 116 124 http://scripts.iucr.org/cgi-bin/paper?dz5179 The usage and control of recent modifications of the program package XDS for the processing of rotation images are described in the context of previous versions. New features include automatic determination of spot size and reflecting range and recognition and assignment of crystal symmetry. Moreover, the limitations of earlier package versions on the number of correction/scaling factors and the representation of pixel contents have been removed. Large program parts have been restructured for parallel processing so that the quality and completeness of collected data can be assessed soon after measurement. Copyright (c) 2010 International Union of Crystallography urn:issn:0907-4449 Kabsch, W. 2010-01-22 doi:10.1107/S0907444909047337 International Union of Crystallography The paper describes the software package XDS for processing of single crystal diffraction data recorded by the rotation method. en XDS The usage and control of recent modifications of the program package XDS for the processing of rotation images are described in the context of previous versions. New features include automatic determination of spot size and reflecting range and recognition and assignment of crystal symmetry. Moreover, the limitations of earlier package versions on the number of correction/scaling factors and the representation of pixel contents have been removed. Large program parts have been restructured for parallel processing so that the quality and completeness of collected data can be assessed soon after measurement. text/html XDS text 2 66 2010-01-22 Copyright (c) 2010 International Union of Crystallography Acta Crystallographica Section D: Biological Crystallography research papers 125 132 http://scripts.iucr.org/cgi-bin/paper?dz5178 Important steps in the processing of rotation data are described that are common to most software packages. These programs differ in the details and in the methods implemented to carry out the tasks. Here, the working principles underlying the data-reduction package XDS are explained, including the new features of automatic determination of spot size and reflecting range, recognition and assignment of crystal symmetry and a highly efficient algorithm for the determination of correction/scaling factors. Copyright (c) 2010 International Union of Crystallography urn:issn:0907-4449 Kabsch, W. 2010-01-22 doi:10.1107/S0907444909047374 International Union of Crystallography The working principles of important steps in processing rotation data are described as employed by the program XDS. en XDS integration scaling space-group assignment post-refinement Important steps in the processing of rotation data are described that are common to most software packages. These programs differ in the details and in the methods implemented to carry out the tasks. Here, the working principles underlying the data-reduction package XDS are explained, including the new features of automatic determination of spot size and reflecting range, recognition and assignment of crystal symmetry and a highly efficient algorithm for the determination of correction/scaling factors. text/html Integration, scaling, space-group assignment and post-refinement text 2 66 2010-01-22 Copyright (c) 2010 International Union of Crystallography Acta Crystallographica Section D: Biological Crystallography research papers 133 144 http://scripts.iucr.org/cgi-bin/paper?mv5032 The MST family is a subclass of mammalian serine/threonine kinases that are related to the yeast sterile-20 protein and are implicated in regulating cell growth and transformation. The MST3 protein contains a 300-residue catalytic domain and a 130-residue regulatory domain, which can be cleaved by caspase and activated by autophosphorylation, promoting apoptosis. Here, five crystal structures of the catalytic domain of MST3 are presented, including a complex with ADP and manganese, a unique cofactor preferred by the enzyme, and a complex with adenine. Similar to other protein kinases, the catalytic domain of MST3 folds into two lobes: the smaller N lobe forms the nucleotide-binding site and the larger C lobe recognizes the polypeptide substrate. The bound ADP and Mn2+ ions are covered by a glycine-rich loop and held in place by Asn149 and Asp162. A different orientation was observed for the ligand in the MST3–adenine complex. In the activation loop, the side chain of Thr178 is phosphorylated and is sandwiched by Arg143 and Arg176. Comparison of this structure with other similar kinase structures shows a 180° rotation of the loop, leading to activation of the enzyme. The well defined protein–ligand interactions also provide useful information for the design of potent inhibitors. Copyright (c) 2010 International Union of Crystallography urn:issn:0907-4449 Ko, T.