The crystal structure of mouse LC3B in complex with the FYCO1 LIR reveals the importance of the flanking region of the LIR motif
FYVE and coiled-coil domain-containing protein 1 (FYCO1), a multidomain autophagy adaptor protein, mediates microtubule plus-end-directed autophagosome transport by interacting with kinesin motor proteins and with the autophagosomal membrane components microtubule-associated protein 1 light chain 3 (LC3), Rab7 and phosphatidylinositol 3-phosphate (PI3P). To establish the structural basis for the recognition of FYCO1 by LC3, the crystal structure of mouse LC3B in complex with the FYCO1 LC3-interacting region (LIR) motif peptide was determined. Structural analysis showed that the flanking sequences N-terminal and C-terminal ...
Source: Acta Crystallographica Section F - February 21, 2017 Category: Biochemistry Authors: Sakurai, S. Tomita, T. Shimizu, T. Ohto, U. Tags: autophagy FYCO1 LC3 LC3-interacting region (LIR) motif research communications Source Type: research
The hyperthermophilic cystathionine γ -synthase from the aerobic crenarchaeon Sulfolobus tokodaii: expression, purification, crystallization and structural insights
Cystathionine γ -synthase (CGS; EC 184.108.40.206), a pyridoxal 5 ′ -phosphate (PLP)-dependent enzyme, catalyzes the formation of cystathionine from an l-homoserine derivative and l-cysteine in the first step of the transsulfuration pathway. Recombinant CGS from the thermoacidophilic archaeon Sulfolobus tokodaii (StCGS) was overexpressed in Escherichia coli and purified to homogeneity by heat treatment followed by hydroxyapatite and gel-filtration column chromatography. The purified enzyme shows higher enzymatic activity at 353 K under basic pH conditions compared with that at 293 K. Crystallization trials yi...
Source: Acta Crystallographica Section F - February 20, 2017 Category: Biochemistry Authors: Sato, D. Shiba, T. Mizuno, S. Kawamura, A. Hanada, S. Yamada, T. Shinozaki, M. Yanagitani, M. Tamura, T. Inagaki, K. Harada, S. Tags: transsulfuration hyperthermophilic enzyme pyridoxal 5 ′ -phosphate methionine biosynthesis Sulfolobus tokodaii cystathionine γ -synthase research communications Source Type: research
Similarities in the structure of the transcriptional repressor AmtR in two different space groups suggest a model for the interaction with GlnK
AmtR belongs to the TetR family of transcription regulators and is a global nitrogen regulator that is induced under nitrogen-starvation conditions in Corynebacterium glutamicum. AmtR regulates the expression of transporters and enzymes for the assimilation of ammonium and alternative nitrogen sources, for example urea, amino acids etc. The recognition of operator DNA by homodimeric AmtR is not regulated by small-molecule effectors as in other TetR-family members but by a trimeric adenylylated PII-type signal transduction protein named GlnK. The crystal structure of ligand-free AmtR (AmtRorth) has been solved at a resoluti...
Source: Acta Crystallographica Section F - February 20, 2017 Category: Biochemistry Authors: Sevvana, M. Hasselt, K. Grau, F.C. Burkovski, A. Muller, Y.A. Tags: nitrogen regulation Corynebacterium glutamicum transcription regulator effector complex AmtR adenylylated GlnK complex stoichiometry crystal-packing comparison research communications Source Type: research
Proteolysis of truncated hemolysin A yields a stable dimerization interface
Wild-type and variant forms of HpmA265 (truncated hemolysin A) from Proteus mirabilis reveal a right-handed, parallel β -helix capped and flanked by segments of antiparallel β -strands. The low-salt crystal structures form a dimeric structure via the implementation of on-edge main-chain hydrogen bonds donated by residues 243 – 263 of adjacent monomers. Surprisingly, in the high-salt structures of two variants, Y134A and Q125A-Y134A, a new dimeric interface is formed via main-chain hydrogen bonds donated by residues 203 – 215 of adjacent monomers, and a previously unobserved tetramer is formed. In addi...
Source: Acta Crystallographica Section F - February 20, 2017 Category: Biochemistry Authors: Novak, W.R.P. Bhattacharyya, B. Grilley, D.P. Weaver, T.M. Tags: hemolysin A two-partner secretion alternate crystal forms proteolysis β -helix Proteus mirabilis research communications Source Type: research
Crystal structure of full-length Zika virus NS5 protein reveals a conformation similar to Japanese encephalitis virus NS5
The rapid spread of the recent Zika virus (ZIKV) epidemic across various countries in the American continent poses a major health hazard for the unborn fetuses of pregnant women. To date, there is no effective medical intervention. The nonstructural protein 5 of Zika virus (ZIKV-NS5) is critical for ZIKV replication through the 5 ′ -RNA capping and RNA polymerase activities present in its N-terminal methyltransferase (MTase) and C-terminal RNA-dependent RNA polymerase (RdRp) domains, respectively. The crystal structure of the full-length ZIKV-NS5 protein has been determined at 3.05 Å resolution from a cryst...
Source: Acta Crystallographica Section F - February 20, 2017 Category: Biochemistry Authors: Upadhyay, A.K. Cyr, M. Longenecker, K. Tripathi, R. Sun, C. Kempf, D.J. Tags: Zika virus NS5 nonstructural protein 5 research communications Source Type: research
Crystallization of FcpA from Leptospira, a novel flagellar protein that is essential for pathogenesis
The protein FcpA is a unique component of the flagellar filament of spirochete bacteria belonging to the genus Leptospira. Although it plays an essential role in translational motility and pathogenicity, no structures of FcpA homologues are currently available in the PDB. Its three-dimensional structure will unveil the novel motility mechanisms that render pathogenic Leptospira particularly efficient at invading and disseminating within their hosts, causing leptospirosis in humans and animals. FcpA from L. interrogans was purified and crystallized, but despite laborious attempts no useful X ray diffraction data could be ob...
