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Acta Crystallographica. Section D, Structural Biology

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https://read.qxmd.com/read/31063153/analysis-and-validation-of-macromolecular-b-values
#1
Rafiga C Masmaliyeva, Garib N Murshudov
This paper describes a global analysis of macromolecular B values. It is shown that the distribution of B values generally follows the shifted inverse-gamma distribution (SIGD). The parameters of the SIGD are estimated using the Fisher scoring technique with the expected Fisher information matrix. It is demonstrated that a contour plot based on the parameters of the SIGD can play a role in the validation of macromolecular structures. The dependence of the peak-height distribution on resolution and atomic B values is also analysed...
May 1, 2019: Acta Crystallographica. Section D, Structural Biology
https://read.qxmd.com/read/31063152/structural-analysis-of-a-replication-protein-encoded-by-a-plasmid-isolated-from-a-multiple-sclerosis-patient
#2
Turgay Kilic, Alexander N Popov, Amelie Burk-Körner, Anna Koromyslova, Harald Zur Hausen, Timo Bund, Grant S Hansman
Bovine meat and milk factors (BMMFs) are circular, single-stranded episomal DNAs that have been detected in bovine meat and milk products. BMMFs are thought to have roles in human malignant and degenerative diseases. BMMFs encode a replication initiator protein (Rep) that is actively transcribed and translated in human cells. In this study, a Rep WH1 domain encoded on a BMMF (MSBI1.176) isolated from a multiple sclerosis human brain sample was determined to 1.53 Å resolution using X-ray crystallography. The overall structure of the MSBI1...
May 1, 2019: Acta Crystallographica. Section D, Structural Biology
https://read.qxmd.com/read/31063151/crystal-structure-of-the-leucine-rich-repeat-ectodomain-of-the-plant-immune-receptor-kinase-sobir1
#3
Ulrich Hohmann, Michael Hothorn
Plant-unique membrane receptor kinases with leucine-rich repeat (LRR) extracellular domains are key regulators of development and immune responses. Here, the 1.55 Å resolution crystal structure of the immune receptor kinase SOBIR1 from Arabidopsis is presented. The ectodomain structure reveals the presence of five LRRs sandwiched between noncanonical capping domains. The disulfide-bond-stabilized N-terminal cap harbours an unusual β-hairpin structure. The C-terminal cap features a highly positively charged linear motif which was found to be largely disordered in this structure...
May 1, 2019: Acta Crystallographica. Section D, Structural Biology
https://read.qxmd.com/read/31063150/structural-and-functional-insights-into-phosphomannose-isomerase-the-role-of-zinc-and-catalytic-residues
#4
Mamata Bangera, Giri Gowda K, S R Sagurthi, M R N Murthy
Phosphomannose isomerase (PMI) is a housekeeping enzyme that is found in organisms ranging from bacteria to fungi to mammals and is important for cell-wall synthesis, viability and signalling. PMI is a zinc-dependent enzyme that catalyses the reversible isomerization between mannose 6-phosphate (M6P) and fructose 6-phosphate (F6P), presumably via the formation of a cis-enediol intermediate. The reaction is hypothesized to involve ring opening of M6P, the transfer of a proton from the C2 atom to the C1 atom and between the O1 and O2 atoms of the substrate, followed by ring closure resulting in the product F6P...
May 1, 2019: Acta Crystallographica. Section D, Structural Biology
https://read.qxmd.com/read/31063149/visualizing-membrane-trafficking-through-the-electron-microscope-cryo-tomography-of-coat-complexes
#5
Evgenia A Markova, Giulia Zanetti
Coat proteins mediate vesicular transport between intracellular compartments, which is essential for the distribution of molecules within the eukaryotic cell. The global arrangement of coat proteins on the membrane is key to their function, and cryo-electron tomography and subtomogram averaging have been used to study membrane-bound coat proteins, providing crucial structural insight. This review outlines a workflow for the structural elucidation of coat proteins, incorporating recent developments in the collection and processing of cryo-electron tomography data...
