forthcoming articles in Acta Crystallographica Section D

The following articles are a selection of those recently accepted for publication in Acta Crystallographica Section D: Biological Crystallography.

See also Forthcoming articles in all IUCr journals.

Structure of Human Bloom's Syndrome Helicase complex with ADP and duplex DNA

M. K. Swan, V. Legris, A. Tanner, P. M. Reaper, S. Vial, R. Bordas, J. R. Pollard, P. A. Charlton, J. M. C. Golec and J. A. Bertrand

Structure determination of human Fas Apoptosis Inhibitory Molecule and identification of the critical residues linking the interdomain interaction to the anti-apoptotic activity

G. Li, L. Qu, S. Ma, Y. Wu, C. Jin and X. Zheng

The structure of class 3 non-symbiotic plant hemoglobin from Arabidopsis thaliana reveals a novel N-terminal helical extension

B. J. Reeder and M. A. Hough

Synopsis: We report the first crystal structure of a class 3 non symbiotic plant haemoglobin to 1.77 Å resolution. The structure reveals a novel N-terminal helical extension that participates extensively in the dimeric interface.

In Cellulo structure determination of a novel Cypovirus Polyhedrin

D. Axford, X. Ji, D. I. Stuart and G. Sutton

Synopsis: The crystal structure of a previously unsolved type of Cypovirus polyhedrin has been determined from data collected directly from frozen live insect cells.

The structure of a novel electron transfer ferredoxin from Rhodopseudomonas palustris HaA2 which contains a histidine residue in its iron-sulfur cluster binding motif

T. Zhang, A. Zhang, S. G. Bell, L.-L. Wong and W. Zhou

Phosphates in Z-DNA dodecamer are flexible, but their P-SAD signal is sufficient for structure solution

Z. Luo, M. Dauter and Z. Dauter

Synopsis: Ultrahigh-resolution structure of the Z-DNA dodecamer, solved from anomalous signal of phosphorus atoms, reveals a substantial flexibility of the backbone phosphate groups.

Structure of the epimerization domain of tyrocidine synthetase A

S. A. Samel, P. Czodrowski and L.-O. Essen

Synopsis: The synthesis of non-ribosomal peptides often introduces D-configured amino acids into the final products. The first crystal structure of the epimerization domain from a non-ribosomal peptide synthetase reveals a bilobal architecture and implies a general acid-base mechanism for the LD isomerization of aminoacyl substrates.

Structure of the nisin leader peptidase NisP revealing a C-terminal autocleavage activity

Y. Xu, X. Li, R. Li, S. Li, H. Ni, H. Wang, H. Xu, W. Zhou, P. E. J. Saris, W. Yang, M. Qiao and Z. Rao

Insights into the binding specificity and catalytic mechanism of N-acetylhexosamine 1-phosphate kinases through multiple-reaction complexes

K.-C. Wang, S.-Y. Lyu, Y.-C. Liu, C.-Y. Chang, C.-J. Wu and T.-L. Li

Structural analysis and insight into metal ion activation of the iron-dependent regulator from Thermoplasma acidophilum

H. K. Yeo, Y. W. Park and J. Y. Lee

Synopsis: Crystal structure of T. acidophilum IdeR

Fingerprinting Redox and Ligand States in Heme Protein Crystal Structures using Resonance Raman Spectroscopy

D. Kekilli, F. S. N. Dworkowski, G. Pompidor, M. R. Fuchs, C. R. Andrew, S. Antonyuk, R. W. Strange, R. R. Eady, S. S. Hasnain and M. A. Hough

Flexible torsion angle non-crystallographic symmetry restraints for improved macromolecular structure refinement

J. J. Headd, N. Echols, P. V. Afonine, N. W. Moriarty, R. J. Gildea and P. D. Adams

Synopsis: Flexible torsion angle-based NCS restraints have been implemented in phenix.refine, allowing for improved model refinement at all resolutions. Rotamer correction and rotamer consistency checks between NCS-related amino acid side chains further improve final model quality.