Source: Acta Crystallographica Section F - February 20, 2017 Category: Biochemistry Authors: San Martin, F. Mechaly, A.E. Larrieux, N. Wunder, E.A. Ko, A.I. Picardeau, M. Trajtenberg, F. Buschiazzo, A. Tags: spirochetes motility flagella SAD phasing Leptospira interrogans Leptospira biflexa FcpA leptospirosis research communications Source Type: research
Crystallization and X-ray crystallographic analysis of recombinant TylP, a putative γ -butyrolactone receptor protein from Streptomyces fradiae
In this report, N-terminally His-tagged recombinant TylP protein (rTylP) was overproduced in Escherichia coli and purified to homogeneity. The rTylP protein was crystallized from a reservoir solution comprising 34%(v/v) ethylene glycol and 5%(v/v) glycerol. The protein crystals diffracted X-rays to 3.05 Å resolution and belonged to the trigonal space group P3121, with unit-cell parameters a = b = 126.62, c = 95.63 Å . (Source: Acta Crystallographica Section F)
Source: Acta Crystallographica Section F - January 30, 2017 Category: Biochemistry Authors: Mohd-Sharif, N. Shaibullah, S. Givajothi, V. Tan, C.-S. Ho, K.L. Teh, A.-H. Baharum, S.N. Waterman, J. Ng, C.L. Tags: Streptomyces fradiae recombinant TylP protein γ -butyrolactone GBL transcription factors tylosin research communications Source Type: research
The crystal structure of PD1, a Haemophilus surface fibril domain
The Haemophilus surface fibril (Hsf) is an unusually large trimeric autotransporter adhesin (TAA) expressed by the most virulent strains of H. influenzae. Hsf is known to mediate adhesion between pathogen and host, allowing the establishment of potentially deadly diseases such as epiglottitis, meningitis and pneumonia. While recent research has suggested that this TAA might adopt a novel `hairpin-like' architecture, the characterization of Hsf has been limited to in silico modelling and electron micrographs, with no high-resolution structural data available. Here, the crystal structure of Hsf putative domain 1 (PD1) is rep...
Source: Acta Crystallographica Section F - January 30, 2017 Category: Biochemistry Authors: Wright, J. Thomsen, M. Kolodziejczyk, R. Ridley, J. Sinclair, J. Carrington, G. Singh, B. Riesbeck, K. Goldman, A. Tags: Hsf putative domain 1 trimeric autotransporter Haemophilus influenzae adhesin cell adhesion Haemophilus surface fibril research communications Source Type: research
A natural, single-residue substitution yields a less active peptaibiotic: the structure of bergofungin A at atomic resolution
Bergofungin is a peptide antibiotic that is produced by the ascomycetous fungus Emericellopsis donezkii HKI 0059 and belongs to peptaibol subfamily 2. The crystal structure of bergofungin A has been determined and refined to 0.84 Å resolution. This is the second crystal structure of a natural 15-residue peptaibol, after that of samarosporin I. The amino-terminal phenylalanine residue in samarosporin I is exchanged to a valine residue in bergofungin A. According to agar diffusion tests, this results in a nearly inactive antibiotic peptide compared with the moderately active samarosporin I. Crystals were obtained f...
Source: Acta Crystallographica Section F - January 26, 2017 Category: Biochemistry Authors: Gessmann, R. Axford, D. Br ü ckner, H. Berg, A. Petratos, K. Tags: crystal structure Emericellopsis donezkii hydrogen bond peptaibols peptide antibiotics 310-helix α research communications Source Type: research
Structure of Methylobacterium extorquens malyl-CoA lyase: CoA-substrate binding correlates with domain shift
Malyl-CoA lyase (MCL) is an Mg2+-dependent enzyme that catalyzes the reversible cleavage of (2S)-4-malyl-CoA to yield acetyl-CoA and glyoxylate. MCL enzymes, which are found in a variety of bacteria, are members of the citrate lyase-like family and are involved in the assimilation of one- and two-carbon compounds. Here, the 1.56 Å resolution X-ray crystal structure of MCL from Methylobacterium extorquens AM1 with bound Mg2+ is presented. Structural alignment with the closely related Rhodobacter sphaeroides malyl-CoA lyase complexed with Mg2+, oxalate and CoA allows a detailed analysis of the domain motion of the ...
Source: Acta Crystallographica Section F - January 26, 2017 Category: Biochemistry Authors: Gonz á lez, J.M. Marti-Arbona, R. Chen, J.C.-H. Unkefer, C.J. Tags: biofuels metabolic engineering methanol malyl-CoA lyase Methylobacterium extorquens research communications Source Type: research
Expression and crystallographic studies of d-glycero- β -d-manno-heptose-1-phosphate adenylyltransferase from Burkholderia pseudomallei
In this study, HldC from B. pseudomallei has been cloned, expressed, purified and crystallized. Synchrotron X-ray data from a selenomethionine-substituted HldC crystal were also collected to 2.8 Å resolution. The crystal belonged to the primitive triclinic space group P1, with unit-cell parameters a = 74.0, b = 74.0, c = 74.9 Å , α = 108.4, β = 108.4, γ = 108.0 ° . Eight protomers are present in the unit cell and three out of five selenomethionines were found in each protomer using the PHENIX software suite. A full structural determination is in progress to elucidate the structure &...
Source: Acta Crystallographica Section F - January 18, 2017 Category: Biochemistry Authors: Park, J. Kim, H. Kim, S. Lee, D. Shin, D.H. Tags: Burkholderia pseudomallei heptose biosynthesis pathway melioidosis d-glycero- β -d-manno-heptose-1-phosphate adenylyltransferase HldC research communications Source Type: research
Crystallization and X-ray analysis of d-threonine aldolase from Chlamydomonas reinhardtii
d-Threonine aldolase from the green alga Chlamydomonas reinhardtii (CrDTA) catalyzes the interconversion of several β -hydroxy-d-amino acids (e.g. d-threonine) and glycine plus the corresponding aldehydes. Recombinant CrDTA was overexpressed in Escherichia coli and purified to homogeneity; it was subsequently crystallized using the hanging-drop vapour-diffusion method at 295 K. Data were collected and processed at 1.85 Å resolution. Analysis of the diffraction pattern showed that the crystal belonged to space group P1, with unit-cell parameters a = 64.79, b = 74.10, c = 89.94 Å , α = 77.0...
Source: Acta Crystallographica Section F - January 18, 2017 Category: Biochemistry Authors: Hirato, Y. Goto, M. Tokuhisa, M. Tanigawa, M. Nishimura, K. Tags: d-threonine aldolase Chlamydomonas reinhardtii d-amino acids crystallization research communications Source Type: research
Crystal structure of the N-terminal anticodon-binding domain of the nondiscriminating aspartyl-tRNA synthetase from Helicobacter pylori
The N-terminal anticodon-binding domain of the nondiscriminating aspartyl-tRNA synthetase (ND-AspRS) plays a crucial role in the recognition of both tRNAAsp and tRNAAsn. Here, the first X-ray crystal structure of the N-terminal domain of this enzyme (ND-AspRS1 – 104) from the human-pathogenic bacterium Helicobacter pylori is reported at 2.0 Å resolution. The apo form of H. pylori ND-AspRS1 – 104 shares high structural similarity with the N-terminal anticodon-binding domains of the discriminating aspartyl-tRNA synthetase (D-AspRS) from Escherichia coli and ND-AspRS from Pseudomonas aeruginosa, allowing...
Source: Acta Crystallographica Section F - January 18, 2017 Category: Biochemistry Authors: Songsiriritthigul, C. Suebka, S. Chen, C.-J. Fuengfuloy, P. Chuawong, P. Tags: nondiscriminating aspartyl-tRNA synthetase anticodon-binding domain Helicobacter pylori crystal structure research communications Source Type: research
Crystallization of a fungal lytic polysaccharide monooxygenase expressed from glycoengineered Pichia pastoris for X-ray and neutron diffraction
Lytic polysaccharide monooxygenases (LPMOs) are carbohydrate-disrupting enzymes secreted by bacteria and fungi that break glycosidic bonds via an oxidative mechanism. Fungal LPMOs typically act on cellulose and can enhance the efficiency of cellulose-hydrolyzing enzymes that release soluble sugars for bioethanol production or other industrial uses. The enzyme PMO-2 from Neurospora crassa (NcPMO-2) was heterologously expressed in Pichia pastoris to facilitate crystallographic studies of the fungal LPMO mechanism. Diffraction resolution and crystal morphology were improved by expressing NcPMO-2 from a glycoengineered strain ...
Source: Acta Crystallographica Section F - January 18, 2017 Category: Biochemistry Authors: O'Dell, W.B. Swartz, P.D. Weiss, K.L. Meilleur, F. Tags: lytic polysaccharide monooxygenases Pichia pastoris glycoengineering neutron protein crystallography research communications Source Type: research
Structural characterization of the Streptococcus pneumoniae carbohydrate substrate-binding protein SP0092
Streptococcus pneumoniae is an opportunistic respiratory pathogen that remains a major cause of morbidity and mortality globally, with infants and the elderly at the highest risk. S. pneumoniae relies entirely on carbohydrates as a source of carbon and dedicates a third of all uptake systems to carbohydrate import. The structure of the carbohydrate-free substrate-binding protein SP0092 at 1.61 Å resolution reveals it to belong to the newly proposed subclass G of substrate-binding proteins, with a ligand-binding pocket that is large enough to accommodate complex oligosaccharides. SP0092 is a dimer in solution and ...
Source: Acta Crystallographica Section F - December 24, 2016 Category: Biochemistry Authors: Culurgioni, S. Tang, M. Walsh, M.A. Tags: Streptococcus pneumoniae substrate-binding protein SP0092 ABC transporters carbohydrate uptake research communications Source Type: research
Expression, purification and crystallization of a protein resulting from the inversion of the amino-acid sequence of a helical bundle
Earlier studies have found that the occurrence of inverse sequence identity in proteins is not indicative of three-dimensional similarity, but rather leads to different folds or unfolded proteins. Short helices, however, frequently keep their conformations when their sequences are inverted. To explore the impact of sequence inversion on long helices, revRM6, with the inverse amino-acid sequence relative to RM6, a highly stable variant of the ColE1 Rop protein, was engineered. RM6 is a highly regular four- α -helical bundle that serves as a model system for protein-folding studies. Here, the crystallization and prelim...
Source: Acta Crystallographica Section F - December 24, 2016 Category: Biochemistry Authors: Kefala, A. Kotsifaki, D. Providaki, M. Amprazi, M. Kokkinidis, M. Tags: Rop protein heptad repeat protein folding sequence – structure relationship hyperthermophilic protein research communications Source Type: research
Recombinant hepatocyte growth factor activator inhibitor 1: expression in Drosophila S2 cells, purification and crystallization
Hepatocyte growth factor activator inhibitor 1 (HAI-1) is a multi-domain membrane-associated protease inhibitor that potently inhibits a variety of serine proteases such as hepatocyte growth factor activator and matriptase. Different truncates of HAI-1 show varying potencies for inhibition of target proteases, suggesting that the domain organization of HAI-1 plays a critical role in its function. Here, the soluble full-length extracellular part of HAI-1 (sHAI-1) was expressed using the Drosophila S2 insect-cell expression system. Diffraction-quality crystals of sHAI-1 were produced using ammonium sulfate as precipitant. Th...
Source: Acta Crystallographica Section F - December 24, 2016 Category: Biochemistry Authors: Liu, M. Yuan, C. Jiang, Y. Jiang, L. Huang, M. Tags: HAI-1 hepatocyte growth factor activator inhibitor Drosophila expression purification crystallization research communications Source Type: research
Structure of a fungal form of aspartate-semialdehyde dehydrogenase from Aspergillus fumigatus
Aspartate-semialdehyde dehydrogenase (ASADH) functions at a critical junction in the aspartate biosynthetic pathway and represents a validated target for antimicrobial drug design. This enzyme catalyzes the NADPH-dependent reductive dephosphorylation of β -aspartyl phosphate to produce the key intermediate aspartate semialdehyde. The absence of this entire pathway in humans and other mammals will allow the selective targeting of pathogenic microorganisms for antimicrobial development. Here, the X-ray structure of a new form of ASADH from the pathogenic fungal species Aspergillus fumigatus has been determined. The over...
Source: Acta Crystallographica Section F - December 24, 2016 Category: Biochemistry Authors: Dahal, G.P. Viola, R.E. Tags: aspartate-semialdehyde dehydrogenase Aspergillus fumigatus pathogenic fungi oligomeric arrangement structural comparison research communications Source Type: research
Crystal structure of a putrescine aminotransferase from Pseudomonas sp. strain AAC
The putrescine aminotransferase KES24511 from Pseudomonas sp. strain AAC was previously identified as an industrially relevant enzyme based on the discovery that it is able to promiscuously catalyse the transamination of 12-aminododecanoic acid. Here, the cloning, heterologous expression, purification and successful crystallization of the KES24511 protein are reported, which ultimately generated crystals adopting space group I2. The crystals diffracted X-rays to 2.07 Å resolution and data were collected using the microfocus beamline of the Australian Synchrotron. The structure was solved using molecular replaceme...
