Acta Crystallographica Section D

Biological Crystallography

Volume 70, Part 4 (April 2014)



[Issue Author Index][Volume Author Index]
[Cover illustration] Cover illustration: Electron cryomicroscopy reconstruction of the plastid-located glutamine synthetase GSII-2a from Medicago truncatula and the fitting of the crystal structure of the cytoplasmic GSII-1a from M. truncatula, with each monomer coloured differently (p. 981).

research papers


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Acta Cryst. (2014). D70, 912-921  [ doi:10.1107/S1399004713033749 ]

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.

PDB references: 3lcm and 4f8y

Online 19 March 2014


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Acta Cryst. (2014). D70, 922-931  [ doi:10.1107/S1399004713033762 ]

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.

PDB references: 4kp1, 4nqy and 4kp2

Online 19 March 2014


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Acta Cryst. (2014). D70, 932-942  [ doi:10.1107/S1399004713033841 ]

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.

PDB references: 3w4r, 3wl1, 3wl0 and 3wkz

Online 19 March 2014


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Acta Cryst. (2014). D70, 943-957  [ doi:10.1107/S139900471303397X ]

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.

PDB references: 4hgy, 4hgz and 4hh4

Online 19 March 2014


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Acta Cryst. (2014). D70, 958-967  [ doi:10.1107/S1399004713034160 ]

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

Synopsis: Paramagnetic NMR data (pseudocontact shifts and self-orientation residual dipolar couplings) and diamagnetic residual dipolar couplings can now be used in the program REFMAC5 from CCP4 as structural restraints together with X-ray crystallographic data. These NMR restraints can reveal differences between solid state and solution conformations of molecules or, in their absence, can be used together with X-ray crystallographic data for structural refinement.

Online 19 March 2014


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Acta Cryst. (2014). D70, 968-980  [ doi:10.1107/S1399004713034391 ]

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 [Delta]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.

PDB references: 4ids, 4idm, 4ihi and 4jdc

Online 19 March 2014


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Acta Cryst. (2014). D70, 981-993  [ doi:10.1107/S1399004713034718 ]

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.

PDB reference: 4is4

Online 19 March 2014


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Acta Cryst. (2014). D70, 994-1004  [ doi:10.1107/S1399004713034925 ]

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.

PDB references: 4jp2, 2ekq, 2ekp and 4jp3

Online 19 March 2014


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Acta Cryst. (2014). D70, 1005-1014  [ doi:10.1107/S1399004714000078 ]

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

Synopsis: The crystal structure of wild-type human neuroglobin reveals two distinct conformations of the CD loop that contains an internal disulfide bridge. The increased affinity for oxygen upon disulfide-bond formation may be explained by the flexibility of the CD loop and the remodelling of the internal cavities.

PDB reference: 4mpm

Online 19 March 2014


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Acta Cryst. (2014). D70, 1015-1025  [ doi:10.1107/S1399004714000091 ]

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.

PDB reference: 4n6v

Online 19 March 2014


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Acta Cryst. (2014). D70, 1026-1036  [ doi:10.1107/S1399004714000121 ]

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

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

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

PDB reference: 4nqw

Online 19 March 2014


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Acta Cryst. (2014). D70, 1037-1049  [ doi:10.1107/S139900471400087X ]

Anomalies in the refinement of isoleucine

K. R. M. Berntsen and G. Vriend

Synopsis: The side-chain torsion angles of isoleucines in X-ray protein structures are a function of resolution, secondary structure and refinement software. Detailing the standard torsion angles used in refinement software can improve protein structure refinement.

Online 19 March 2014


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Acta Cryst. (2014). D70, 1050-1060  [ doi:10.1107/S1399004714000972 ]

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

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 [beta] with the zinc-finger-type transcription regulator Snail1 is reported.

PDB reference: 3w5k

Online 19 March 2014


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Acta Cryst. (2014). D70, 1061-1073  [ doi:10.1107/S1399004714000996 ]

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.

PDB references: 4nu2, 4nu3 and 4nuh

Online 19 March 2014


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Acta Cryst. (2014). D70, 1074-1085  [ doi:10.1107/S1399004714000911 ]

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

R. Torres, B. Lan, Y. Latif, N. Chim and C. W. Goulding

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

PDB references: 4n8h, 4n8i, 4n8j, 4n8k and 4n8l

Online 20 March 2014


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Acta Cryst. (2014). D70, 1086-1093  [ doi:10.1107/S1399004714001084 ]

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.

PDB reference: 4chi

Online 20 March 2014


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Acta Cryst. (2014). D70, 1094-1103  [ doi:10.1107/S1399004714001242 ]

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

Synopsis: The first crystal structure of the VgrG3CCD-TsiV3 complex has been determined. The detailed biochemical, biophysical and functional studies delineated the structural basis for self-protection in Vibrio cholerae.

PDB reference: 4noo

Online 20 March 2014


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Acta Cryst. (2014). D70, 1104-1114  [ doi:10.1107/S1399004714001308 ]

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

Synopsis: The solvent-picking procedure in phenix.refine has been extended and combined with Phaser anomalous substructure completion and analysis of coordination geometry to identify and place elemental ions.

Online 20 March 2014


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Acta Cryst. (2014). D70, 1115-1123  [ doi:10.1107/S1399004714001497 ]

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

C. G. Frankaer, 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.

PDB references: 4cfy, 4cfz and 4cg0

Online 21 March 2014


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Acta Cryst. (2014). D70, 1124-1135  [ doi:10.1107/S1399004714001606 ]

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.

PDB reference: 4hic

Online 21 March 2014


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Acta Cryst. (2014). D70, 1136-1146  [ doi:10.1107/S1399004714001928 ]

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.

Online 21 March 2014


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Acta Cryst. (2014). D70, 1147-1154  [ doi:10.1107/S1399004714001916 ]

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.

PDB references: 4brh, 4bvo and 4bvp

Online 21 March 2014


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Acta Cryst. (2014). D70, 1155-1165  [ doi:10.1107/S1399004714001904 ]

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.

PDB reference: 4lhm

Online 21 March 2014


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Acta Cryst. (2014). D70, 1166-1172  [ doi:10.1107/S1399004713034275 ]

Threonine 57 is required for the post-translational activation of Escherichia coli aspartate [alpha]-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.

PDB reference: 4azd

Online 21 March 2014


addenda and errata


 

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Acta Cryst. (2014). D70, 1173  [ doi:10.1107/S1399004714006130 ]

The structure of an authentic spore photoproduct lesion in DNA suggests a basis for recognition. Corrigendum

I. Singh, Y. Jian, L. Li and M. M. Georgiadis

Synopsis: A correction is made to the article by Singh et al. [(2014). Acta Cryst. D70, 752-759].

Online 26 March 2014


 

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Acta Cryst. (2014). D70, 1174  [ doi:10.1107/S1399004714006154 ]

AMPLE: a cluster-and-truncate approach to solve the crystal structures of small proteins using rapidly computed ab initio models. Corrigendum

J. Bibby, R. M. Keegan, O. Mayans, M. D. Winn and D. J. Rigden

Synopsis: A number of corrections are made to the article by Bibby et al. (2012). Acta Cryst. D68, 1622-1631.

Online 26 March 2014


book reviews


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Acta Cryst. (2014). D70, 1175-1176  [ doi:10.1107/S1399004714005719 ]

Small Angle X-Ray and Neutron Scattering from Solutions of Biological Macromolecules

Online 26 March 2014


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