Acta Crystallographica Section D

Biological Crystallography

Volume 70, Part 5 (May 2014)



[Issue Author Index][Volume Author Index]
[Cover illustration] Cover illustration: The active site of the enzyme riboflavin synthase from the pathogenic bacterium Brucella abortus, with two molecules of the product analogue 5-nitro-6-ribitylamino-2,4(1H,3H)-pyrimidinedione bound in an antiparallel way (p. 1419). Interestingly, the active site of this enzyme is formed by two substrate-binding sites bearing pseudo-C2 symmetry that are located at the interface between two neighbouring chains.

research papers


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Acta Cryst. (2014). D70, 1177-1189  [ doi:10.1107/S1399004713034603 ]

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

Synopsis: A method is presented for screening fragment libraries using acoustic droplet ejection to co-crystallize proteins and chemicals directly on micromeshes with as little as 2.5 nl of each component. This method was used to identify previously unreported fragments that bind to lysozyme, thermolysin, and trypsin.

PDB references: 4m65, 4ncy and 4n8z

Online 30 April 2014


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Acta Cryst. (2014). D70, 1190-1201  [ doi:10.1107/S1399004714001400 ]

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.

PDB references: 4hsq and 4hss

Online 26 April 2014


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Acta Cryst. (2014). D70, 1202-1211  [ doi:10.1107/S1399004714002004 ]

An improved integration method in serial femtosecond crystallography

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

Synopsis: An improved integration method enhances the quality of electron-density maps and decreases the number of diffraction patterns that are needed in serial femtosecond crystallography.

Online 26 April 2014


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Acta Cryst. (2014). D70, 1212-1223  [ doi:10.1107/S1399004714002016 ]

Structural basis of a novel activity of bacterial 6-pyruvoyltetrahydropterin synthase homologues distinct from mammalian 6-pyruvoyltetrahydro­pterin synthase activity

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

Synopsis: Crystal structures show how bacterial PTPS homologues possess an unusual activity that differs from that of mammalian PTPS enzymes.

PDB references: 3qn9, 3qn0 and 3qna

Online 26 April 2014


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Acta Cryst. (2014). D70, 1224-1232  [ doi:10.1107/S1399004714002223 ]

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.

Online 26 April 2014


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Acta Cryst. (2014). D70, 1233-1247  [ doi:10.1107/S1399004714002260 ]

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. I. Martin, K. M. Merz and L. M. Westerhoff

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

Online 26 April 2014


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Acta Cryst. (2014). D70, 1248-1256  [ doi:10.1107/S1399004714005379 ]

Exploiting fast detectors to enter a new dimension in room-temperature crystallography

R. L. Owen, N. Paterson, D. Axford, J. Aishima, C. Schulze-Briese, J. Ren, E. E. Fry, D. I. Stuart and G. Evans

Synopsis: A departure from a linear or an exponential decay in the diffracting power of macromolecular crystals is observed and accounted for through consideration of a multi-state sequential model.

Online 26 April 2014


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Acta Cryst. (2014). D70, 1257-1270  [ doi:10.1107/S1399004714002351 ]

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

Synopsis: The first comprehensive analysis of the sunitinib malate crystal structure and charge-density distribution in the context of sunitinib complexes with a series of protein kinases is reported. The aspherical atom databank approach, Hirshfeld surface analysis and quantum theory of atoms in molecules are used as a foundation for the investigations of interactions between an inhibitor and a protein.

Online 29 April 2014


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Acta Cryst. (2014). D70, 1271-1280  [ doi:10.1107/S1399004714002363 ]

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 unique structural features of the enzyme were compared with those of a glucose dehydrogenase showing broad substrate specificity.

PDB references: 3wic, 3wid and 3wie

Online 29 April 2014


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Acta Cryst. (2014). D70, 1281-1288  [ doi:10.1107/S1399004714004118 ]

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: The crystal structure of T. acidophilum IdeR is reported.

PDB references: 4o5v and 4o6j

Online 29 April 2014


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Acta Cryst. (2014). D70, 1289-1296  [ doi:10.1107/S1399004714004039 ]

Fingerprinting redox and ligand states in haemprotein 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

Synopsis: High-resolution X-ray crystallography has been effectively combined with resonance Raman spectroscopy to `fingerprint' and validate different redox and ligand states in structures of Alcaligenes xylosoxidans cytochrome c'.

