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.

Accepted 18 November 2014

A national facility for biological cryo-electron microscopy

H. R. Saibil, K. Grünewald and D. I. Stuart

Synopsis: This review provides a brief update on the use of cryo-electron microscopy for integrated structural biology, along with an overview of the plans for the UK national facility for electron microscopy being built at the Diamond synchrotron.

Accepted 17 November 2014

Ligand bound structures of 3-de­oxy-D-manno-octulosonate 8-phosphate phosphatase from Moraxella catarrhalis reveals water channel connecting the active site for the second step of catalysis

S. Dhindwal, P. Priyadarshini, D. N. Patil, S. Tapas, P. Kumar, S. Tomar and P. Kumar

Synopsis: For the first time, the crystal structure of KdsC from Moraxella catarhallis reveals an intersubunit water tunnel, proposed to provide water molecule at the active site for catalysis.

Accepted 17 November 2014

Analysis of the HindIII catalyzed reaction by Time-Resolved Crystallography

T. Kawamura, T. Kobayashi and N. Watanabe

Synopsis: Time-resolved study with the freeze trap method elucidates the mechanism of DNA-cleaving reaction of HindIII.

Accepted 17 November 2014

Insight into cofactor recognition in arylamine N-acetyltransferase enzymes: Crystal structure of Mesorhizobium loti arylamine N-acetyltransferase in complex with coenzyme A

X. Xu, I. Li de la Sierra-Gallay, X. Kubiak, R. Duval, A. F. Chaffotte, J.-M. Dupret, A. Haouz and F. Rodrigues-Lima

Accepted 17 November 2014

Nitrogenase MoFe-Protein from Clostridium pasteurianum at 1.08 Å Resolution: Comparison to the Azotobacter vinelandii MoFe-protein

L. Zhang, C. N. Morrison, J. T. Kaiser and D. C. Rees

Synopsis: Determination of the nitrogenase MoFe-protein from Clostridium pasteurianum at 1.08 Å resolution and comparison to its distinct ortholog from Azotobacter vinelandii at atomic resolution reveals conserved structural arrangements that are significant to the function of nitrogenase.

Accepted 15 November 2014

Crystallization of lysozyme with (R)-, (S)- and (RS)-2-methyl-2,4-pentanediol

M. Stauber, J. Jakoncic, J. Berger, J. M. Karp, A. Axelbaum, D. Sastow, S. V. Buldyrev, B. J. Hrnjez and N. Asherie

Synopsis: Crystallization of lysozyme with (R)-2-methyl-2,4-pentanediol produces more ordered crystals and a higher resolution protein structure than crystallization with (S)-2-methyl-2,4-pentanediol. The results suggest that chiral interactions with chiral additives are important in protein crystal formation.

Accepted 15 November 2014

Structure of [gamma]-conglutin: insight into quaternary structure of 7S basic globulins from legumes

J. Czubinski, J. Barciszewski, M. Gilski, K. Szpotkowski, J. Debski, E. Lampart-Szczapa and M. Jaskolski

Synopsis: 4pph, [gamma]-conglutin, 7S basic globulin. The crystal structure of 45 kDa [gamma]-conglutin from lupine seeds was determined at 2 Å resolution, showing that in variance with the tetrameric structure of another 7S basic globulin from a legume plant (soybean) it forms a ring-like hexamer.

Accepted 14 November 2014

Biochemical and structural investigation of two paralogous glycoside hydrolases from Zobellia galactanivorans: novel insights into the evolution, dimerization plasticity and catalytic mechanism of the GH117 family

E. Ficko-Blean, D. Duffieux, É. Rebuffet, R. Larocque, A. Groisillier, G. Michel and M. Czjzek

Synopsis: Structural, functional and phylogenetic analyses reveal enzyme diversity within family 117 of the glycoside hydrolases, which remove terminal [alpha]-1,3-linked 3,6-anhydro-L-galactose from neoagaro-oligosaccharides produced by [beta]-agarases. A product complex with the unique [beta]-3,6-anhydro-L-galactose provides strong crystallographic evidence for an inverting mechanism in this family of enzymes.