May 1, 2019: Acta Crystallographica. Section D, Structural Biology
https://read.qxmd.com/read/31063148/design-guidelines-for-an-electron-diffractometer-for-structural-chemistry-and-structural-biology
#6
Jonas Heidler, Radosav Pantelic, Julian T C Wennmacher, Christian Zaubitzer, Ariane Fecteau-Lefebvre, Kenneth N Goldie, Elisabeth Müller, Julian J Holstein, Eric van Genderen, Sacha De Carlo, Tim Gruene
3D electron diffraction has reached a stage where the structures of chemical compounds can be solved productively. Instrumentation is lagging behind this development, and to date dedicated electron diffractometers for data collection based on the rotation method do not exist. Current studies use transmission electron microscopes as a workaround. These are optimized for imaging, which is not optimal for diffraction studies. The beam intensity is very high, it is difficult to create parallel beam illumination and the detectors used for imaging are of only limited use for diffraction studies...
May 1, 2019: Acta Crystallographica. Section D, Structural Biology
https://read.qxmd.com/read/31063147/findable-accessible-interoperable-re-usable-fair-diffraction-data-are-coming-to-protein-crystallography
#7
John R Helliwell, Wladek Minor, Manfred S Weiss, Elspeth F Garman, Randy J Read, Janet Newman, Mark J van Raaij, Janos Hajdu, Edward N Baker
No abstract text is available yet for this article.
May 1, 2019: Acta Crystallographica. Section D, Structural Biology
https://read.qxmd.com/read/30988261/announcing-mandatory-submission-of-pdbx-mmcif-format-files-for-crystallographic-depositions-to-the-protein-data-bank-pdb
#8
Paul D Adams, Pavel V Afonine, Kumaran Baskaran, Helen M Berman, John Berrisford, Gerard Bricogne, David G Brown, Stephen K Burley, Minyu Chen, Zukang Feng, Claus Flensburg, Aleksandras Gutmanas, Jeffrey C Hoch, Yasuyo Ikegawa, Yumiko Kengaku, Eugene Krissinel, Genji Kurisu, Yuhe Liang, Dorothee Liebschner, Lora Mak, John L Markley, Nigel W Moriarty, Garib N Murshudov, Martin Noble, Ezra Peisach, Irina Persikova, Billy K Poon, Oleg V Sobolev, Eldon L Ulrich, Sameer Velankar, Clemens Vonrhein, John Westbrook, Marcin Wojdyr, Masashi Yokochi, Jasmine Y Young
No abstract text is available yet for this article.
April 1, 2019: Acta Crystallographica. Section D, Structural Biology
https://read.qxmd.com/read/30988260/nitrosative-stress-sensing-in-porphyromonas-gingivalis-structure-of-and-heme-binding-by-the-transcriptional-regulator-hcpr
#9
B Ross Belvin, Faik N Musayev, John Burgner, J Neel Scarsdale, Carlos R Escalante, Janina P Lewis
Although the HcpR regulator plays a vital step in initiation of the nitrosative stress response in many Gram-negative anaerobic bacteria, the molecular mechanisms that it uses to mediate gas sensing are not well understood. Here, a 2.6 Å resolution crystal structure of the N-terminal sensing domain of the anaerobic periodontopathogen Porphyromonas gingivalis HcpR is presented. The protein has classical features of the regulators belonging to the FNR-CRP family and contains a hydrophobic pocket in its N-terminal sensing domain...
April 1, 2019: Acta Crystallographica. Section D, Structural Biology
https://read.qxmd.com/read/30988259/high-resolution-crystal-structures-of-the-glycoside-hydrolase-family-45-endoglucanase-eg27ii-from-the-snail-ampullaria-crossean
#10
Taisuke Nomura, Hisamu Iwase, Naoki Saka, Nobuyuki Takahashi, Bunzo Mikami, Kimihiko Mizutani
Although endogenous animal cellulases have great potential for industrial applications such as bioethanol production, few investigations have focused on these enzymes. In this study, the glycoside hydrolase family 45 (GH45) subfamily B endoglucanase EG27II from the snail Ampullaria crossean was expressed using a Pichia pastoris expression system and the crystal structure of the apo form was determined at 1.00 Å resolution; this is the highest resolution structure of an animal endoglucanase. The results showed that EG27II has a double-ψ six-stranded β-barrel and that the structure of EG27II more closely resembles those of subfamily C enzymes than those of subfamily A enzymes...
