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.
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.
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.
Synopsis: Time-resolved study with the freeze trap method elucidates the mechanism of DNA-cleaving reaction of HindIII.
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.
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.
Synopsis: 4pph, -conglutin, 7S basic globulin. The crystal structure of 45 kDa -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.
Synopsis: Structural, functional and phylogenetic analyses reveal enzyme diversity within family 117 of the glycoside hydrolases, which remove terminal -1,3-linked 3,6-anhydro-L-galactose from neoagaro-oligosaccharides produced by -agarases. A product complex with the unique -3,6-anhydro-L-galactose provides strong crystallographic evidence for an inverting mechanism in this family of enzymes.
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.
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.
Synopsis: The storage polysaccharide of brown algae is laminarin, a -1,3-glucan with occasional -1,6-branches. The catalytic module of the -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--glucan analogue suggests a specific recognition of the branched domains of laminarin.
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.
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 -arm flexibility is a major determinant.
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.
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.
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.
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.
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.
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.
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.
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.
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.
Synopsis: A description is given of new tools to facilitate model building and refinement into electron cryo-microscopy reconstructions.
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.
Synopsis: The advantages of perdeuteration with regard to solvent visibility in macromolecules is demonstrated through the comparison of two neutron protein structures.
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.
Synopsis: The crystal structure of a novel human norovirus polymerase replication complex reveals changes in conformation similar to a state following nucleotide incorporation.
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.
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.
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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