-P. Jeng, W.-Y. Liu, C.-I. Lai, M.-D. Wu, C.-L. Chang, W.-J. Shr, H.-L. Lu, T.-J. Wang, A.H.-J. 2010-01-22 doi:10.1107/S0907444909047507 International Union of Crystallography The structure of human apoptosis-related protein kinase MST3 in its active form was determined with various bound ligands including Mn-ADP. en signal transduction caspases apoptosis ligand interactions metal cofactors The MST family is a subclass of mammalian serine/threonine kinases that are related to the yeast sterile-20 protein and are implicated in regulating cell growth and transformation. The MST3 protein contains a 300-residue catalytic domain and a 130-residue regulatory domain, which can be cleaved by caspase and activated by autophosphorylation, promoting apoptosis. Here, five crystal structures of the catalytic domain of MST3 are presented, including a complex with ADP and manganese, a unique cofactor preferred by the enzyme, and a complex with adenine. Similar to other protein kinases, the catalytic domain of MST3 folds into two lobes: the smaller N lobe forms the nucleotide-binding site and the larger C lobe recognizes the polypeptide substrate. The bound ADP and Mn2+ ions are covered by a glycine-rich loop and held in place by Asn149 and Asp162. A different orientation was observed for the ligand in the MST3–adenine complex. In the activation loop, the side chain of Thr178 is phosphorylated and is sandwiched by Arg143 and Arg176. Comparison of this structure with other similar kinase structures shows a 180° rotation of the loop, leading to activation of the enzyme. The well defined protein–ligand interactions also provide useful information for the design of potent inhibitors. text/html Structures of human MST3 kinase in complex with adenine, ADP and Mn2+ text 2 66 2010-01-22 Copyright (c) 2010 International Union of Crystallography Acta Crystallographica Section D: Biological Crystallography research papers 145 154 http://scripts.iucr.org/cgi-bin/paper?hm5080 Purine nucleoside phosphorylase (PNP) catalyzes the reversible phosphorolysis of purine ribonucleosides to the corresponding free bases and ribose 1-phosphate. The crystal structure of grouper iridovirus PNP (givPNP), corresponding to the first PNP gene to be found in a virus, was determined at 2.4 Å resolution. The crystals belonged to space group R3, with unit-cell parameters a = 193.0, c = 105.6 Å, and contained four protomers per asymmetric unit. The overall structure of givPNP shows high similarity to mammalian PNPs, having an α/β structure with a nine-stranded mixed β-barrel flanked by a total of nine α-helices. The predicted phosphate-binding and ribose-binding sites are occupied by a phosphate ion and a Tris molecule, respectively. The geometrical arrangement and hydrogen-bonding patterns of the phosphate-binding site are similar to those found in the human and bovine PNP structures. The enzymatic activity assay of givPNP on various substrates revealed that givPNP can only accept 6-oxopurine nucleosides as substrates, which is also suggested by its amino-acid composition and active-site architecture. All these results suggest that givPNP is a homologue of mammalian PNPs in terms of amino-acid sequence, molecular mass, substrate specificity and overall structure, as well as in the composition of the active site. Copyright (c) 2010 International Union of Crystallography urn:issn:0907-4449 Kang, Y.-N. Zhang, Y. Allan, P.W. Parker, W.B. Ting, J.-W. Chang, C.