当前位置： SCI文献检索 > JOURNAL OF MOLECULAR BIOLOGY期刊下所有文献 > Crystal structures of an oligopeptide-binding protein from the biosynthetic pathway of the beta-lactamase inhibitor clavulanic acid.

Crystal structures of an oligopeptide-binding protein from the biosynthetic pathway of the beta-lactamase inhibitor clavulanic acid.

Abstract：

:Clavulanic acid (CA) is a clinically important beta-lactamase inhibitor that is produced by fermentation of Streptomyces clavuligerus. The CA biosynthesis pathway starts from arginine and glyceraldehyde-3-phosphate and proceeds via (3S,5S)-clavaminic acid, which is converted to (3R,5R)-clavaldehyde, the immediate precursor of (3R,5R)-CA. Open reading frames 7 (orf7) and 15 (orf15) of the CA biosynthesis cluster encode oligopeptide-binding proteins (OppA1 and OppA2), which are essential for CA biosynthesis. OppA1/2 are proposed to be involved in the binding and/or transport of peptides across the S. clavuligerus cell membrane. Peptide binding assays reveal that recombinant OppA1 and OppA2 bind di-/tripeptides containing arginine and certain nonapeptides including bradykinin. Crystal structures of OppA2 in its apo form and in complex with arginine or bradykinin were solved to 1.45, 1.7, and 1.7 A resolution, respectively. The overall fold of OppA2 consists of two lobes with a deep cavity in the center, as observed for other oligopeptide-binding proteins. The large cavity creates a peptide/arginine binding cleft. The crystal structures of OppA2 in complex with arginine or bradykinin reveal that the C-terminal arginine of bradykinin binds similarly to arginine. The results are discussed in terms of the possible roles of OppA1/2 in CA biosynthesis.

journal_name

J Mol Biol

journal_title

Journal of molecular biology

authors

Mackenzie AK,Valegård K,Iqbal A,Caines ME,Kershaw NJ,Jensen SE,Schofield CJ,Andersson I

doi

10.1016/j.jmb.2009.11.045

subject

Has Abstract

pub_date

2010-02-19 00:00:00

pages

332-44

issue

2

eissn

0022-2836

issn

1089-8638

pii

S0022-2836(09)01439-9

journal_volume

396

pub_type

杂志文章

相关文献

JOURNAL OF MOLECULAR BIOLOGY文献大全
  • Determining the critical nucleus and mechanism of fibril elongation of the Alzheimer's Abeta(1-40) peptide.

    abstract：:We use a coarse-grained protein model to characterize the critical nucleus, structural stability, and fibril elongation propensity of Abeta(1-40) oligomers for the C(2x) and C(2z) quaternary forms proposed by solid-state NMR. By estimating equilibrium populations of structurally stable and unstable protofibrils, we de...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2006.10.011

    authors： Fawzi NL,Okabe Y,Yap EH,Head-Gordon T

    更新日期：2007-01-12 00:00:00

  • Molecular structure of the "low molecular weight antigen" of Toxoplasma gondii: a glucose alpha 1-4 N-acetylgalactosamine makes free glycosyl-phosphatidylinositols highly immunogenic.

    abstract：:Toxoplasma gondii is a ubiquitous parasitic protozoan causing congenital infection and severe encephalitis in the course of the acquired immunodeficiency syndrome. Glycosyl-phosphatidylinositols of T. gondii have been shown to be identical with the low molecular weight antigen which elicits an early immunoglobulin M i...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1006/jmbi.1996.0806

    authors： Striepen B,Zinecker CF,Damm JB,Melgers PA,Gerwig GJ,Koolen M,Vliegenthart JF,Dubremetz JF,Schwarz RT

    更新日期：1997-03-07 00:00:00

  • Phenotypic suppression by incorporation of an alien amino acid.

    abstract：:Azaleucine is a naturally occurring amino acid antibiotic that can be incorporated into proteins by mimicking leucine. In spite of its highly toxic character, the contrast between the hydrophobic side-chain of leucine and the basic side-chain of azaleucine suggested a mechanism for rescuing certain mutants. We constru...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1006/jmbi.1993.1269

    authors： Lemeignan B,Sonigo P,Marlière P

    更新日期：1993-05-20 00:00:00

  • Stability of Escherichia coli transcription complexes near an intrinsic terminator.

    abstract：:Transcription complexes containing Escherichia coli RNA polymerase terminate RNA synthesis in response to intrinsic (rho-independent) terminators encoded in the DNA template. This type of termination involves the formation of a hairpin structure in the nascent RNA, leading to release of the RNA and polymerase from the...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1006/jmbi.1994.1702

    authors： Wilson KS,von Hippel PH

    更新日期：1994-11-18 00:00:00

  • Two-dimensional kinetics of inter-connexin interactions from single-molecule force spectroscopy.

    abstract：:Gap junction channels are intercellular channels that form by docking the extracellular loops of connexin protein subunits. While the structure and function of gap junctions as intercellular channels have been characterized using different techniques, the physics of the inter-connexin interaction remain unknown. Moreo...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2011.07.013

    authors： Rico F,Oshima A,Hinterdorfer P,Fujiyoshi Y,Scheuring S

    更新日期：2011-09-09 00:00:00

  • Genomic organization and physical mapping of the transfer RNA genes in Escherichia coli K12.

    abstract：:By using a set of 476 ordered DNA clones (in lambda phage vector) that covers the entire chromosome of Escherichia coli K12, we have made an exhaustive survey of tRNA genes in the E. coli genome. Ultraviolet-irradiated bacteria were separately infected with each of the 476 clones and the RNA molecules produced upon in...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/0022-2836(90)90224-A

    authors： Komine Y,Adachi T,Inokuchi H,Ozeki H

    更新日期：1990-04-20 00:00:00

  • Antisense-RNA mediated transcriptional attenuation: importance of a U-turn loop structure in the target RNA of plasmid pIP501 for efficient inhibition by the antisense RNA.

    abstract：:Antisense-RNA mediated gene regulation has been found and studied in detail mainly in prokaryotic accessory DNA elements. In spite of different regulatory mechanisms, in all cases a rapid interaction between antisense and target RNA has been shown to be crucial for efficient regulation. Recently, a sequence comparison...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2003.09.020

    authors： Heidrich N,Brantl S

    更新日期：2003-11-07 00:00:00

  • Different intrastrand and interstrand contributions to stacking account for roll variations at the alternating purine-pyrimidine sequences in A-DNA and A-RNA.

    abstract：:An explanation is suggested for the roll alternation between low and high values in A-type nucleic acid duplexes containing alternating sequences of purine and pyrimidine residues. The explanation combines two points. (1) Roll inevitably occurs in A-type duplexes due to geometrical reasons. (2) Intrastrand base stacki...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/0022-2836(91)80172-q

    authors： