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Acta Crystallographica. Section F, Structural Biology Communications

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https://www.readbyqxmd.com/read/28580926/crystal-structure-of-recombinant-phosphoribosylpyrophosphate-synthetase-2-from-thermus-thermophilus-hb27-complexed-with-adp-and-sulfate-ions
#1
Vladimir I Timofeev, Ekaterina V Sinitsyna, Maria A Kostromina, Tatiana I Muravieva, Dmitry A Makarov, Olga O Mikheeva, Inna P Kuranova, Roman S Esipov
Phosphoribosylpyrophosphate synthetase (PRPPS) from the thermophilic bacterial strain Thermus thermophilus HB27 catalyzes the synthesis of phosphoribosylpyrophosphate from ribose 5-phosphate and ATP, and belongs to the class I PRPPSs. The three-dimensional structure of the recombinant enzyme was solved at 2.2 Å resolution using crystals grown in microgravity from protein solution containing ATP, magnesium and sulfate ions. An ADP molecule was located in the active site of each subunit of the hexameric enzyme molecule and sulfate ions were located in both the active and allosteric sites...
June 1, 2017: Acta Crystallographica. Section F, Structural Biology Communications
https://www.readbyqxmd.com/read/28580925/crystal-structure-of-the-multiple-antibiotic-resistance-regulator-marr-from-clostridium-difficile
#2
J W Peng, H Yuan, X S Tan
Regulators of multiple antibiotic resistance (MarRs) are key players against toxins in prokaryotes. MarR homologues have been identified in many bacterial and archaeal species which pose daunting antibiotic resistance issues that threaten public health. The continuous prevalence of Clostridium difficile infection (CDI) throughout the world is associated with the abuse of antibiotics, and antibiotic treatments of CDI have limited effect. In the genome of C. difficile strain 630, the marR gene (ID 4913953) encodes a MarR protein...
June 1, 2017: Acta Crystallographica. Section F, Structural Biology Communications
https://www.readbyqxmd.com/read/28580924/crystal-structure-of-n-acetylmannosamine-kinase-from-fusobacterium-nucleatum
#3
Rhawnie Caing-Carlsson, Parveen Goyal, Amit Sharma, Swagatha Ghosh, Thanuja Gangi Setty, Rachel A North, Rosmarie Friemann, S Ramaswamy
Sialic acids comprise a varied group of nine-carbon amino sugars that are widely distributed among mammals and higher metazoans. Some human commensals and bacterial pathogens can scavenge sialic acids from their environment and degrade them for use as a carbon and nitrogen source. The enzyme N-acetylmannosamine kinase (NanK; EC 2.7.1.60) belongs to the transcriptional repressors, uncharacterized open reading frames and sugar kinases (ROK) superfamily. NanK catalyzes the second step of the sialic acid catabolic pathway, transferring a phosphate group from adenosine 5'-triphosphate to the C6 position of N-acetylmannosamine to generate N-acetylmannosamine 6-phosphate...
June 1, 2017: Acta Crystallographica. Section F, Structural Biology Communications
https://www.readbyqxmd.com/read/28580923/the-crystal-structure-of-human-deah-box-rna-helicase-15-reveals-a-domain-organization-of-the-mammalian-deah-rha-family
#4
Karin Murakami, Kenji Nakano, Toshiyuki Shimizu, Umeharu Ohto
DEAH-box RNA helicase 15 (DHX15) plays important roles in RNA metabolism, including in splicing and in ribosome biogenesis. In addition, mammalian DHX15 also mediates the innate immune sensing of viral RNA. However, structural information on this protein is not available, although the structure of the fungal orthologue of this protein, Prp43, has been elucidated. Here, the crystal structure of the ADP-bound form of human DHX15 is reported at a resolution of 2.0 Å. This is the first structure to be revealed of a member of the mammalian DEAH-box RNA helicase (DEAH/RHA) family in a nearly complete form, including the catalytic core consisting of the two N-terminal RecA domains and the C-terminal regulatory domains (CTD)...
June 1, 2017: Acta Crystallographica. Section F, Structural Biology Communications
https://www.readbyqxmd.com/read/28580922/phosphate-binding-protein-from-polaromonas-js666-purification-characterization-crystallization-and-sulfur-sad-phasing
#5
Vanessa R Pegos, Louis Hey, Jacob LaMirande, Rachel Pfeffer, Rosalie Lipsh, Moshe Amitay, Daniel Gonzalez, Mikael Elias
Phosphate-binding proteins (PBPs) are key proteins that belong to the bacterial ABC-type phosphate transporters. PBPs are periplasmic (or membrane-anchored) proteins that capture phosphate anions from the environment and release them to the transmembrane transporter. Recent work has suggested that PBPs have evolved for high affinity as well as high selectivity. In particular, a short, unique hydrogen bond between the phosphate anion and an aspartate residue has been shown to be critical for selectivity, yet is not strictly conserved in PBPs...