Source: Acta Crystallographica Section F - December 24, 2016 Category: Biochemistry Authors: Wilding, M. Scott, C. Newman, J. Peat, T.S. Tags: aminotransferases 12-aminododecanoic acid transaminase PLP-dependent research communications Source Type: research
X-ray crystal structure of a malonate-semialdehyde dehydrogenase from Pseudomonas sp. strain AAC
The NAD-dependent malonate-semialdehyde dehydrogenase KES23460 from Pseudomonas sp. strain AAC makes up half of a bicistronic operon responsible for β -alanine catabolism to produce acetyl-CoA. The KES23460 protein has been heterologously expressed, purified and used to generate crystals suitable for X-ray diffraction studies. The crystals belonged to space group P212121 and diffracted X-rays to beyond 3 Å resolution using the microfocus beamline of the Australian Synchrotron. The structure was solved using molecular replacement, with a monomer from PDB entry 4zz7 as the search model. (Source: Acta Crystallographica Section F)
Source: Acta Crystallographica Section F - December 24, 2016 Category: Biochemistry Authors: Wilding, M. Scott, C. Peat, T.S. Newman, J. Tags: malonate-semialdehyde dehydrogenase β -alanine catabolism Pseudomonas sp. strain AAC research communications Source Type: research
Crystal structure of an IclR homologue from Microbacterium sp. strain HM58-2
The bacterial transcription factor IclR (isocitrate lyase regulator) is a member of a one-component signal transduction system, which shares the common motif of a helix – turn – helix (HTH)-type DNA-binding domain (DBD) connected to a substrate-binding domain (SBD). Here, the crystal structure of an IclR homologue (Mi-IclR) from Microbacterium sp. strain HM58-2, which catabolizes acylhydrazide as the sole carbon source, is reported. Mi-IclR is expected to regulate an operon responsible for acylhydrazide degradation as an initial step. Native single-wavelength anomalous diffraction (SAD) experiments were perform...
Source: Acta Crystallographica Section F - December 16, 2016 Category: Biochemistry Authors: Akiyama, T. Yamada, Y. Takaya, N. Ito, S. Sasaki, Y. Yajima, S. Tags: isocitrate lyase regulator transcription factor Microbacterium hydrazide one-component system research communications Source Type: research
Crystal structure of the ATPase-C domain of the chromatin remodeller Fun30 from Saccharomyces cerevisiae
Fun30 (Function unknown now 30) is a chromatin remodeller belonging to the Snf2 family. It has previously been reported to be a regulator of several cellular activities, including DNA repair, gene silencing and maintenance of chromatin structure. Here, the crystal structure of the Fun30 ATPase-C domain (the C-lobe of the ATPase domain) is reported at 1.95 Å resolution. Although the structure displays overall similarities to those of other Snf2 family members, a new structural module was found to be specific to the Fun30 subfamily. Fun30 ATPase-C was shown be monomeric in solution and showed no detectable affinity...
Source: Acta Crystallographica Section F - December 16, 2016 Category: Biochemistry Authors: Liu, L. Jiang, T. Tags: Fun30 Snf2 structure remodeller ATPase research communications Source Type: research
Crystal structure of truncated human coatomer protein complex subunit ζ 1 (Cop ζ 1)
The majority of modern anticancer approaches target DNA/protein targets involved in tumour-cell proliferation. Such approaches have a major drawback, as nonproliferating cancer cells remain unaffected and may cause relapse or remission. Human coatomer protein complex I (COPI) subunit ζ (Cop ζ ), a component of the coat protein involved in cell apoptosis and intracellular trafficking, has recently been proposed as a potential anticancer drug target. Previous studies have shown that two different isoforms of the Cop ζ subunit exist in mammalian cells. While normal cells express both Cop ζ 1 and Cop ζ...
Source: Acta Crystallographica Section F - December 14, 2016 Category: Biochemistry Authors: Lunev, S. Semmelink, M.F.W. Xian, J.L. Ma, K.Y. Leenders, A.J.A. D ö mling, A.S.S. Shtutman, M. Groves, M.R. Tags: cancer dormant cells human COPI crystal structure ζ 1 2 research communications Source Type: research
Protein production, crystallization and preliminary crystallographic analysis of the four N-terminal immunoglobulin domains of Down syndrome cell adhesion molecule 1. Corrigendum
An extra author is added to the article by Chen et al. [(2015), Acta Cryst. F71, 775 – 778]. (Source: Acta Crystallographica Section F)
Source: Acta Crystallographica Section F - November 29, 2016 Category: Biochemistry Authors: Cheng, L. Li, S.-A. Wang, J. Yu, Y. Chen, Q. Tags: Dscam1 RNA splicing homophilic dimer horseshoe configuration crystallization corrigendum addenda and errata Source Type: research
Characterization and 1.57 Å resolution structure of the key fire blight phosphatase AmsI from Erwinia amylovora
AmsI is a low-molecular-weight protein tyrosine phosphatase that regulates the production of amylovoran in the Gram-negative bacterium Erwinia amylovora, a specific pathogen of rosaceous plants such as apple, pear and quince. Amylovoran is an exopolysaccharide that is necessary for successful infection. In order to shed light on AmsI, its structure was solved at 1.57 Å resolution at the same pH as its highest measured activity (pH 5.5). In the active site, a water molecule, bridging between the catalytic Arg15 and the reaction-product analogue sulfate, might be representative of the water molecule attacking the p...
Source: Acta Crystallographica Section F - November 29, 2016 Category: Biochemistry Authors: Salomone-Stagni, M. Musiani, F. Benini, S. Tags: hydrolases amylovoran low-molecular-weight protein tyrosine phosphatase kinetics fire blight Enterobacteriaceae Erwinia amylovora research communications Source Type: research
Overcoming a hemihedral twinning problem in tetrahydrofolate-dependent O-demethylase crystals by the microseeding method
A tetrahydrofolate-dependent O-demethylase, LigM, from Sphingobium sp. SYK-6 was crystallized by the hanging-drop vapour-diffusion method. However, the obtained P3121 or P3221 crystals, which diffracted to 2.5 – 3.3 Å resolution, were hemihedrally twinned. To overcome the twinning problem, microseeding using P3121/P3221 crystals as microseeds was performed with optimization of the reservoir conditions. As a result, another crystal form was obtained. The newly obtained crystal diffracted to 2.5 – 3.0 Å resolution and belonged to space group P21212, with unit-cell parameters a = 102.0, b = 117...