April 1, 2019: Acta Crystallographica. Section D, Structural Biology
https://read.qxmd.com/read/30988258/building-and-rebuilding-n-glycans-in-protein-structure-models
#11
Bart van Beusekom, Natasja Wezel, Maarten L Hekkelman, Anastassis Perrakis, Paul Emsley, Robbie P Joosten
N-Glycosylation is one of the most common post-translational modifications and is implicated in, for example, protein folding and interaction with ligands and receptors. N-Glycosylation trees are complex structures of linked carbohydrate residues attached to asparagine residues. While carbohydrates are typically modeled in protein structures, they are often incomplete or have the wrong chemistry. Here, new tools are presented to automatically rebuild existing glycosylation trees, to extend them where possible, and to add new glycosylation trees if they are missing from the model...
April 1, 2019: Acta Crystallographica. Section D, Structural Biology
https://read.qxmd.com/read/30988257/crystal-structure-of-the-pseudoenzyme-pdx1-2-in-complex-with-its-cognate-enzyme-pdx1-3-a-total-eclipse
#12
Graham C Robinson, Markus Kaufmann, Céline Roux, Jacobo Martinez-Font, Michael Hothorn, Stéphane Thore, Teresa B Fitzpatrick
Pseudoenzymes have burst into the limelight recently as they provide another dimension to regulation of cellular protein activity. In the eudicot plant lineage, the pseudoenzyme PDX1.2 and its cognate enzyme PDX1.3 interact to regulate vitamin B6 biosynthesis. This partnership is important for plant fitness during environmental stress, in particular heat stress. PDX1.2 increases the catalytic activity of PDX1.3, with an overall increase in vitamin B6 biosynthesis. However, the mechanism by which this is achieved is not known...
April 1, 2019: Acta Crystallographica. Section D, Structural Biology
https://read.qxmd.com/read/30988256/the-third-structural-switch-in-the-archaeal-translation-initiation-factor-2-aif2-molecule-and-its-possible-role-in-the-initiation-of-gtp-hydrolysis-and-the-removal-of-aif2-from-the-ribosome
#13
Oleg Nikonov, Olesya Kravchenko, Natalia Nevskaya, Elena Stolboushkina, Maria Garber, Stanislav Nikonov
The structure of the γ subunit of archaeal translation initiation factor 2 (aIF2) from Sulfolobus solfataricus (SsoIF2γ) was determined in complex with GDPCP (a GTP analog). Crystals were obtained in the absence of magnesium ions in the crystallization solution. They belonged to space group P1, with five molecules in the unit cell. Four of these molecules are related in pairs by a common noncrystallographic twofold symmetry axis, while the fifth has no symmetry equivalent. Analysis of the structure and its comparison with other known aIF2 γ-subunit structures in the GTP-bound state show that (i) the magnesium ion is necessary for the formation and the maintenance of the active form of SsoIF2γ and (ii) in addition to the two previously known structural switches 1 and 2, eukaryotic translation initiation factor 2 (eIF2) and aIF2 molecules have another flexible region (switch 3), the function of which may consist of initiation of the hydrolysis of GTP and the removal of e/aIF2 from the ribosome after codon-anticodon recognition...
April 1, 2019: Acta Crystallographica. Section D, Structural Biology
https://read.qxmd.com/read/30988255/conformational-changes-in-the-third-pdz-domain-of-the-neuronal-postsynaptic-density-protein-95
#14
Ana Camara-Artigas, Javier Murciano-Calles, Jose C Martínez
PDZ domains are protein-protein recognition modules that interact with other proteins through short sequences at the carboxyl terminus. These domains are structurally characterized by a conserved fold composed of six β-strands and two α-helices. The third PDZ domain of the neuronal postsynaptic density protein 95 has an additional α-helix (α3), the role of which is not well known. In previous structures, a succinimide was identified in the β2-β3 loop instead of Asp332. The presence of this modified residue results in conformational changes in α3...