An arginine tetrad as mediator of input-dependent and input-independent ATPases in the clock protein KaiC

R. Pattanayek, Y. Xu, A. Lamichhane, C. H. Johnson and M. Egli

Structure of a three-dimensional domain-swapped dimer of the Helicobacter pylori type IV secretion system pilus protein CagL

S. Barden, B. Schomburg, J. Conradi, S. Backert, N. Sewald and H. H. Niemann

Synopsis: CagL mediates contact of the pathogen H. pylori with host cell integrins. A domain-swapped structure of CagL shows the RGD motif to act as a hinge region embedded in a helix and reveals the structure of the functionally important C-terminus.

Structural Basis of Sialidase in Complex with Geranylated Flavonoids as Potent Natural Inhibitors

Y. Lee, Y. B. Ryu, H.-S. Youn, J. K. Cho, Y. M. Kim, J.-Y. Park, W. S. Lee, K. H. Park and S. H. Eom

Synopsis: The crystal structure of sialidase from Clostridium perfringens, a pathogenic bacterium causing various gastrointestinal diseases, in complex with the potent natural polyphenolic geranylated flavonoid-based inhibitor was determined. The complex structure and comparative kinetic studies revealed that the geranyl group and C3' hydroxyl group of the flavonoid backbone contribute to inhibit the bacterial sialidase and make the stable enzyme-inhibitor complex.

Structure of the ubiquitin activating enzyme loaded with two ubiquitin molecules

A. Schäfer, M. Kuhn and H. Schindelin

Synopsis: The structure of a ternary complex consisting of the ubiquitin activating enzyme Uba1 and two differently bound ubiquitin molecules has been determined by X-ray crystallography. For the first time the formation of the ubiquitin-acyladenylate could be structurally visualized together with the attachment of a second ubiquitin covalently linked to the active site cysteine of Uba1. Model building studies provide insights into the recruitment of ubiquitin conjugating enzymes.

A novel -xylosidase structure from Geobacillus thermoglucosidasius. The first crystal structure of a glycoside-hydrolase family GH52 enzyme reveals unpredicted similarity with other glycoside-hydrolase folds.

G. Espina, K. Eley, G. Pompidor, T. R. Schneider, S. J. Crennell and M. J. Danson

Synopsis: The first structure of a CAZy glycoside-hydrolase family 52 enzyme, of Geobacillus thermoglucosidasius-xylosidase, reveals structural similarities with other families with which it shares less than 13% sequence identity. The substrate-bound complex confirms the active site residues and is consistent with a retaining mechanism.

Structure of Sulfamidase Provides Insight into the Molecular Pathology of Mucopolysaccharidosis IIIA

N. S. Sidhu, K. Schreiber, K. Pröpper, S. Becker, I. Usón, G. M. Sheldrick, J. Gärtner, R. Krätzner and R. Steinfeld

Synopsis: Mucopolysaccharidosis IIIA is a fatal neurodegenerative disease that typically manifests itself in childhood, and is caused by mutations in the gene for the lysosomal enzyme sulfamidase. We present the first structure of this enzyme, which provides insight into the molecular basis of disease-causing mutations, and propose the enzymatic mechanism.

Bacteriophage P22 Tailspike: Crystal Structure of the Complete Protein and Function of the Interdomain Linker

A. Seul, J. J. Müller, D. Andres, E. Stettner, U. Heinemann and R. Seckler

Synopsis: A single mutation in the linker region renders intact P22 tailspike crystallizable, allowing the analysis of the crystal structure of the complete tailspike at high resolution. The mutant protein is still functional, but has to be distorted to fit into a published cryo-EM map, and the structure suggests an important role of the highly conserved linker in intramolecular signal transmission.

Divalent metal ion-based catalysis mechanism of the Nudix hydrolase Orf153 (YmfB) from Escherichia coli

M.-K. Hong, A. J. M. Ribeiro, J.-K. Kim, P.-T.H. Ngo, J. Kim, C. H. Lee, Y.-J. Ahn, P. A. Fernandes, Q. Li, M. J. Ramos and L.-W. Kang

Structural insight into glucose dehydrogenase from the thermoacidophilic archaeon Thermoplasma volcanium

Y. Kanoh, S. Uehara, H. Iwata, K. Yoneda, T. Ohshima and H. Sakuraba

Synopsis: The structure of a medium-chain dehydrogenase reductase-type glucose dehydrogenase showing narrow substrate specificity was determined, and the enzyme's unique structural features were compared with those of a glucose dehydrogenase showing broad substrate specificity.

