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: The crystal structures of Plasmodium vivax SHMT in complex with L-serine and with D-serine and 5-formyl-tetrahydrofolate provide better understanding of ligand binding and the catalytic mechanism. Features important for controlling PvSHMT activity and specificity such as stereoselectivity and redox status are addressed.
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 a hydrogen atom bound to the flavin N5 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 structure, molecular simulation and directed mutagenesis data. Based on this structural-functional evaluation, short and long/extralong manganese peroxidase subfamilies are accepted, the latter being characterized by exceptional stability, while we shown for the first time that the former are able to oxidize other substrates at the same site where Mn(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 the 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 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 of thermal stability of the Cwc27 PPIase domain of 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 a strained conformation 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: A novel protein fold and the first crystal structure of a gas vesicle protein are described.
Synopsis: EhIPPase is probably the inositol polyphosphate 1-phosphatase of E. histolytica.
Synopsis: The first structure of B. anthracis PurK with a bicarbonate ion in the active site is reported. Based on several enzyme structures with different ligands in the active site, a mechanism for the enzymatic reaction is proposed.
Synopsis: The enzyme-adenylate structure of a bacterial ATP-dependent DNA ligase (ADL), which does not have any additional DNA-binding domains, is similar to minimal viral ADLs that comprise only the core catalytic domains. The bacterial ADL also lacks the unstructured loops which are involved in DNA binding in the viral ADLs, implying that it must instead use short well structured motifs of the core domains to engage its substrate.
Synopsis: The structural bases of the inactivation of methionine -lyase by a new suicide substrate were determined.
Synopsis: The structures of the ascomycetous B. aclada laccase and its L499M T1-site mutant have been solved at 1.7 Å resolution. The mutant enzyme shows a 140 mV lower redox potential of the type 1 copper and altered kinetic behaviour. The wild type and the mutant have very similar structures, which makes it possible to relate the changes in the redox potential to the L499M mutation
Synopsis: X-ray and solution structures of the human RyR2 N-terminal region were obtained under near-physiological conditions. The structure exhibits a unique network of interactions between its three domains, revealing an important stabilizing role of the central helix.
Synopsis: The crystal structures of a first fungal glycoside hydrolase family 5 -mannosidase from Rhizomucor miehei (RmMan5B) and of its inactive E202A mutant in complex with mannobiose, mannotriose and mannosyl-fructose are presented. Structural analyses reveal the structural basis of substrates binding.
Synopsis: Nuclease A (NucA) is an extracellular nuclease secreted from S. agalactiae and is required for full virulence during infection. Crystal structures and biochemical characterization of NucA mutants reveal possible roles for surface residues in DNA substrate binding and catalysis. These results may serve as a foundation for the design of targeted antibacterial therapeutic compounds.
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: A GH30 subfamily 8 (GH30-8) xylanase with functional properties different from the canonical GH30-8 glucuronoxylan xylanohydrolases has been biochemically and structurally characterized. The findings highlight the diversity of xylanolytic activities that derive from the GH30 family of glycoside hydrolases.
Synopsis: The crystal structure of ADC-68 reveals new mechanisms for expanding its substrate spectrum to extended-spectrum cephalosporins and carbapenems.
Synopsis: The current and the attainable coverage by X-ray structures of proteins and their functions on the scale of the `protein universe' are estimated. A detailed analysis of the coverage across nearly 2000 proteomes from all superkingdoms of life and functional annotations is performed, with particular focus on the human proteome and the family of GPCR proteins.
Synopsis: Mycobacterium tuberculosis MenB, or 1, 4-dihydroxynaphthoyl coenzyme A synthase, is found to undergo induced-fit conformational changes that play an important role in substrate recognition and catalytic mechanism.
Synopsis: The three-dimensional structure of the GH27 arabinopyranosidase (Abp) from G. stearothermophilus T6 has been determined by molecular replacement, leading to full structural analysis of wild-type Abp (at 2.28 Å resolution) and its catalytic mutant Abp-D197A with (at 2.20 Å resolution) and without (at 2.30 Å resolution) bound L-arabinose product. The structures demonstrate that Abp is a tetramer built of two pincer-like dimers, as also confirmed by SAXS.
Synopsis: The present work illustrates that small-angle neutron scattering, deuteration and contrast variation, combined with in vitro particle reconstruction, constitutes a very efficient approach to determine subunit architectures in large, symmetric protein complexes. In the case of the 468 kDa heterododecameric TET peptidase machine, it was demonstrated that the assembly of the 12 subunits is a highly controlled process and represents a way to optimize the catalytic efficiency of the enzyme.
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.
Synopsis: The rate of global radiation damage to 70S ribosome crystals has been measured at 100, 180 and 300 K. At 100 and 300 K, damage rates are comparable to and much larger than those of model proteins, respectively. The larger damage rates at 300 K cannot explain the dramatically higher diffraction quality observed at 100 K.
Synopsis: The biophysical characterization of protein-ligand interactions in solution using techniques such as thermal shift assay, or on surfaces using, for example, dual polarization interferometry, plays an increasingly important role in complementing crystal structure determinations.
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