Accepted 12 November 2014

The design and structural characterization of a synthetic pentatricopeptide repeat protein

B. S. Gully, K. R. Shah, M. Lee, K. Shearston, N. M. Smith, A. Sadowska, A. J. Blythe, K. Bernath-Levin, W. A. Stanley, I. D. Small and C. S. Bond

Accepted 11 November 2014

Structures of lactate de­hydrogenase A (LDHA) in apo, ternary and inhibitor-bound forms

S. Kolappan, D. L. Shen, R. Mosi, J. Sun, E. J. McEachern, D. J. Vocadlo and L. Craig

Synopsis: X-ray crystal structures of LDHA in complex with two quinoline-based inhibitors show the inhibitors bound to a site overlapping the NADH-binding site. Apo, oxalate/NADH-bound and oxalate/kanamycin-bound LDHA structures are also reported.

Accepted 8 November 2014

ACHESYM: an algorithm and server for standardized placement of macromolecular models in the unit cell

M. Kowiel, M. Jaskolski and Z. Dauter

Synopsis: An algorithm is proposed for selecting a unique description of macromolecular crystal structures. It is recommended that authors use the procedure before deposition and publication, so that crystal structures are easier to interpret and compare by noncrystallographers.

Accepted 7 November 2014

Structural and biochemical characterization of the laminarinase ZgLamCGH16 from Zobellia galactanivorans suggests preferred recognition of branched laminarin

A. Labourel, M. Jam, L. Legentil, B. Sylla, J.-H. Hehemann, V. Ferrières, M. Czjzek and G. Michel

Synopsis: The storage polysaccharide of brown algae is laminarin, a [beta]-1,3-glucan with occasional [beta]-1,6-branches. The catalytic module of the [beta]-glucanase ZgLamC from the marine bacterium Z. galactanivorans has been characterized. Notably, the structure of an inactive mutant of ZglamC in complex with a thio-[beta]-glucan analogue suggests a specific recognition of the branched domains of laminarin.

Accepted 1 November 2014

Improved crystal orientation and physical properties from single-shot XFEL stills

N. K. Sauter, J. Hattne, A. S. Brewster, N. Echols, P. H. Zwart and P. D. Adams

Accepted 31 October 2014

High-syn conformation of uridine and asymmetry of the hexameric molecule revealed in the high-resolution structures of Shewanella oneidensis MR-1 uridine phosphorylase in the free form and in complex with uridine

T. N. Safonova, S. N. Mikhailov, V. P. Veiko, N. N. Mordkovich, V. A. Manuvera, C. S. Alekseev, M. V. Kovalchuk, V. O. Popov and K. M. Polyakov

Synopsis: The three-dimensional structures of uridine phosphorylase from S. oneidensis MR-1 in the free form and in complex with uridine were determined at atomic resolution (0.95 Å) and high resolution (1.6 Å), respectively. The uridine molecule has an energetically unfavourable high-syn conformation with a nearly planar ribose ring. The hexamer of uridine phosphorylase was found to be asymmetric.

Accepted 30 October 2014

[beta]-Arm flexibility of HU from Staphylococcus aureus dictates the DNA-binding and recognition mechanism

D.-H. Kim, H. Im, J.-G. Jee, S.-B. Jang, H.-J. Yoon, A.-R. Kwon, S.-M. Kang and B.-J. Lee

Synopsis: Structural analysis of apo and DNA-bound HU from S. aureus (SHU) revealed that conformational changes occur in both the protein and DNA upon DNA binding. Base-readout and shape-readout mechanisms are involved in DNA binding and recognition by SHU, in which [beta]-arm flexibility is a major determinant.

Accepted 30 October 2014

The structural basis of the Tle4-Tli4 complex reveals the self-protection mechanism of H2-T6SS in Pseudomonas aeruginosa

D. Lu, Y. Zheng, N. Liao, L. Wei, B. Xu, X. Liu and J. Liu

Accepted 30 October 2014

A cautionary tale of structure-guided inhibitor development against an essential enzyme in the aspartate-biosynthetic pathway

A. G. Pavlovsky, B. Thangavelu, P. Bhansali and R. E. Viola

Accepted 29 October 2014

Structures of holo wild-type human cellular retinol-binding protein II (hCRBPII) bound to retinol and retinal

Z. Nossoni, Z. Assar, I. Yapici, M. Nosrati, W. Wang, T. Berbasova, C. Vasileiou, B. Borhan and J. Geiger

Synopsis: The structures of retinal-bound and retinol-bound hCRBPII are reported. The X-ray flux-dependent and wavelength-dependent rearrangement of retinol in the binding pocket of hCRBPII is demonstrated. The binding modes of retinol and retinal in CRBPI and CRBPII are contrasted.