Sunitinib: from charge density studies to interaction with proteins

M. Malinska, K. N. Jarzembska, A. M. Goral, A. Kutner, K. Wozniak and P. M. Dominiak

Coiled-coil deformations in crystal structures: the measles virus phosphoprotein multimerization domain as an illustrative example

D. Blocquel, J. Habchi, E. Durand, M. Sevajol, F. Ferron, J. Erales, N. Papageorgiou and S. Longhi

Accurate macromolecular crystallographic refinement: incorporation of the linear scaling, semiempirical quantum-mechanics program DivCon into the PHENIX refinement package

O. Y. Borbulevych, J. A. Plumley, R. M. Martin, K. M. Merz and L. M. Westerhoff

Synopsis: Semiempirical quantum-chemical X-ray macromolecular refinement using the program DivCon integrated with PHENIX.

IR-laser induced protein crystal transformation

R. Kiefersauer, B. Grandl, S. Krapp and R. Huber

Synopsis: A novel method and the associated instrumentation for improving crystalline order (higher resolution of X-ray diffraction and reduced mosaicity) of protein crystals by precisely controlled heating is demonstrated. Crystal transformation is optically controlled by a video system.

An improved integration method in serial femtosecond crystallography

K. Qu, L. Zhou and Y.-H. Dong

Structural basis of a novel activity of bacterial 6-pyruvoyl tetrahydropterin synthase homologues distinguished from mammalian 6-pyruvoyl tetrahydropterin synthase activity

K. H. Seo, N. N. Zhuang, Y. S. Park, K. H. Park and K. H. Lee

Synopsis: Crystal structures show how bacterial PTPS homologues possess an unusual activity different from the mammalian PTPS.

The active site of hen egg-white lysozyme: flexibility and chemical bonding

J. Held and S. van Smaalen

Synopsis: Chemical bonding at the active site of lysozyme is analyzed on the basis of a multipole model employing transferable multipole parameters from a database. Large B factors at low temperatures reflect frozen-in disorder, but therefore prevent a meaningful free refinement of multipole parameters.

Structures of Legionella pneumophila NTPDase1 in complex with polyoxometallates

M. Zebisch, M. Krauss, P. Schäfer and N. Sträter

Synopsis: Crystal structures of L. pneumophila NTPDase1 in complex with three polyoxometallate clusters suggest different inhibitory mechanisms.

3'-Azidothymidine in the active site of Escherichia coli thymidine phosphorylase: the peculiarity of the binding on the basis of X-ray study

V. Timofeev, Y. Abramchik, N. Zhukhlistova, T. Muravieva, I. Fateev, R. Esipov and I. Kuranova

Synopsis: X-ray crystallography shows that 3'-azidothymidine, a reversible inhibitor of E. coli thymidine phosphorylase, is bound in the active site of the enzyme in an orientation different from that of the thymidine substrate and nucleoside analogues in known complexes of pyrimidine nucleoside phosphorylases. The possible role of the 3'-azido group as a trigger of reorientation of the ligand is discussed.

A conformational landscape for alginate secretion across the outer membrane of Pseudomonas aeruginosa

J. Tan, S. L. Rouse, D. Li, V. E. Pye, L. Vogeley, A. R. Brinth, J. C. Whitney, P. L. Howell, M. S. P. Sansom and M. Caffrey

Synopsis: Crystal structures of the -barrel porin AlgE reveal a mechanism whereby alginate is exported from P. aeruginosa for biofilm formation.

The type IV secretion protein TraK from the Enterococcus conjugative plasmid pIP501 exhibits a novel fold

N. Goessweiner-Mohr, C. Fercher, K. Arends, R. Birner-Gruenberger, D. Laverde-Gomez, J. Huebner, E. Grohmann and W. Keller

Synopsis: The 3 Å resolution structure of the type IV secretion system protein TraK from Gram-positive conjugative plasmid pIP501 is reported.

Analysis of an industrial production suspension of Bacillus lentus subtilisin crystals by powder diffraction: a powerful quality-control tool

C. G. Frankær, O. V. Moroz, J. P. Turkenburg, S. I. Aspmo, M. Thymark, E. P. Friis, K. Stahl, J. E. Nielsen, K. S. Wilson and P. Harris

Synopsis: A combination of powder diffraction and macromolecular crystallography demonstrated the presence of at least three different crystal forms of B. lentus subtilisin in a suspension from a large-scale industrial production. The application of powder diffraction is a powerful tool for quality control in enzyme production.