PDB references: 4cda, 4cdv, 4cdy, 4cip, 4cjg and 4cjo

Online 29 April 2014


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Acta Cryst. (2014). D70, 1297-1310  [ doi:10.1107/S1399004714002570 ]

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

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

Synopsis: The structures of Escherichia coli YmfB on its own and in complex with three sulfates and two manganese ions, when compared with the structures of other Nudix hydrolases such as MutT, Ap4Aase and DR1025, provide insight into the unique hydrolysis mechanism of YmfB.

PDB references: 4nfx and 4nfw

Online 29 April 2014


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Acta Cryst. (2014). D70, 1311-1320  [ doi:10.1107/S1399004714002910 ]

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.

PDB reference: 4nnj

Online 30 April 2014


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Acta Cryst. (2014). D70, 1321-1335  [ doi:10.1107/S1399004714002739 ]

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. The first structure of this enzyme is presented, which provides insight into the molecular basis of disease-causing mutations, and the enzymatic mechanism is proposed.

PDB references: 4mhx and 4miv

Online 30 April 2014


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Acta Cryst. (2014). D70, 1336-1345  [ doi:10.1107/S1399004714002685 ]

Bacteriophage P22 tailspike: 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 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.

PDB references: 2vky, 2vnl and 2xc1

Online 30 April 2014


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Acta Cryst. (2014). D70, 1346-1356  [ doi:10.1107/S1399004714003277 ]

Flexible torsion-angle noncrystallographic 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 improved model refinement at all resolutions. Rotamer correction and rotamer consistency checks between NCS-related amino-acid side chains further improve the final model quality.

Online 30 April 2014


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Acta Cryst. (2014). D70, 1357-1365  [ doi:10.1107/S1399004714002971 ]

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

PDB reference: 4l2e

Online 30 April 2014


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Acta Cryst. (2014). D70, 1366-1374  [ doi:10.1107/S1399004714002788 ]

A novel [beta]-xylosidase structure from Geobacillus thermoglucosidasius: the first crystal structure of a glycoside hydrolase family GH52 enzyme reveals unpredicted similarity to 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, that of G. thermoglucosidasius [beta]-xylosidase, reveals structural similarities to 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.

PDB references: 4c1o and 4c1p

Online 30 April 2014


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Acta Cryst. (2014). D70, 1375-1390  [ doi:10.1107/S1399004714003228 ]

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

Synopsis: The crystal structure of KaiC from Thermosynechococcus elongatus allows insight into the different anatomies of the CI and CII ATPases.

PDB reference: 4o0m

Online 30 April 2014


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Acta Cryst. (2014). D70, 1391-1400  [ doi:10.1107/S1399004714003150 ]

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.

PDB reference: 4cii

Online 30 April 2014


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Acta Cryst. (2014). D70, 1401-1410  [ doi:10.1107/S1399004714004209 ]

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

Synopsis: The seven crystal structures presented in this work represent the first multiple reaction complexes (GlcNAc/GalNAc, GlcNAc-1P/GalNAc-1P, ATP/ADP and Mg2+) of NahK in the lacto-N-biose (LNB)/galacto-N-biose (GNB) pathway, providing the molecular basis for the recognition of substrates and gaining insights into the catalytic mechanism at the molecular level.

PDB references: 4ocj, 4ock, 4oco, 4ocp, 4ocq, 4ocu and 4ocv

Online 30 April 2014


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Acta Cryst. (2014). D70, 1411-1418  [ doi:10.1107/S1399004714004878 ]

The structure of a class 3 nonsymbiotic plant haemoglobin from Arabidopsis thaliana reveals a novel N-terminal helical extension

B. J. Reeder and M. A. Hough

Synopsis: The first crystal structure of a class 3 nonsymbiotic plant haemoglobin is reported to 1.77 Å resolution. The structure revealed a novel N-terminal helical extension that participates extensively in the dimeric interface.