June 1, 2017: Acta Crystallographica. Section F, Structural Biology Communications
https://www.readbyqxmd.com/read/28580921/crystal-structure-of-the-active-form-of-native-human-thymidylate-synthase-in-the-absence-of-bound-substrates
#6
P Deschamps, S Réty, J Bareille, N Leulliot
Human thymidylate synthase (hTS) provides the sole de novo intracellular source of thymidine 5'-monophosphate (dTMP). hTS is required for DNA replication prior to cell division, making it an attractive target for anticancer chemotherapy and drug discovery. hTS binds 2'-deoxyuridine 5'-monophosphate (dUMP) and the folate co-substrate N(5),N(10)-methylenetetrahydrofolate (meTHF) in a pocket near the catalytic residue Cys195. The catalytic loop, which is composed of amino-acid residues 181-197, can adopt two distinct conformations related by a 180° rotation...
June 1, 2017: Acta Crystallographica. Section F, Structural Biology Communications
https://www.readbyqxmd.com/read/28580920/crystal-structure-of-the-thermoplasma-acidophilum-protein-ta1207
#7
Ganesh Ramnath Pathare, István Nagy, Ágnes Hubert, Dennis R Thomas, Andreas Bracher
The crystal structure of the Ta1207 protein from Thermoplasma acidophilum is reported. Ta1207 was identified in a screen for high-molecular-weight protein complexes in T. acidophilum. In solution, Ta1207 forms homopentamers of 188 kDa. The crystal structure of recombinant Ta1207 solved by Se-MAD at 2.4 Å resolution revealed a complex with fivefold symmetry. In the crystal lattice, calcium ions induce the formation of a nanocage from two pentamers. The Ta1207 protomers comprise two domains with the same novel α/β topology...
June 1, 2017: Acta Crystallographica. Section F, Structural Biology Communications
https://www.readbyqxmd.com/read/28580919/crystallization-and-x-ray-diffraction-analysis-of-spae-a-basal-pilus-protein-from-the-gut-adapted-lactobacillus-rhamnosus-gg
#8
Arjun K Mishra, Abhin Kumar Megta, Airi Palva, Ingemar von Ossowski, Vengadesan Krishnan
SpaE is the predicted basal pilin subunit in the sortase-dependent SpaFED pilus from the gut-adapted and commensal Lactobacillus rhamnosus GG. Thus far, structural characterization of the cell-wall-anchoring basal pilins has remained difficult and has been limited to only a few examples from pathogenic genera and species. To gain a further structural understanding of the molecular mechanisms that are involved in the anchoring and assembly of sortase-dependent pili in less harmful bacteria, L. rhamnosus GG SpaE for crystallization was produced by recombinant expression in Escherichia coli...
June 1, 2017: Acta Crystallographica. Section F, Structural Biology Communications
https://www.readbyqxmd.com/read/28580918/crystal-structure-of-rv1220c-a-sam-dependent-o-methyltransferase-from-mycobacterium-tuberculosis
#9
Qiaoling Yan, Neil Shaw, Lanfang Qian, Dunquan Jiang
Rv1220c from Mycobacterium tuberculosis is annotated as an O-methyltransferase (MtbOMT). Currently, no structural information is available for this protein. Here, the crystal structure of MtbOMT refined to 2.0 Å resolution is described. The structure reveals the presence of a methyltransferase fold and shows clear electron density for one molecule of S-adenosylmethionine (SAM), which was apparently bound by the protein during its production in Escherichia coli. Although the overall structure of MtbOMT resembles the structures of O-methyltransferases from Cornybacterium glutamicum, Coxiella burnetti and Alfa alfa, differences are observed in the residues that make up the active site...
June 1, 2017: Acta Crystallographica. Section F, Structural Biology Communications
https://www.readbyqxmd.com/read/28580917/crystal-structures-of-human-fabs-targeting-the-bexsero-meningococcal-vaccine-antigen-nhba
#10
Martina Maritan, Roberta Cozzi, Paola Lo Surdo, Daniele Veggi, Matthew James Bottomley, Enrico Malito
Neisserial heparin-binding antigen (NHBA) is a surface-exposed lipoprotein from Neisseria meningitidis and is a component of the meningococcus B vaccine Bexsero. As part of a study to characterize the three-dimensional structure of NHBA and the molecular basis of the human immune response to Bexsero, the crystal structures of two fragment antigen-binding domains (Fabs) isolated from human monoclonal antibodies targeting NHBA were determined. Through a high-resolution analysis of the organization and the amino-acid composition of the CDRs, these structures provide broad insights into the NHBA epitopes recognized by the human immune system...