A slow-forming isopeptide bond in the structure of the major pilin SpaD from Corynebacterium diphtheriae has implications for pilus assembly

H. J. Kang, N. G. Paterson, C. U. Kim, M. Middleditch, C. Chang, H. Ton-That and E. N. Baker

Synopsis: Two crystal structures of the major pilin SpaD from C. diphtheriae have been determined at 1.87 and 2.5 Å resolution. The N-terminal domain is found to contain an isopeptide bond that forms slowly over time in the recombinant protein. Given its structural context, this provides insight into the relationship between internal isopeptide-bond formation and pilus assembly.

Automated identification of elemental ions in macromolecular crystal structures

N. Echols, N. Morshed, P. V. Afonine, A. J. McCoy, M. D. Miller, R. J. Read, J. S. Richardson, T. C. Terwilliger and P. D. Adams

Molecular mechanism for self-protection against the type VI secretion system in Vibrio cholerae

X. Yang, M. Xu, Y. Wang, P. Xia, S. Wang, B. Ye, L. Tong, T. Jiang and Z. Fan

Structure-based characterization and antifreeze properties of a hyperactive ice-binding protein from the Antarctic bacterium Flavobacterium frigoris PS1

H. Do, S.-J. Kim, H. J. Kim and J. H. Lee

Synopsis: The high-resolution crystal structure of FfIBP was determined and the structure showed an intramolecular disulfide bond in the capping head loop region and a T-A/G-X-T/N ice-binding motif. The rigid capping head loop region and greater surface area of the ice-binding site are important for the antifreeze activity of FfIBP.

Crystallographic characterization of the (R)-selective amine transaminase from Aspergillus fumigatus

M. Thomsen, L. Skalden, G. J. Palm, M. Höhne, U. T. Bornscheuer and W. Hinrichs

Synopsis: The X-ray crystal structure of the (R)-selective amine transaminase from A. fumigatus at 1.27 Å resolution was determined via S-SAD phasing at 1.84 Å resolution.

Anomalies in the refinement of isoleucine

K. R. M. Berntsen and G. Vriend

Structural snapshots along the reaction pathway of Yersinia pestis RipA, a putative butyryl-CoA transferase

R. Torres, B. Lan, N. Çhim and C. W. Goulding

Synopsis: The crystal structures of Y. pestis RipA mutants were determined to provide insights into the CoA transferase reaction pathway.

Structural basis for the selective nuclear import of the C2H2 zinc-finger protein Snail by importin

S. Choi, E. Yamashita, N. Yasuhara, J. Song, S.-Y. Son, Y. H. Won, H. R. Hong, Y. S. Shin, T. Sekimoto, I. Y. Park, Y. Yoneda and S. J. Lee

Synopsis: The X-ray structure of the complex of the nuclear transporter importin with the zinc-finger-type transcription regulator Snail1 is reported.

Structural basis for the redox sensitivity of the Mycobacterium tuberculosis SigK-RskA -anti- complex

J. Shukla, R. Gupta, K. G. Thakur, R. Gokhale and B. Gopal

Synopsis: A disulfide bond in the -35 promoter-binding domain of ^K regulates its interaction with the anti- factor RskA.

The crystal structure of wild-type human brain neuroglobin reveals flexibility of the disulfide bond that regulates oxygen affinity

B. G. Guimarães, D. Hamdane, C. Lechauve, M. C. Marden and B. Golinelli-Pimpaneau

Partial rotational lattice order-disorder in stefin B crystals

M. Renko, A. Taler-Vercic, M. Mihelic, E. Zerovnik and D. Turk

Synopsis: Crystal lattice disorders are a phenomenon which may hamper the determination of macromolecular crystal structures. Using the case of the crystal structure of stefin B, identification of rotational order-disorder and structure determination are described.

The first crystal structure of NAD-dependent 3-dehydro-2-deoxy-D-gluconate dehydrogenase from Thermus thermophilus HB8

K. J. Pampa, N. K. Lokanath, N. Kunishima and R. V. Rai

Synopsis: The crystal structure of 3-dehydro-3-deoxy-D-gluconate 5-dehydrogenase from T. thermophilus HB8 has been determined in the apo form, as well as in complexes with the cofactor and with citrate, by X-ray diffraction methods. The citrate molecule and the cofactor have been identified deep in the cleft formed between the interface of two adjacent subunits. These structures provide insights into the substrate recognition and catalytic machinery of 3-dehydro-3-deoxy-D-gluconate 5-dehydrogenase.