Source: Acta Crystallographica Section F - November 29, 2016 Category: Biochemistry Authors: Harada, A. Sato, Y. Kamimura, N. Venugopalan, N. Masai, E. Senda, T. Tags: hemihedral twinning microseeding cryoprotectant tetrahydrofolate Sphingobium sp. SYK-6 O-demethylase research communications Source Type: research
Purification, crystallization and characterization of the Pseudomonas outer membrane protein FapF, a functional amyloid transporter
Bacteria often produce extracellular amyloid fibres via a multi-component secretion system. Aggregation-prone, unstructured subunits cross the periplasm and are secreted through the outer membrane, after which they self-assemble. Here, significant progress is presented towards solving the high-resolution crystal structure of the novel amyloid transporter FapF from Pseudomonas, which facilitates the secretion of the amyloid-forming polypeptide FapC across the bacterial outer membrane. This represents the first step towards obtaining structural insight into the products of the Pseudomonas fap operon. Initial attempts at crys...
Source: Acta Crystallographica Section F - November 29, 2016 Category: Biochemistry Authors: Rouse, S.L. Hawthorne, W.J. Lambert, S. Morgan, M.L. Hare, S.A. Matthews, S. Tags: amyloid transporter bacterial outer membrane FapF Pseudomonas C8E4 research communications Source Type: research
The crystal structure of dihydrodipicolinate reductase from the human-pathogenic bacterium Bartonella henselae strain Houston-1 at 2.3 Å resolution
In bacteria, the second committed step in the diaminopimelate/lysine anabolic pathways is catalyzed by the enzyme dihydrodipicolinate reductase (DapB). DapB catalyzes the reduction of dihydrodipicolinate to yield tetrahydrodipicolinate. Here, the cloning, expression, purification, crystallization and X-ray diffraction analysis of DapB from the human-pathogenic bacterium Bartonella henselae, the causative bacterium of cat-scratch disease, are reported. Protein crystals were grown in conditions consisting of 5%(w/v) PEG 4000, 200 mM sodium acetate, 100 mM sodium citrate tribasic pH 5.5 and were shown to diffract to &...
Source: Acta Crystallographica Section F - November 24, 2016 Category: Biochemistry Authors: Cala, A.R. Nadeau, M.T. Abendroth, J. Staker, B.L. Reers, A.R. Weatherhead, A.W. Dobson, R.C.J. Myler, P.J. Hudson, A.O. Tags: Bartonella henselae dihydrodipicolinate reductase diaminopimelate lysine biosynthesis cat-scratch disease research communications Source Type: research
Coxsackievirus B3 protease 3C: expression, purification, crystallization and preliminary structural insights
Viral proteases are proteolytic enzymes that orchestrate the assembly of viral components during the viral life cycle and proliferation. Here, the expression, purification, crystallization and preliminary X-ray diffraction analysis are presented of protease 3C, the main protease of an emerging enterovirus, coxsackievirus B3, that is responsible for many cases of viral myocarditis. Polycrystalline protein precipitates suitable for X-ray powder diffraction (XRPD) measurements were produced in the presence of 22 – 28%(w/v) PEG 4000, 0.1 M Tris – HCl, 0.2 M MgCl2 in a pH range from 7.0 to 8.5. A polymorph o...
Source: Acta Crystallographica Section F - November 24, 2016 Category: Biochemistry Authors: Fili, S. Valmas, A. Christopoulou, M. Spiliopoulou, M. Nikolopoulos, N. Lichi è re, J. Logotheti, S. Karavassili, F. Rosmaraki, E. Fitch, A. Wright, J. Beckers, D. Degen, T. Nenert, G. Hilgenfeld, R. Papageorgiou, N. Canard, B. Coutard, B. Margiolaki, I. Tags: 3C protease coxsackievirus B3 powder diffraction research communications Source Type: research
The crystal structure of the endoglucanase Cel10, a family 8 glycosyl hydrolase from Klebsiella pneumoniae
Cellulases are produced by microorganisms that grow on cellulose biomass. Here, a cellulase, Cel10, was identified in a strain of Klebsiella pneumoniae isolated from Chinese bamboo rat gut. Analysis of substrate specificity showed that Cel10 is able to hydrolyze amorphous carboxymethyl cellulose (CMC) and crystalline forms of cellulose (Avicel and xylan) but is unable to hydrolyze p-nitrophenol β -d-glucopyranoside (p-NPG), proving that Cel10 is an endoglucanase. A phylogenetic tree analysis indicates that Cel10 belongs to the glycoside hydrolase 8 (GH8) subfamily. In order to further understanding of its substrate sp...
Source: Acta Crystallographica Section F - November 24, 2016 Category: Biochemistry Authors: Attigani, A. Sun, L. Wang, Q. Liu, Y. Bai, D. Li, S. Huang, X. Tags: cellulases Klebsiella pneumoniae carboxymethyl cellulase cellulose biosynthesis crystal structure Cel10 research communications Source Type: research
Crystal structure of the toxin Msmeg_6760, the structural homolog of Mycobacterium tuberculosis Rv2035, a novel type II toxin involved in the hypoxic response
The structure of Msmeg_6760, a protein of unknown function, has been determined. Biochemical and bioinformatics analyses determined that Msmeg_6760 interacts with a protein encoded in the same operon, Msmeg_6762, and predicted that the operon is a toxin – antitoxin (TA) system. Structural comparison of Msmeg_6760 with proteins of known function suggests that Msmeg_6760 binds a hydrophobic ligand in a buried cavity lined by large hydrophobic residues. Access to this cavity could be controlled by a gate – latch mechanism. The function of the Msmeg_6760 toxin is unknown, but structure-based predictions revealed th...