June 1, 2017: Acta Crystallographica. Section F, Structural Biology Communications
https://www.readbyqxmd.com/read/28471363/crystallization-and-biochemical-characterization-of-an-archaeal-lectin-from-methanococcus-voltae-a3
#11
N Sivaji, K V Abhinav, M Vijayan
A lectin from Methanococcus voltae A3 has been cloned, expressed, purified and characterized. The lectin appears to be specific for complex sugars. The protein crystallized in a tetragonal space group, with around 16 subunits in the asymmetric unit. Sequence comparisons indicate the lectin to have a β-prism I fold, with poor homology to lectins of known three-dimensional structure.
May 1, 2017: Acta Crystallographica. Section F, Structural Biology Communications
https://www.readbyqxmd.com/read/28471362/crystal-structure-of-cd27-in-complex-with-a-neutralizing-noncompeting-antibody
#12
Alexey Teplyakov, Galina Obmolova, Thomas J Malia, Gary L Gilliland
CD27 is a T-cell and B-cell co-stimulatory glycoprotein of the tumor necrosis factor (TNF) receptor superfamily that is dependent on the availability of the TNF-like ligand CD70. Therapeutic approaches to treating autoimmune diseases and cancers with antagonistic and agonistic anti-CD27 monoclonal antibodies (mAbs), respectively, have recently been developed. Mouse anti-human CD27 mAb 2177 shows potency in neutralizing CD70-induced signaling; however, it does not block the binding of soluble CD70. To provide insight into the mechanism of action of the mAb, the crystal structure of the CD27 extracellular domain in complex with the Fab fragment of mAb 2177 was determined at 1...
May 1, 2017: Acta Crystallographica. Section F, Structural Biology Communications
https://www.readbyqxmd.com/read/28471361/camelid-nanobodies-used-as-crystallization-chaperones-for-different-constructs-of-porm-a-component-of-the-type-ix-secretion-system-from-porphyromonas-gingivalis
#13
Yoan Duhoo, Jennifer Roche, Thi Trang Nhung Trinh, Aline Desmyter, Anaïs Gaubert, Christine Kellenberger, Christian Cambillau, Alain Roussel, Philippe Leone
PorM is a membrane protein that is involved in the assembly of the type IX secretion system (T9SS) in Porphyromonas gingivalis, a major bacterial pathogen that is responsible for periodontal disease in humans. In the context of structural studies of PorM to better understand T9SS assembly, four camelid nanobodies were selected, produced and purified, and their specific interaction with the N-terminal or C-terminal part of the periplasmic domain of PorM was investigated. Diffracting crystals were also obtained, and the structures of the four nanobodies were solved by molecular replacement...
May 1, 2017: Acta Crystallographica. Section F, Structural Biology Communications
https://www.readbyqxmd.com/read/28471360/transcription-factor-rv0081-from-mycobacterium-tuberculosis-purification-crystallization-and-initial-crystallographic-analysis
#14
Shishang Dong, Zhenzhen Ding, Yu Wang, Yan Yang, Yonghong Mao, Ying Wang
Because of its high infectivity and pathogenicity, Mycobacterium tuberculosis is a serious threat to human health. While the transcription-regulatory system of M. tuberculosis remains incompletely understood, Rv0081, an essential regulatory hub, is known to mediate the initial response to hypoxia in the long-term survival of M. tuberculosis. Here, the production, crystallization and initial X-ray crystallographic analysis of Rv0081 are reported. The crystals of Rv0081 belonged to space group P62, with unit-cell parameters a = 67...
May 1, 2017: Acta Crystallographica. Section F, Structural Biology Communications
https://www.readbyqxmd.com/read/28471359/crystal-structure-of-the-rna-2-3-cyclic-phosphodiesterase-from-deinococcus-radiodurans
#15
Wanchun Han, Jiahui Cheng, Congli Zhou, Yuejin Hua, Ye Zhao
2',3'-Cyclic phosphodiesterase (CPDase) homologues have been found in all domains of life and are involved in diverse RNA and nucleotide metabolisms. The CPDase from Deinococcus radiodurans was crystallized and the crystals diffracted to 1.6 Å resolution, which is the highest resolution currently known for a CPDase structure. Structural comparisons revealed that the enzyme is in an open conformation in the absence of substrate. Nevertheless, the active site is well formed, and the representative motifs interact with sulfate ion, which suggests a conserved catalytic mechanism...