The structures of cytosolic and plastid-located glutamine synthetases from Medicago truncatula reveal a common and dynamic architecture

E. Torreira, A. R. Seabra, H. Marriott, M. Zhou, Ó. Llorca, C. V. Robinson, H. G. Carvalho, C. Fernández-Tornero and P. J. B. Pereira

Synopsis: The experimental models of dicotyledonous cytoplasmic and plastid-located glutamine synthetases unveil a conserved eukaryotic-type decameric architecture, with subtle structural differences in M. truncatula isoenzymes that account for their distinct herbicide resistance.

Hitting the target: fragment screening with acoustic in situ co-crystallization of proteins plus fragment libraries on pin-mounted data-collection micromeshes

X. Yin, A. Scalia, L. Leroy, C. M. Cuttitta, G. M. Polizzo, D. L. Ericson, C. G. Roessler, O. Campos, M. Y. Ma, R. Agarwal, R. Jackimowicz, M. Allaire, A. M. Orville, R. M. Sweet and A. S. Soares

Characterization of the proline-utilization pathway in Mycobacterium tuberculosis through structural and functional studies

T. Lagautriere, G. Bashiri, N. G. Paterson, M. Berney, G. M. Cook and E. N. Baker

Synopsis: The structure of ¹-pyrroline-5-carboxylic dehydrogenase (PruA), involved in proline utilization in M. tuberculosis, has been determined in apo and NAD⁺-bound forms. Opportunities for inhibitor development are identified and the proline-utilization pathway has been characterized with a novel use of NMR.

Threonine 57 is required for the post-translational activation of Escherichia coli aspartate -decarboxylase

M. E. Webb, B. A. Yorke, T. Kershaw, S. Lovelock, C. M. C. Lobley, M. L. Kilkenny, A. G. Smith, T. L. Blundell, A. R. Pearson and C. Abell

Synopsis: Threonine 57 is identified as the key residue required for the post-translational activation of E. coli aspartate decarboxylase. The crystal structure of the site-directed mutant T57V is reported.

Simultaneous use of solution NMR and X-ray data in REFMAC5 for joint refinement/detection of structural differences

M. Rinaldelli, E. Ravera, V. Calderone, G. Parigi, G. N. Murshudov and C. Luchinat

Structure and possible mechanism of the CcbJ methyltransferase from Streptomyces caelestis

J. Bauer, G. Ondrovicová, L. Najmanová, V. Pevala, Z. Kameník, J. Kostan, J. Janata and E. Kutejová

Synopsis: The 2.7 Å resolution crystal structure of the CcbJ methyltransferase from S. caelestis, which is part of the biosynthetic pathway of the lincosamide antibiotic celesticetin, is reported along with its complex with S-adenosyl-L-homocysteine at 2.9 Å resoution. Mutational and docking studies based on these structures are used to propose a plausible mechanism for its activity.

Structural and biochemical characterization of MdaB from cariogenic Streptococcus mutans reveals an NADPH-specific quinone oxidoreductase

Z. Wang, L. Li, Y.-H. Dong and X.-D. Su

Synopsis: The putative gene smu.1420 from S. mutans is demonstrated to encode the MdaB protein with NADPH-specific quinone oxidoreductase activity. Crystal structures of Smu.1420 with NADP⁺ and menadione reveal the substrate-selection and catalytic mechanisms, and shed light on future drug development against S. mutans.

Structural characterization and comparison of the large subunits of IPM isomerase and homoaconitase from Methanococcus jannaschii

E. H. Lee, K. Lee and K. Y. Hwang

Synopsis: IPM isomerase and homoaconitase belong to the aconitase family of enzymes and are composed of large and small subunits. The large subunits of the two enzymes adopt different active-site states before Fe-S cluster binding.

Structural characteristics of an insect group I chitinase, an enzyme indispensable to moulting

L. Chen, T. Liu, Y. Zhou, Q. Chen, X. Shen and Q. Yang

Synopsis: The first crystal structure of an insect chitinase that is indispensable to moulting is revealed.

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