April 1, 2019: Acta Crystallographica. Section D, Structural Biology
https://read.qxmd.com/read/30988254/refinement-of-protein-structures-using-a-combination-of-quantum-mechanical-calculations-with-neutron-and-x-ray-crystallographic-data
#15
Octav Caldararu, Francesco Manzoni, Esko Oksanen, Derek T Logan, Ulf Ryde
Neutron crystallography is a powerful method to determine the positions of H atoms in macromolecular structures. However, it is sometimes hard to judge what would constitute a chemically reasonable model, and the geometry of H atoms depends more on the surroundings (for example the formation of hydrogen bonds) than heavy atoms, so that the empirical geometry information for the H atoms used to supplement the experimental data is often less accurate. These problems may be reduced by using quantum-mechanical calculations...
April 1, 2019: Acta Crystallographica. Section D, Structural Biology
https://read.qxmd.com/read/30988253/a-structural-overview-of-the-zinc-transporters-in-the-cation-diffusion-facilitator-family
#16
Camila A Cotrim, Russell J Jarrott, Jennifer L Martin, David Drew
The cation diffusion facilitators (CDFs) are a family of membrane-bound proteins that maintain cellular homeostasis of essential metal ions. In humans, the zinc-transporter CDF family members (ZnTs) play important roles in zinc homeostasis. They do this by facilitating zinc efflux from the cytoplasm to the extracellular space across the plasma membrane or into intracellular organelles. Several ZnTs have been implicated in human health owing to their association with type 2 diabetes and neurodegenerative diseases...
April 1, 2019: Acta Crystallographica. Section D, Structural Biology
https://read.qxmd.com/read/30950406/thomas-a-steitz-1940-2018
#17
Poul Nissen
No abstract text is available yet for this article.
March 1, 2019: Acta Crystallographica. Section D, Structural Biology
https://read.qxmd.com/read/30950405/coping-with-strong-translational-noncrystallographic-symmetry-and-extreme-anisotropy-in-molecular-replacement-with-phaser-human-rab27a
#18
Mostafa Jamshidiha, Inmaculada Pérez-Dorado, James W Murray, Edward W Tate, Ernesto Cota, Randy J Read
Data pathologies caused by effects such as diffraction anisotropy and translational noncrystallographic symmetry (tNCS) can dramatically complicate the solution of the crystal structures of macromolecules. Such problems were encountered in determining the structure of a mutant form of Rab27a, a member of the Rab GTPases. Mutant Rab27a constructs that crystallize in the free form were designed for use in the discovery of drugs to reduce primary tumour invasiveness and metastasis. One construct, hRab27aMut , crystallized within 24 h and diffracted to 2...
March 1, 2019: Acta Crystallographica. Section D, Structural Biology
https://read.qxmd.com/read/30950404/a-60-heme-reductase-complex-from-an-anammox-bacterium-shows-an-extended-electron-transfer-pathway
#19
Andreas Dietl, Wouter J Maalcke, Christina Ferousi, Mike S M Jetten, Boran Kartal, Thomas R M Barends
The hydroxylamine oxidoreductase/hydrazine dehydrogenase (HAO/HDH) protein family constitutes an important group of octaheme cytochromes c (OCCs). The majority of these proteins form homotrimers, with their subunits being covalently attached to each other via a rare cross-link between the catalytic heme moiety and a conserved tyrosine residue in an adjacent subunit. This covalent cross-link has been proposed to modulate the active-site heme towards oxidative catalysis by distorting the heme plane. In this study, the crystal structure of a stable complex of an HAO homologue (KsHAOr) with its diheme cytochrome c redox partner (KsDH) from the anammox bacterium Kuenenia stuttgartiensis was determined...
March 1, 2019: Acta Crystallographica. Section D, Structural Biology
https://read.qxmd.com/read/30950403/x-ray-structure-of-an-inactive-zymogen-clostripain-like-protease-from-parabacteroides-distasonis
#20
Gonzalo E González-Páez, Emily J Roncase, Dennis W Wolan
The clostripain-like (C11) family of cysteine proteases are ubiquitously produced by the vast majority of the bacterial strains that make up the human distal gut microbiome. Recent reports show that some C11 proteases promote host immune responses and bacterial pathogenesis, including the induction of neutrophil phagocytosis and the activation of bacterial pathogenic toxins, respectively. The crystal structure of distapain, the only C11 protease predicted within the genome of the commensal bacterium Parabacteroides distasonis, was determined in the inactive zymogen state to 1...
March 1, 2019: Acta Crystallographica. Section D, Structural Biology
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