Source: Acta Crystallographica Section F - November 18, 2016 Category: Biochemistry Authors: Bajaj, R.A. Arbing, M.A. Shin, A. Cascio, D. Miallau, L. Tags: Mycobacterium smegmatis Mycobacterium tuberculosis X-ray crystallography protein structure toxin – antitoxin complexes bacterial latency macrophage infection novel folds research communications Source Type: research
1.45 Å resolution structure of SRPN18 from the malaria vector Anopheles gambiae
Serine protease inhibitors (serpins) in insects function within development, wound healing and immunity. The genome of the African malaria vector, Anopheles gambiae, encodes 23 distinct serpin proteins, several of which are implicated in disease-relevant physiological responses. A. gambiae serpin 18 (SRPN18) was previously categorized as non-inhibitory based on the sequence of its reactive-center loop (RCL), a region responsible for targeting and initiating protease inhibition. The crystal structure of A. gambiae SRPN18 was determined to a resolution of 1.45 Å , including nearly the entire RCL in one of the two m...
Source: Acta Crystallographica Section F - November 17, 2016 Category: Biochemistry Authors: Meekins, D.A. Zhang, X. Battaile, K.P. Lovell, S. Michel, K. Tags: serpins serine proteases insect immunity enzyme inhibitors mosquito Anopheles gambiae malaria vector research communications Source Type: research
Structural characterization of the thermostable Bradyrhizobium japonicumd-sorbitol dehydrogenase
Bradyrhizobium japonicum sorbitol dehydrogenase is NADH-dependent and is active at elevated temperatures. The best substrate is d-glucitol (a synonym for d-sorbitol), although l-glucitol is also accepted, giving it particular potential in industrial applications. Crystallization led to a hexagonal crystal form, with crystals diffracting to 2.9 Å resolution. In attempts to phase the data, a molecular-replacement solution based upon PDB entry 4nbu (33% identical in sequence to the target) was found. The solution contained one molecule in the asymmetric unit, but a tetramer similar to that found in other short-chain...
Source: Acta Crystallographica Section F - October 26, 2016 Category: Biochemistry Authors: Fredslund, F. Otten, H. Gemperlein, S. Poulsen, J.-C.N. Carius, Y. Kohring, G.-W. Lo Leggio, L. Tags: sorbitol dehydrogenase thermostability glucitol research communications Source Type: research
Development of a high-throughput crystal structure-determination platform for JAK1 using a novel metal-chelator soaking system
Crystals of phosphorylated JAK1 kinase domain were initially generated in complex with nucleotide (ADP) and magnesium. The tightly bound Mg2+-ADP at the ATP-binding site proved recalcitrant to ligand displacement. Addition of a molar excess of EDTA helped to dislodge the divalent metal ion, promoting the release of ADP and allowing facile exchange with ATP-competitive small-molecule ligands. Many kinases require the presence of a stabilizing ligand in the ATP site for crystallization. This procedure could be useful for developing co-crystallization systems with an exchangeable ligand to enable structure-based drug design o...
Source: Acta Crystallographica Section F - October 26, 2016 Category: Biochemistry Authors: Caspers, N.L. Han, S. Rajamohan, F. Hoth, L.R. Geoghegan, K.F. Subashi, T.A. Vazquez, M.L. Kaila, N. Cronin, C.N. Johnson, E. Kurumbail, R.G. Tags: Janus kinase kinases crystal soaking ligand exchange structure-based drug design research communications Source Type: research
Crystal structure of fuculose aldolase from the Antarctic psychrophilic yeast Glaciozyma antarctica PI12
In this study, the gene encoding FucA from Glaciozyma antarctica PI12 (GaFucA) was cloned and the enzyme was overexpressed in Escherichia coli, purified and crystallized. The tetrameric structure of GaFucA was determined to 1.34 Å resolution. The overall architecture of GaFucA and its catalytically essential histidine triad are highly conserved among other fuculose aldolases. Comparisons of structural features between GaFucA and its mesophilic and thermophilic homologues revealed that the enzyme has typical psychrophilic attributes, indicated by the presence of a high number of nonpolar residues at the surface an...
Source: Acta Crystallographica Section F - October 26, 2016 Category: Biochemistry Authors: Jaafar, N.R. Littler, D. Beddoe, T. Rossjohn, J. Illias, R.M. Mahadi, N.M. Mackeen, M.M. Murad, A.M.A. Abu Bakar, F.D. Tags: psychrophiles crystallization metalloenzymes fuculose aldolase l-fuculose metabolism Glaciozyma antarctica imino cyclitols research communications Source Type: research
Natural and non-natural amino-acid side-chain substitutions: affinity and diffraction studies of meditope – Fab complexes
Herein, multiple crystal structures of meditope peptide derivatives incorporating natural and unnatural amino acids bound to the cetuximab Fab domain are presented. The affinity of each derivative was determined by surface plasmon resonance and correlated to the atomic structure. Overall, it was observed that the hydrophobic residues in the meditope peptide, Phe3, Leu5 and Leu10, could accommodate a number of moderate substitutions, but these invariably reduced the overall affinity and half-life of the interaction. In one case, the substitution of Phe3 by histidine led to a change in the rotamer conformation, in which the ...
Source: Acta Crystallographica Section F - October 23, 2016 Category: Biochemistry Authors: Bzymek, K.P. Avery, K.A. Ma, Y. Horne, D.A. Williams, J.C. Tags: meditope monoclonal antibody cetuximab unnatural amino acids X-ray crystallography surface plasmon resonance research communications Source Type: research
The structure of the metallo- β -lactamase VIM-2 in complex with a triazolylthioacetamide inhibitor
In this study, three triazolylthioacetamides were tested as inhibitors of VIM-2. One of the tested compounds showed clear inhibition of VIM-2, with an IC50 of 20 µ M. The crystal structure of the inhibitor in complex with VIM-2 was obtained by DMSO-free co-crystallization and was solved at a resolution of 1.50 Å . To our knowledge, this is the first structure of a triazolylthioacetamide inhibitor in complex with an MBL. Analysis of the structure shows that the inhibitor binds to the two zinc ions in the active site of VIM-2 and revealed detailed information on the interactions involved. Furthermore, the...
Source: Acta Crystallographica Section F - October 23, 2016 Category: Biochemistry Authors: Christopeit, T. Yang, K.-W. Yang, S.-K. Leiros, H.-K.S. Tags: antibiotic resistance DMSO-free co-crystallization carbapenemases VIM-2 metallo- β -lactamases research communications Source Type: research
Crystal structure of a phosphoribosyl anthranilate isomerase from the hyperthermophilic archaeon Thermococcus kodakaraensis
A phosphoribosyl anthranilate isomerase, TkTrpF, from Thermococcus kodakaraensis was expressed in Escherichia coli and purified to homogeneity. TkTrpF was crystallized and its structure was determined by molecular replacement in two different space groups (C2 and P1) using data to 1.85 and 1.75 Å resolution, respectively. TkTrpF belongs to the class of TIM-barrel proteins. Structural comparison with other phosphoribosyl anthranilate isomerases (TrpFs) showed the highest structural similarity to Pyrococcus furiosus TrpF. Similarly to P. furiosus TrpF, TkTrpF is a monomer in solution, in contrast to other thermophi...