-Y. Ealick, S.E. 2010-01-22 doi:10.1107/S0907444909048276 International Union of Crystallography The crystal structure of purine nucleoside phosphorylase from grouper iridovirus was solved at 2.38 Å resolution. en purine salvage phosphorolysis viral proteins Tris-binding site Purine nucleoside phosphorylase (PNP) catalyzes the reversible phosphorolysis of purine ribonucleosides to the corresponding free bases and ribose 1-phosphate. The crystal structure of grouper iridovirus PNP (givPNP), corresponding to the first PNP gene to be found in a virus, was determined at 2.4 Å resolution. The crystals belonged to space group R3, with unit-cell parameters a = 193.0, c = 105.6 Å, and contained four protomers per asymmetric unit. The overall structure of givPNP shows high similarity to mammalian PNPs, having an α/β structure with a nine-stranded mixed β-barrel flanked by a total of nine α-helices. The predicted phosphate-binding and ribose-binding sites are occupied by a phosphate ion and a Tris molecule, respectively. The geometrical arrangement and hydrogen-bonding patterns of the phosphate-binding site are similar to those found in the human and bovine PNP structures. The enzymatic activity assay of givPNP on various substrates revealed that givPNP can only accept 6-oxopurine nucleosides as substrates, which is also suggested by its amino-acid composition and active-site architecture. All these results suggest that givPNP is a homologue of mammalian PNPs in terms of amino-acid sequence, molecular mass, substrate specificity and overall structure, as well as in the composition of the active site. text/html Structure of grouper iridovirus purine nucleoside phosphorylase text 2 66 2010-01-22 Copyright (c) 2010 International Union of Crystallography Acta Crystallographica Section D: Biological Crystallography research papers 155 162 http://scripts.iucr.org/cgi-bin/paper?yt5020 HIV/SIV Nef mediates many cellular processes through interactions with various cytoplasmic and membrane-associated host proteins, including the signalling ζ subunit of the T-cell receptor (TCRζ). Here, the crystallization strategy, methods and refinement procedures used to solve the structures of the core domain of the SIVmac239 isolate of Nef (Nefcore) in complex with two different TCRζ fragments are described. The structure of SIVmac239 Nefcore bound to the longer TCRζ polypeptide (Leu51–Asp93) was determined to 3.7 Å resolution (Rwork = 28.7%) in the tetragonal space group P43212. The structure of SIVmac239 Nefcore in complex with the shorter TCRζ polypeptide (Ala63–Arg80) was determined to 2.05 Å resolution (Rwork = 17.0%), but only after the detection of nearly perfect pseudo-merohedral crystal twinning and proper assignment of the orthorhombic space group P212121. The reduction in crystal space-group symmetry induced by the truncated TCRζ polypeptide appears to be caused by the rearrangement of crystal-contact hydrogen-bonding networks and the substitution of crystallographic symmetry operations by similar noncrystallographic symmetry (NCS) operations. The combination of NCS rotations that were nearly parallel to the twin operation (k, h, −l) and a and b unit-cell parameters that were nearly identical predisposed the P212121 crystal form to pseudo-merohedral twinning. Copyright (c) 2010 International Union of Crystallography urn:issn:0907-4449 Kim, W.M. Sigalov, A.B. Stern, L.J. 2010-01-22 doi:10.1107/S090744490904880X International Union of Crystallography P212121 crystals of SIV Nef core domain bound to a peptide fragment of the T-cell receptor ζ subunit exhibited noncrystallographic symmetry and nearly perfect pseudo-merohedral twinning simulating tetragonal symmetry. For a different peptide fragment, nontwinned tetragonal crystals were observed but diffracted to lower resolution. The structure was determined after assignment of the top molecular-replacement solutions to various twin or NCS domains followed by refinement under the appropriate twin law. en pseudo-merohedral twinning noncrystallographic symmetry pseudosymmetry human immunodeficiency virus Nef T-cell receptor HIV/SIV Nef mediates many cellular processes through interactions with various cytoplasmic and membrane-associated host proteins, including the signalling ζ subunit of the T-cell receptor (TCRζ). Here, the crystallization strategy, methods and refinement procedures used to solve the structures of the core domain of the SIVmac239 isolate of Nef (Nefcore) in complex with two different TCRζ fragments are described. The structure of SIVmac239 Nefcore bound to the longer TCRζ polypeptide (Leu51–Asp93) was determined to 3.7 Å resolution (Rwork = 28.7%) in the tetragonal space group P43212. The structure of SIVmac239 Nefcore in complex with the shorter TCRζ polypeptide (Ala63–Arg80) was determined to 2.05 Å resolution (Rwork = 17.0%), but only after the detection