PDB reference: 4c0n

Online 30 April 2014


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Acta Cryst. (2014). D70, 1419-1434  [ doi:10.1107/S1399004714005161 ]

Crystallographic and kinetic study of riboflavin synthase from Brucella abortus, a chemotherapeutic target with an enhanced intrinsic flexibility

M. I. Serer, H. R. Bonomi, B. G. Guimarães, R. C. Rossi, F. A. Goldbaum and S. Klinke

Synopsis: This work reports crystal structures of trimeric riboflavin synthase from the pathogen B. abortus both as the apo protein and in complex with several ligands of interest. It is shown that ligand binding drives the assembly of the unique active site of the trimer, and these findings are complemented by a detailed kinetic study on this enzyme, in which marked inhibition by substrate and product was observed.

PDB references: 4fxu, 4e0f, 4g6i and 4gqn

Online 30 April 2014


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Acta Cryst. (2014). D70, 1435-1441  [ doi:10.1107/S1399004714004714 ]

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.

PDB references: 4otv and 4ots

Online 30 April 2014


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Acta Cryst. (2014). D70, 1442-1452  [ doi:10.1107/S1399004714004398 ]

Structure of the epimerization domain of tyrocidine synthetase A

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

Synopsis: The synthesis of nonribosomal peptides often introduces D-configured amino acids into the final products. The first crystal structure of the epimerization domain of a nonribosomal peptide synthetase reveals a bilobal architecture and implies a general acid-base mechanism for the L[left right arrow]D isomerization of aminoacyl substrates.

PDB reference: 2xhg

Online 30 April 2014


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Acta Cryst. (2014). D70, 1453-1464  [ doi:10.1107/S139900471400474X ]

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

Synopsis: The crystal structure of the ferredoxin HaPuxC has been solved at 2.3 Å resolution.

PDB references: 4id8 and 4ov1

Online 30 April 2014


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Acta Cryst. (2014). D70, 1465-1475  [ doi:10.1107/S139900471400501X ]

Structure of human Bloom's syndrome helicase in 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

Synopsis: The crystal structure of the human BLM helicase in complex with ADP and a 3'-overhang DNA duplex is reported.

PDB reference: 4o3m

Online 30 April 2014


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Acta Cryst. (2014). D70, 1476-1483  [ doi:10.1107/S1399004714005227 ]

Structure of the unique SEFIR domain from human interleukin 17 receptor A reveals a composite ligand-binding site containing a conserved [alpha]-helix for Act1 binding and IL-17 signaling

B. Zhang, C. Liu, W. Qian, Y. Han, X. Li and J. Deng

Synopsis: Crystal structure of the SEFIR domain from human IL-17 receptor A provides new insights into IL-17 signaling.

PDB reference: 4nux

Online 30 April 2014


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Acta Cryst. (2014). D70, 1484-1490  [ doi:10.1107/S1399004714005422 ]

Structural characterization of the apo form and NADH binary complex of human lactate dehydrogenase

S. Dempster, S. Harper, J. E. Moses and I. Dreveny

Synopsis: A crystal structure of the human lactate dehydrogenase A apo form suitable for ligand soaking and a NADH binary-complex structure are presented.

PDB references: 4l4r and 4l4s

Online 30 April 2014


short communications


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Acta Cryst. (2014). D70, 1491-1497  [ doi:10.1107/S1399004714005318 ]

Diamonds in the rough: a strong case for the inclusion of weak-intensity X-ray diffraction data

J. Wang and R. A. Wing

Synopsis: Here, new evidence is provided to show that the inclusion of weak-intensity, high-resolution X-ray diffraction data helps to improve the quality of experimental phases by imposing proper constraints on electron-density models during noncrystallographic symmetry averaging.

PDB reference: 4lr3

Online 30 April 2014


addenda and errata


 

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Acta Cryst. (2014). D70, 1498  [ doi:10.1107/S1399004714007391 ]

Structural and functional characterization of an Isd-type haem-degradation enzyme from Listeria monocytogenes. Corrigendum

T. Duong, K. Park, T. Kim, S. W. Kang, M. J. Hahn, H.-Y. Hwang, I. Jang, H. B. Oh and K. K. Kim

Synopsis: A correction is made to the article by Duong et al. [(2014). Acta Cryst. D70, 615-626].

Online 30 April 2014


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