Source: Acta Crystallographica Section F - October 23, 2016 Category: Biochemistry Authors: Perveen, S. Rashid, N. Papageorgiou, A.C. Tags: tryptophan biosynthesis protein stability TIM barrel hyperthermophilic archaea Pyrococcus furiosus Thermococcus kodakaraensis phosphoribosyl anthranilate isomerase research communications Source Type: research
Crystal structures of a yeast 14-3-3 protein from Lachancea thermotolerans in the unliganded form and bound to a human lipid kinase PI4KB-derived peptide reveal high evolutionary conservation
14-3-3 proteins bind phosphorylated binding partners to regulate several of their properties, including enzymatic activity, stability and subcellular localization. Here, two crystal structures are presented: the crystal structures of the 14-3-3 protein (also known as Bmh1) from the yeast Lachancea thermotolerans in the unliganded form and bound to a phosphopeptide derived from human PI4KB (phosphatidylinositol 4-kinase B). The structures demonstrate the high evolutionary conservation of ligand recognition by 14-3-3 proteins. The structural analysis suggests that ligand recognition by 14-3-3 proteins evolved very early in t...
Source: Acta Crystallographica Section F - October 23, 2016 Category: Biochemistry Authors: Eisenreichova, A. Klima, M. Boura, E. Tags: 14-3-3 proteins Bmh1 Bmh2 crystal structure phosphopeptide PI4KB Lachancea thermotolerans research communications Source Type: research
Expression and crystallographic studies of the Arabidopsis thaliana GDP-d-mannose pyrophosphorylase VTC1
GDP-d-mannose pyrophosphorylase catalyzes the production of GDP-d-mannose, an intermediate product in the plant ascorbic acid (AsA) biosynthetic pathway. This enzyme is a key regulatory target in AsA biosynthesis and is encoded by VITAMIN C DEFECTIVE 1 (VTC1) in the Arabidopsis thaliana genome. Here, recombinant VTC1 was expressed, purified and crystallized. Diffraction data were obtained from VTC1 crystals grown in the absence and presence of substrate using X-rays. The ligand-free VTC1 crystal diffracted X-rays to 3.3 Å resolution and belonged to space group R32, with unit-cell parameters a = b = 183.6, c = 368...
Source: Acta Crystallographica Section F - September 26, 2016 Category: Biochemistry Authors: Zhao, S. Liu, L. Tags: ascorbic acid biosynthesis GDP-d-mannose pyrophosphorylase Arabidopsis thaliana research communications Source Type: research
Biochemical, spectroscopic and X-ray structural analysis of deuterated multicopper oxidase CueO prepared from a new expression construct for neutron crystallography
Multicopper oxidases oxidize various phenolic and nonphenolic compounds by using molecular oxygen as an electron acceptor to produce water. A multicopper oxidase protein, CueO, from Escherichia coli is involved in copper homeostasis in the bacterial cell. Although X-ray crystallographic studies have been conducted, the reduction mechanism of oxygen and the proton-transfer pathway remain unclear owing to the difficulty in identifying H atoms from X-ray diffraction data alone. To elucidate the reaction mechanism using neutron crystallography, a preparation system for obtaining large, high-quality single crystals of deuterate...
Source: Acta Crystallographica Section F - September 21, 2016 Category: Biochemistry Authors: Akter, M. Inoue, C. Komori, H. Matsuda, N. Sakurai, T. Kataoka, K. Higuchi, Y. Shibata, N. Tags: multicopper oxidase CueO deuteration X-ray diffraction neutron diffraction research communications Source Type: research
X-ray crystallographic studies of the extracellular domain of the first plant ATP receptor, DORN1, and the orthologous protein from Camelina sativa
Does not respond to nucleotides 1 (DORN1) has recently been identified as the first membrane-integral plant ATP receptor, which is required for ATP-induced calcium response, mitogen-activated protein kinase activation and defense responses in Arabidopsis thaliana. In order to understand DORN1-mediated ATP sensing and signal transduction, crystallization and preliminary X-ray studies were conducted on the extracellular domain of DORN1 (atDORN1-ECD) and that of an orthologous protein, Camelina sativa lectin receptor kinase I.9 (csLecRK-I.9-ECD or csI.9-ECD). A variety of deglycosylation strategies were employed to optimize t...
Source: Acta Crystallographica Section F - September 21, 2016 Category: Biochemistry Authors: Li, Z. Chakraborty, S. Xu, G. Tags: plant ATP receptor DORN1 lectin receptor kinase I.9 glycosylation Arabidopsis thaliana Camelina sativa research communications Source Type: research
Crystallographic study of the 2-thioribothymidine-synthetic complex TtuA – TtuB from Thermus thermophilus
In this study, the TtuA – TtuB complex from Thermus thermophilus was expressed, purified and crystallized. To mimic the thiocarboxylated TtuB, the C-terminal Gly residue was replaced with Cys (G65C) to obtain crystals of the TtuA – TtuB complex. A Zn-MAD data set was collected to a resolution of 2.5 Å . MAD analysis successfully determined eight Zn sites, and a partial structure model composed of four TtuA – TtuB complexes in the asymmetric unit was constructed. (Source: Acta Crystallographica Section F)
Source: Acta Crystallographica Section F - September 21, 2016 Category: Biochemistry Authors: Chen, M. Narai, S. Omura, N. Shigi, N. Chimnaronk, S. Tanaka, Y. Yao, M. Tags: post-transcriptional modification sulfur transfer ubiquitin-like protein Zn-MAD TtuA TtuB research communications Source Type: research
Crystal structure of rofecoxib bound to human cyclooxygenase-2
Rofecoxib (Vioxx) was one of the first selective cyclooxygenase-2 (COX-2) inhibitors (coxibs) to be approved for use in humans. Within five years after its release to the public, Vioxx was withdrawn from the market owing to the adverse cardiovascular effects of the drug. Despite the widespread knowledge of the development and withdrawal of Vioxx, relatively little is known at the molecular level about how the inhibitor binds to COX-2. Vioxx is unique in that the inhibitor contains a methyl sulfone moiety in place of the sulfonamide moiety found in other coxibs such as celecoxib and valdecoxib. Here, new crystallization con...