of nearly perfect pseudo-merohedral crystal twinning and proper assignment of the orthorhombic space group P212121. The reduction in crystal space-group symmetry induced by the truncated TCRζ polypeptide appears to be caused by the rearrangement of crystal-contact hydrogen-bonding networks and the substitution of crystallographic symmetry operations by similar noncrystallographic symmetry (NCS) operations. The combination of NCS rotations that were nearly parallel to the twin operation (k, h, −l) and a and b unit-cell parameters that were nearly identical predisposed the P212121 crystal form to pseudo-merohedral twinning. text/html Pseudo-merohedral twinning and noncrystallographic symmetry in orthorhombic crystals of SIVmac239 Nef core domain bound to different-length TCRζ fragments text 2 66 2010-01-22 Copyright (c) 2010 International Union of Crystallography Acta Crystallographica Section D: Biological Crystallography research papers 163 175 http://scripts.iucr.org/cgi-bin/paper?dz5185 Endosialidase NF (endoNF) is a bacteriophage-derived endosialidase that specifically degrades α-2,8-linked polysialic acid. The structure of a new crystal form of endoNF in complex with sialic acid has been refined at 0.98 Å resolution. The 210 kDa homotrimeric multi-domain enzyme displays outstanding stability and resistance to SDS. Even at atomic resolution, only a minor fraction of side chains possess alternative conformations. However, multiple conformations of an active-site residue imply that it has an important catalytic function in the cleavage mechanism of polysialic acid. Copyright (c) 2010 International Union of Crystallography urn:issn:0907-4449 Schulz, E.C. Neumann, P. Gerardy-Schahn, R. Sheldrick, G.M. Ficner, R. 2010-01-22 doi:10.1107/S0907444909048720 International Union of Crystallography The 0.98 Å resolution crystal structure of the 210 kDa protein endosialidase NF in complex with sialic acid is presented in a new polymorphic form. en endosialidase NF polysialic acid atomic resolution Endosialidase NF (endoNF) is a bacteriophage-derived endosialidase that specifically degrades α-2,8-linked polysialic acid. The structure of a new crystal form of endoNF in complex with sialic acid has been refined at 0.98 Å resolution. The 210 kDa homotrimeric multi-domain enzyme displays outstanding stability and resistance to SDS. Even at atomic resolution, only a minor fraction of side chains possess alternative conformations. However, multiple conformations of an active-site residue imply that it has an important catalytic function in the cleavage mechanism of polysialic acid. text/html Structure analysis of endosialidase NF at 0.98 Å resolution text 2 66 2010-01-22 Copyright (c) 2010 International Union of Crystallography Acta Crystallographica Section D: Biological Crystallography research papers 176 180 http://scripts.iucr.org/cgi-bin/paper?hm5079 The polyamines putrescine, spermidine and spermine are ubiquitous aliphatic cations and are essential for cellular growth and differentiation. S-Adenosylmethionine decarboxylase (AdoMetDC) is a critical pyruvoyl-dependent enzyme in the polyamine-biosynthetic pathway. The crystal structures of AdoMetDC from humans and plants and of the AdoMetDC proenzyme from Thermotoga maritima have been obtained previously. Here, the crystal structures of activated T. maritima AdoMetDC (TmAdoMetDC) and of its complexes with S-adenosylmethionine methyl ester and 5′-deoxy-5′-dimethylthioadenosine are reported. The results demonstrate for the first time that TmAdoMetDC autoprocesses without the need for additional factors and that the enzyme contains two complete active sites, both of which use residues from both chains of the homodimer. The complexes provide insights into the substrate specificity and ligand binding of AdoMetDC in prokaryotes. The conservation of the ligand-binding mode and the active-site residues between human and T. maritima AdoMetDC provides insight into the evolution of AdoMetDC. Copyright (c) 2010 International Union of Crystallography urn:issn:0907-4449 Bale, S. Baba, K. McCloskey, D.E. Pegg, A.E. Ealick, S.E. 2010-01-22 doi:10.1107/S090744490904877X International Union of Crystallography The crystal structures of activated S-adenosylmethionine decarboxylase (AdoMetDC) from T. maritima and of its complexes with S-adenosylmethionine methyl ester and 5′-deoxy-5′-dimethylthioadenosine