May 1, 2017: Acta Crystallographica. Section F, Structural Biology Communications
https://www.readbyqxmd.com/read/28471358/structural-insights-into-the-mechanism-of-the-drastic-changes-in-enzymatic-activity-of-the-cytochrome-p450-vitamin-d3-hydroxylase-cyp107br1-caused-by-a-mutation-distant-from-the-active-site
#16
Yoshiaki Yasutake, Tomoshi Kameda, Tomohiro Tamura
Cytochromes P450 (P450s) are haem-containing enzymes that catalyze medically and industrially important oxidative reactions, and many P450s have been subjected to directed evolution and site-directed mutagenesis to improve their activity and substrate specificity. Nonetheless, in most cases the mechanism that leads to drastic changes in specific activity after the introduction of an amino-acid substitution distant from the active-site pocket is unclear. Here, two crystal structures of inactive mutants of the P450 vitamin D3 hydroxylase (Vdh), Vdh-F106V and Vdh-L348M, which were obtained in the course of protein-engineering experiments on Vdh, are reported...
May 1, 2017: Acta Crystallographica. Section F, Structural Biology Communications
https://www.readbyqxmd.com/read/28471357/crystal-structure-of-d-ccggggtaccccgg-2-at-1-4%C3%A2-%C3%A3-resolution
#17
Selvam Karthik, Arunachalam Thirugnanasambandam, Pradeep Kumar Mandal, Namasivayam Gautham
The X-ray crystal structure of the DNA tetradecamer sequence d(CCGGGGTACCCCGG)2 is reported at 1.4 Å resolution in the tetragonal space group P41212. The sequence was designed to fold as a four-way junction. However, it forms an A-type double helix in the presence of barium chloride. The metal ion could not be identified in the electron-density map. The crystallographic asymmetric unit consists of one A-type double helix with 12 base pairs per turn, in contrast to 11 base pairs per turn for canonical A-DNA...
May 1, 2017: Acta Crystallographica. Section F, Structural Biology Communications
https://www.readbyqxmd.com/read/28471356/increasing-the-soluble-expression-and-crystallization-of-the-escherichia-coli-quorum-sensing-protein-lsrk
#18
Jung Hye Ha, Yumi Eo, Hee Chul Ahn, Kyoung Seok Ryu
LsrK is one of the key components of the luxS-regulated (lsr) operon in Escherichia coli and plays an important role during the quorum-sensing (QS) process mediated by autoinducer-2 (AI-2). The AI-2 molecule is imported into the cell by the LsrACB transporter and is subsequently phosphorylated (to AI-2-P) by LsrK. AI-2-P binds to the repressor protein of the lsr operon (LsrR) and triggers various cellular responses related to QS by dissociating LsrR from the DNA. Although a large amount of purified LsrK is required for structural studies, recombinant GST-LsrK was mostly expressed in an insoluble form...
May 1, 2017: Acta Crystallographica. Section F, Structural Biology Communications
https://www.readbyqxmd.com/read/28471355/structure-of-nadp-bound-7%C3%AE-hydroxysteroid-dehydrogenase-reveals-two-cofactor-binding-modes
#19
Rui Wang, Jiaquan Wu, David Kin Jin, Yali Chen, Zhijia Lv, Qian Chen, Qiwei Miao, Xiaoyu Huo, Feng Wang
In mammals, bile acids/salts and their glycine and taurine conjugates are effectively recycled through enterohepatic circulation. 7β-Hydroxysteroid dehydrogenases (7β-HSDHs; EC 1.1.1.201), including that from the intestinal microbe Collinsella aerofaciens, catalyse the NADPH-dependent reversible oxidation of secondary bile-acid products to avoid potential toxicity. Here, the first structure of NADP(+) bound to dimeric 7β-HSDH is presented. In one active site, NADP(+) adopts a conventional binding mode similar to that displayed in related enzyme structures...
May 1, 2017: Acta Crystallographica. Section F, Structural Biology Communications
https://www.readbyqxmd.com/read/28368284/x-ray-diffraction-analysis-and-in-vitro-characterization-of-the-uam2-protein-from-oryza-sativa
#20
Ditte Hededam Welner, Alex Yi Lin Tsai, Andy M DeGiovanni, Henrik Vibe Scheller, Paul D Adams
The role of seemingly non-enzymatic proteins in complexes interconverting UDP-arabinopyranose and UDP-arabinofuranose (UDP-arabinosemutases; UAMs) in the plant cytosol remains unknown. To shed light on their function, crystallographic and functional studies of the seemingly non-enzymatic UAM2 protein from Oryza sativa (OsUAM2) were undertaken. Here, X-ray diffraction data are reported, as well as analysis of the oligomeric state in the crystal and in solution. OsUAM2 crystallizes readily but forms highly radiation-sensitive crystals with limited diffraction power, requiring careful low-dose vector data acquisition...
April 1, 2017: Acta Crystallographica. Section F, Structural Biology Communications
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