Source: Acta Crystallographica Section F - September 21, 2016 Category: Biochemistry Authors: Orlando, B.J. Malkowski, M.G. Tags: cyclooxygenase rofecoxib nonsteroidal anti-inflammatory drugs Vioxx crystal structure research communications Source Type: research
Comparative analysis of anti-polyglutamine Fab crystals grown on Earth and in microgravity
Huntington's disease is one of nine neurodegenerative diseases caused by a polyglutamine (polyQ)-repeat expansion. An anti-polyQ antigen-binding fragment, MW1 Fab, was crystallized both on Earth and on the International Space Station, a microgravity environment where convection is limited. Once the crystals returned to Earth, the number, size and morphology of all crystals were recorded, and X-ray data were collected from representative crystals. The results generally agreed with previous microgravity crystallization studies. On average, microgravity-grown crystals were 20% larger than control crystals grown on Earth, and ...
Source: Acta Crystallographica Section F - September 21, 2016 Category: Biochemistry Authors: Owens, G.E. New, D.M. Olvera, A.I. Manzella, J.A. Macon, B.L. Dunn, J.C. Cooper, D.A. Rouleau, R.L. Connor, D.S. Bjorkman, P.J. Tags: Huntington's disease International Space Station microgravity polyglutamine X-ray crystallography huntingtin crystallization research communications Source Type: research
The structure of a glycoside hydrolase 29 family member from a rumen bacterium reveals unique, dual carbohydrate-binding domains
Glycoside hydrolase (GH) family 29 consists solely of α -l-fucosidases. These enzymes catalyse the hydrolysis of glycosidic bonds. Here, the structure of GH29_0940, a protein cloned from metagenomic DNA from the rumen of a cow, has been solved, which reveals a multi-domain arrangement that has only recently been identified in bacterial GH29 enzymes. The microbial species that provided the source of this enzyme is unknown. This enzyme contains a second carbohydrate-binding domain at its C-terminal end in addition to the typical N-terminal catalytic domain and carbohydrate-binding domain arrangement of GH29-family prot...
Source: Acta Crystallographica Section F - September 21, 2016 Category: Biochemistry Authors: Summers, E.L. Moon, C.D. Atua, R. Arcus, V.L. Tags: GH29 glycoside hydrolase α -l-fucosidase carbohydrate-binding domain CBM32 PDB5K9H research communications Source Type: research
Crystal and solution structural studies of mouse phospholipid hydroperoxide glutathione peroxidase 4
The mammalian glutathione peroxidase (GPx) family is a key component of the cellular antioxidative defence system. Within this family, GPx4 has unique features as it accepts a large class of hydroperoxy lipid substrates and has a plethora of biological functions, including sperm maturation, regulation of apoptosis and cerebral embryogenesis. In this paper, the structure of the cytoplasmic isoform of mouse phospholipid hydroperoxide glutathione peroxidase (O70325-2 GPx4) with selenocysteine 46 mutated to cysteine is reported solved at 1.8 Å resolution using X-ray crystallography. Furthermore, solution data of an i...
Source: Acta Crystallographica Section F - September 21, 2016 Category: Biochemistry Authors: Janowski, R. Scanu, S. Niessing, D. Madl, T. Tags: phospholipid hydroperoxide glutathione peroxidase 4 reactive oxidative species NMR spectroscopy small-angle X-ray scattering research communications Source Type: research
Arabidopsis receptor-like cytoplasmic kinase BIK1: purification, crystallization and X-ray diffraction analysis
In this study, the purification and crystallization of a first member of the class VI family of RLCK proteins, BIK1, are reported. BIK1 was crystallized using the microbatch-under-oil method. X-ray diffraction data were collected to 2.35 Å resolution. The crystals belonged to the monoclinic space group C2, with two monomers per asymmetric unit. (Source: Acta Crystallographica Section F)
Source: Acta Crystallographica Section F - September 21, 2016 Category: Biochemistry Authors: Lal, N.K. Fisher, A.J. Dinesh-Kumar, S.P. Tags: receptor-like kinase receptor-like cytoplasmic kinases RLCK BIK1 BOTRYTIS-INDUCED KINASE 1 PAMP-triggered immunity Arabidopsis research communications Source Type: research
Crystal structure of yeast monothiol glutaredoxin Grx6 in complex with a glutathione-coordinated [2Fe – 2S] cluster
Glutaredoxins (Grxs) constitute a superfamily of proteins that perform diverse biological functions. The Saccharomyces cerevisiae glutaredoxin Grx6 not only serves as a glutathione (GSH)-dependent oxidoreductase and as a GSH transferase, but also as an essential [2Fe – 2S]-binding protein. Here, the dimeric structure of the C-terminal domain of Grx6 (holo Grx6C), bridged by one [2Fe – 2S] cluster coordinated by the active-site Cys136 and two external GSH molecules, is reported. Structural comparison combined with multiple-sequence alignment demonstrated that holo Grx6C is similar to the [2Fe – 2S] cluster...
Source: Acta Crystallographica Section F - September 21, 2016 Category: Biochemistry Authors: Abdalla, M. Dai, Y.-N. Chi, C.-B. Cheng, W. Cao, D.-D. Zhou, K. Ali, W. Chen, Y. Zhou, C.-Z. Tags: glutaredoxin iron – sulfur cluster Saccharomyces cerevisiae crystal structure oxidoreductase research communications Source Type: research
1.65 Å resolution structure of the AraC-family transcriptional activator ToxT from Vibrio cholerae
In this study, a crystal structure of ToxT at 1.65 Å resolution with a similar overall structure to the previously determined structure is reported. However, there are distinct differences between the two structures, particularly in the region that extends from Asp101 to Glu110. This region, which can influence ToxT activity but was disordered in the previous structure, can be traced entirely in the current structure. (Source: Acta Crystallographica Section F)
Source: Acta Crystallographica Section F - August 25, 2016 Category: Biochemistry Authors: Li, J. Wehmeyer, G. Lovell, S. Battaile, K.P. Egan, S.M. Tags: AraC ToxT Vibrio cholerae crystal structure palmitoleic acid pathogenesis research communications Source Type: research