have been obtained. Comparison of the structures with that of human AdoMetDC provides insights into the substrate specificity, binding mode, autoprocessing and evolution of the enzyme. en protein evolution proenzymes pyruvoyl cofactor cation–π interactions The polyamines putrescine, spermidine and spermine are ubiquitous aliphatic cations and are essential for cellular growth and differentiation. S-Adenosylmethionine decarboxylase (AdoMetDC) is a critical pyruvoyl-dependent enzyme in the polyamine-biosynthetic pathway. The crystal structures of AdoMetDC from humans and plants and of the AdoMetDC proenzyme from Thermotoga maritima have been obtained previously. Here, the crystal structures of activated T. maritima AdoMetDC (TmAdoMetDC) and of its complexes with S-adenosylmethionine methyl ester and 5′-deoxy-5′-dimethylthioadenosine are reported. The results demonstrate for the first time that TmAdoMetDC autoprocesses without the need for additional factors and that the enzyme contains two complete active sites, both of which use residues from both chains of the homodimer. The complexes provide insights into the substrate specificity and ligand binding of AdoMetDC in prokaryotes. The conservation of the ligand-binding mode and the active-site residues between human and T. maritima AdoMetDC provides insight into the evolution of AdoMetDC. text/html Complexes of Thermotoga maritimaS-adenosylmethionine decarboxylase provide insights into substrate specificity text 2 66 2010-01-22 Copyright (c) 2010 International Union of Crystallography Acta Crystallographica Section D: Biological Crystallography research papers 181 189 http://scripts.iucr.org/cgi-bin/paper?be5135 The anaphylatoxin C5a is derived from the complement component C5 during activation of the complement cascade. It is an important component in the pathogenesis of a number of inflammatory diseases. NMR structures of human and porcine C5a have been reported; these revealed a four-helix bundle stabilized by three disulfide bonds. The crystal structure of human desArg-C5a has now been determined in two crystal forms. Surprisingly, the protein crystallizes as a dimer and each monomer in the dimer has a three-helix core instead of the four-helix bundle noted in the NMR structure determinations. Furthermore, the N-terminal helices of the two monomers occupy different positions relative to the three-helix core and are completely different from the NMR structures. The physiological significance of these structural differences is unknown. Copyright (c) 2010 International Union of Crystallography urn:issn:0907-4449 Cook, W.J. Galakatos, N. Boyar, W.C. Walter, R.L. Ealick, S.E. 2010-01-22 doi:10.1107/S0907444909049051 International Union of Crystallography The structure of human desArg-C5a has been determined using molecular replacement to 2.58 Å. The structure is a dimer, and the N-terminal helices in each monomer differ from each other and occupy completely different positions from the NMR structures. en complement factor 5 anaphylatoxins desArg-C5a The anaphylatoxin C5a is derived from the complement component C5 during activation of the complement cascade. It is an important component in the pathogenesis of a number of inflammatory diseases. NMR structures of human and porcine C5a have been reported; these revealed a four-helix bundle stabilized by three disulfide bonds. The crystal structure of human desArg-C5a has now been determined in two crystal forms. Surprisingly, the protein crystallizes as a dimer and each monomer in the dimer has a three-helix core instead of the four-helix bundle noted in the NMR structure determinations. Furthermore, the N-terminal helices of the two monomers occupy different positions relative to the three-helix core and are completely different from the NMR structures. The physiological significance of these structural differences is unknown. text/html Structure of human desArg-C5a text 2 66 2010-01-22 Copyright (c) 2010 International Union of Crystallography Acta Crystallographica Section D: Biological Crystallography research papers 190 197 http://scripts.iucr.org/cgi-bin/paper?be5130 Mouse 3(17)α-hydroxysteroid dehydrogenase (AKR1C21) is the only aldo–keto reductase that catalyzes the stereospecific reduction of 3- and 17-ketosteroids to the corresponding 3(17)α-hydroxysteroids. The Y224D mutation of AKR1C21 reduced the Km