Accepted 28 October 2014

Neutron scattering from myelin revisited: bilayer asymmetry and water-exchange kinetics

A. R. Denninger, B. Demé, V. Cristiglio, G. LeDuc, W. B. Feller and D. A. Kirschner

Synopsis: The structure of internodal myelin in the rodent central and peripheral nervous systems has been determined using neutron diffraction. The kinetics of water exchange in these tissues is also described.

Accepted 28 October 2014

The crystal structure of human mitochondrial 3-keto­acyl-CoA thiolase (T1): insight into the reaction mechanism of its thiolase and thioesterase activities

T.-R. Kiema, R. K. Harijan, M. Strozyk, T. Fukao, S. Alexson and R. K. Wierenga

Synopsis: Structural and enzymological characterization of the human degradative medium-chain-specific 3-ketoacyl-CoA thiolase (hT1) shows that its structure is highly similar to the short-chain-specific tetrameric biosynthetic thiolases, except for small structural differences in two loops at the active site, which provide extra space for a medium-chain fatty-acyl tail to bind. The intrinsic thioesterase activity of hT1 is also discussed.

Accepted 23 October 2014

Structural and functional insights into an archaeal L-asparaginase obtained through the linker-less assembly of constituent domains

R. Tomar, P. Sharma, A. Srivastava, S. Bansal, Ashish and B. Kundu

Accepted 20 October 2014

Structures of Plasmodium vivax serine hydroxymethyltransferase: implications for ligand-binding specificity and functional control

P. Chitnumsub, A. Jaruwat, P. Riangrungroj, W. Ittarat, K. Noytanom, W. Oonanant, J. Vanichthanankul, P. Chuankhayan, S. Maenpuen, C.-J. Chen, P. Chaiyen, Y. Yuthavong and U. Leartsakulpanich

Synopsis: Crystal structures of P. vivax serine hydroxymethyltransferase (PvSHMT) in complex with L-serine and with D-serine and 5-formyltetrahydrofolate provide better understanding of ligand binding and the catalytic mechanism. Features that are important for controlling the activity and specificity of PvSHMT such as stereoselectivity and redox status are addressed.

Accepted 18 October 2014

Multi-lamellar organization of fully deuterated lipid extracts of yeast membranes

Y. Gerelli, A. de Ghellinck, J. Jouhet, V. Laux, M. Haertlein and G. Fragneto

Synopsis: This first structural characterization of fully deuterated natural lipid extracts has revealed that the membrane stack is complex and regulated mainly by electrostatic repulsion between adjacent membranes. Structural differences with respect to hydrogenous analogues are investigated as a function of temperature and humidity.

Accepted 17 October 2014

High-resolution structures of cholesterol oxidase in the reduced state provide insights into redox stabilization

E. Golden, A. Karton and A. Vrielink

Synopsis: The atomic resolution X-ray diffraction structure of the reduced state of the redox flavoenzyme cholesterol oxidase is presented. The structure indicates the presence of an H atom bound to the flavin N5 atom, suggesting that a hydride transfer has occurred.

Accepted 16 October 2014

Structural implications of the C-terminal tail in the catalytic and stability properties of manganese peroxidases from ligninolytic fungi

E. Fernández-Fueyo, S. Acebes, F. J. Ruiz-Dueñas, M. J. Martínez, A. Romero, F. J. Medrano, V. Guallar and A. T. Martínez

Synopsis: The variable C-terminal tail of manganese peroxidases, a group of enzymes involved in lignin degradation, is implicated in their catalytic and stability properties, as shown by new crystal structures, molecular-simulation and directed-mutagenesis data. Based on this structural-functional evaluation, short and long/extralong manganese peroxidase subfamilies have been accepted; the latter are characterized by exceptional stability, while it is shown for the first time that the former are able to oxidize other substrates at the same site where manganese(II) is oxidized.

Accepted 16 October 2014

The structure of vanin 1: a key enzyme linking metabolic disease and inflammation

Y. L. Boersma, J. Newman, T. E. Adams, N. Cowieson, G. Krippner, K. Bozaoglu and T. S. Peat

Accepted 13 October 2014

Structures of trehalose synthase from Deinococcus radiodurans reveal that a closed conformation is involved in catalysis of the intramolecular isomerization

Y.-L. Wang, S.-Y. Chow, Y.-T. Lin, Y.-C. Hsieh, G.-C. Lee and S.-H. Liaw

Synopsis: Crystal structures of the wild type and the N253A mutant of trehalose synthase from D. radiodurans in complex with the inhibitor Tris have been determined at 2.7 and 2.21 Å resolution, respectively, and they display a closed conformation for catalysis of the intramolecular isomerization.