value for NADP(H) by up to 80-fold and completely reversed the 17α stereospecificity of the enzyme. The crystal structure of the Y224D mutant at 2.3 Å resolution revealed that the mutation resulted in a change in the conformation of the flexible loop B, including the V-shaped groove, which is a unique feature of the active-site architecture of wild-type AKR1C21 and is formed by the side chains of Tyr224 and Trp227. Furthermore, mutations (Y224F and Q222N) of residues involved in forming the safety belt for binding of the coenzyme showed similar alterations in kinetic constants for 3α-hydroxy/3-ketosteroids and 17-hydroxy/ketosteroids compared with the wild type. Copyright (c) 2010 International Union of Crystallography urn:issn:0907-4449 Dhagat, U. Endo, S. Mamiya, H. Hara, A. El-Kabbani, O. 2010-01-22 doi:10.1107/S0907444909051464 International Union of Crystallography The structure of the Y224D mutant of mouse 3(17)α-hydroxysteroid dehydrogenase revealed that the mutation resulted in a change in the conformation of the flexible loop B. This loop is a unique feature of the active-site architecture of the wild type and is formed by the side chains of Tyr224 and Trp227. en aldo–keto reductases hydroxysteroid dehydrogenases AKR1C21 Mouse 3(17)α-hydroxysteroid dehydrogenase (AKR1C21) is the only aldo–keto reductase that catalyzes the stereospecific reduction of 3- and 17-ketosteroids to the corresponding 3(17)α-hydroxysteroids. The Y224D mutation of AKR1C21 reduced the Km value for NADP(H) by up to 80-fold and completely reversed the 17α stereospecificity of the enzyme. The crystal structure of the Y224D mutant at 2.3 Å resolution revealed that the mutation resulted in a change in the conformation of the flexible loop B, including the V-shaped groove, which is a unique feature of the active-site architecture of wild-type AKR1C21 and is formed by the side chains of Tyr224 and Trp227. Furthermore, mutations (Y224F and Q222N) of residues involved in forming the safety belt for binding of the coenzyme showed similar alterations in kinetic constants for 3α-hydroxy/3-ketosteroids and 17-hydroxy/ketosteroids compared with the wild type. text/html Studies on a Tyr residue critical for the binding of coenzyme and substrate in mouse 3(17)α-hydroxysteroid dehydrogenase (AKR1C21): structure of the Y224D mutant enzyme text 2 66 2010-01-22 Copyright (c) 2010 International Union of Crystallography Acta Crystallographica Section D: Biological Crystallography research papers 198 204 http://scripts.iucr.org/cgi-bin/paper?hm5081 The enzyme aspartate semialdehyde dehydrogenase (ASADH) catalyzes a critical transformation that produces the first branch-point intermediate in an essential microbial amino-acid biosynthetic pathway. The first structure of an ASADH isolated from a fungal species (Candida albicans) has been determined as a complex with its pyridine nucleotide cofactor. This enzyme is a functional dimer, with a similar overall fold and domain organization to the structurally characterized bacterial ASADHs. However, there are differences in the secondary-structural elements and in cofactor binding that are likely to cause the lower catalytic efficiency of this fungal enzyme. Alterations in the dimer interface, through deletion of a helical subdomain and replacement of amino acids that participate in a hydrogen-bonding network, interrupt the intersubunit-communication channels required to support an alternating-site catalytic mechanism. The detailed functional information derived from this new structure will allow an assessment of ASADH as a possible target for antifungal drug development. Copyright (c) 2010 International Union of Crystallography urn:issn:0907-4449 Arachea, B.T. Liu, X. Pavlovsky, A.G. Viola, R.E. 2010-01-22 doi:10.1107/S0907444909052834 International Union of Crystallography This first structure of a fungal ortholog of ASA dehydrogenase has a similar overall fold and domain organization to the other members of this enzyme family. However, differences in the binding of the nucleotide cofactor and changes in the nature of the subunit interface are proposed to account for the lower catalytic efficiency of this enzyme from C. albicans. en aspartate β-semialdehyde dehydrogenases Candida albicans amino-acid biosynthesis The enzyme aspartate semialdehyde dehydrogenase (ASADH) catalyzes a critical transformation that produces the first branch-point intermediate in an essential microbial amino-acid biosynthetic pathway. The first structure of an ASADH isolated from a fungal species (Candida albicans) has been determined as a complex with its pyridine nucleotide cofactor. This enzyme is a functional dimer, with a similar overall fold and domain organization to the structurally characterized bacterial ASADHs. However, there are differences in the secondary-structural elements and in cofactor binding that are likely to cause the lower catalytic efficiency of this fungal enzyme. Alterations in the dimer interface, through deletion of a helical subdomain and replacement of amino acids that participate in a hydrogen-bonding network, interrupt the intersubunit-communication channels required to support an alternating-site catalytic mechanism. The detailed functional information derived from this new structure will allow an assessment of ASADH as a possible target for antifungal drug development. text/html Expansion of the aspartate β-semialdehyde dehydrogenase family: the first structure of a fungal ortholog text 2 66 2010-01-22 Copyright (c) 2010 International Union of Crystallography Acta Crystallographica Section D: Biological Crystallography research papers 205 212 http://scripts.iucr.org/cgi-bin/paper?dz5186 Macromolecular X-ray crystallography is routinely applied to understand biological processes at a molecular level. However, significant time and effort are still required to solve and complete many of these structures because of the need for manual interpretation of complex numerical data using many software packages and the repeated use of interactive three-dimensional graphics. PHENIX has been developed to provide a comprehensive system for macromolecular crystallographic structure solution with an emphasis on the automation of all procedures. This has relied on the development of algorithms that minimize or eliminate subjective input, the development of algorithms that automate procedures that are traditionally performed by hand and, finally, the development of a framework that allows a tight integration between the algorithms. Copyright (c) 2010 International Union of Crystallography urn:issn:0907-4449 Adams, P.D. Afonine, P.V. Bunkóczi, G. Chen, V.B. Davis, I.W. Echols, N. Headd, J.J. Hung, L.-W. Kapral, G.J. Grosse-Kunstleve, R.W. McCoy, A.J. Moriarty, N.W. Oeffner, R. Read, R.J. Richardson, D.C. Richardson, J.S. Terwilliger, T.C. Zwart, P.H. 2010-01-22 doi:10.1107/S0907444909052925 International Union of Crystallography The PHENIX software for macromolecular structure determination is described. en PHENIX Python macromolecular crystallography algorithms Macromolecular X-ray crystallography is routinely applied to understand biological processes at a molecular level. However, significant time and effort are still required to solve and complete many of these structures because of the need for manual interpretation of complex numerical data using many software packages and the repeated use of interactive three-dimensional graphics. PHENIX has been developed to provide a comprehensive system for macromolecular crystallographic structure solution with an emphasis on the automation of all procedures. This has relied on the development of algorithms that minimize or eliminate subjective input, the development of algorithms that automate procedures that are traditionally performed by hand and, finally, the development of a framework that allows a tight integration between the algorithms. text/html PHENIX: a comprehensive Python-based system for macromolecular structure solution text 2 66 2010-01-22 Copyright (c) 2010 International Union of Crystallography Acta Crystallographica Section D: Biological Crystallography research papers 213 221 http://scripts.iucr.org/cgi-bin/paper?me0411 Two papers by H. M. Krishna Murthy et al. are retracted. Copyright (c) 2010 International Union of Crystallography urn:issn:0907-4449 2010-01-22 doi:10.1107/S0907444910000259 International Union of Crystallography Retraction of two articles by H. M. Krishna Murthy et al.. en Two papers by H. M. Krishna Murthy et al. are retracted. text/html Retraction of articles by H. M. Krishna Murthy et al. text 2 66 2010-01-22 Copyright (c) 2010 International Union of Crystallography Acta Crystallographica Section D: Biological Crystallography addenda and errata 222 222