Accepted 6 October 2014

Structures of an Eph receptor tyrosine kinase and its potential activation mechanism

Q. Wei, J. Liu, N. Wang, X. Zhang, J. Jin, I. Chin-Sang, J. Zheng and Z. Jia

Synopsis: Structures of EphA2 representing three activation states reveal that EphA2 probably possesses an alternate activation mechanism distinct from those of other Eph receptor tyrosine kinases.

Accepted 1 October 2014

Tools for macromolecular model building and refinement into electron cryo-microscopy reconstructions

A. Brown, F. Long, R. A. Nicholls, J. Toots, P. Emsley and G. Murshudov

Synopsis: A description is given of new tools to facilitate model building and refinement into electron cryo-microscopy reconstructions.

Accepted 1 October 2014

Structure and evolution of the spliceosomal peptidyl-prolyl cis-trans isomerase Cwc27

A. Ulrich and M. C. Wahl

Synopsis: Evolutionary comparisons suggest that Cwc27 evolved from a prolyl isomerase to a pure proline binder. The increase in the thermal stability of the PPIase domain of Cwc27 from C. thermophilum compared with its human counterpart is based on the additive effects of several amino-acid changes, which result in the removal of long side chains in strained conformations and additional intramolecular interactions.

Accepted 30 September 2014

Perdeuteration: improved visualization of solvent structure in neutron macromolecular crystallography

S. J. Fisher, M. P. Blakeley, E. I. Howard, I. Petit-Haertlein, M. Haertlein, A. Mitschler, A. Cousido-Siah, A. G. Salvay, A. Popov, C. Muller-Dieckmann, T. Petrova and A. Podjarny

Synopsis: The advantages of perdeuteration with regard to solvent visibility in macromolecules is demonstrated through the comparison of two neutron protein structures.

Accepted 29 September 2014

X-ray structures of eIF5B and the eIF5B-eIF1A complex: the conformational flexibility of eIF5B is restricted on the ribosome by interaction with eIF1A

A. Zheng, J. Yu, R. Yamamoto, T. Ose, I. Tanaka and M. Yao

Synopsis: Two crystal forms of eIF5B and one crystal form of the eIF5B-eIF1A complex exhibit four different conformations of eIF5B, indicating that the conformation of eIF5B is highly flexible. The interaction between eIF5B domain IV and the eIF1A C-terminal tail may restrict the flexibility of eIF5B on the ribosome and stabilize the interface for ribosome subunit joining.

Accepted 29 September 2014

Structure of a backtracked state reveals conformational changes similar to the state following nucleotide incorporation in human norovirus polymerase

D. Zamyatkin, C. Rao, E. Hoffarth, G. Jurca, H. Rho, F. Parra, P. Grochulski and K.K.-S. Ng

Synopsis: The crystal structure of a novel human norovirus polymerase replication complex reveals changes in conformation similar to a state following nucleotide incorporation.

Accepted 25 September 2014

Free kick instead of cross-validation in maximum-likelihood refinement of macromolecular crystal structures

J. Praznikar and D. Turk

Synopsis: The maximum-likelihood free-kick target, which calculates model error estimates from the work set and a randomly displaced model, proved superior in the accuracy and consistency of refinement of crystal structures compared with the maximum-likelihood cross-validation target, which calculates error estimates from the test set and the unperturbed model.

Accepted 29 August 2014

ISPyB for BioSAXS, the gateway to user autonomy in solution scattering experiments

A. De Maria Antolinos, P. Pernot, M. Brennich, J. Kieffer, M. W. Bowler, S. Delageniere, S. Ohlsson, S. Malbet Monaco, A. Ashton, D. Franke, D. Svergun, S. McSweeney, E. Gordon and A. Round

Synopsis: The ISPyB information-management system for crystallography has been adapted to include data from small-angle X-ray scattering of macromolecules in solution experiments.

Accepted 6 August 2014

Collaborative Computational Project for Electron cryo-Microscopy

C. Wood, T. Burnley, A. Patwardhan, S. Scheres, M. Topf, A. Roseman and M. Winn

Synopsis: The Collaborative Computational Project for Electron cryo-Microscopy (CCP-EM) is a new initiative for the structural biology community, following the success of CCP4 for macromolecular crystallography. Progress in supporting the users and developers of cryoEM software is reported.

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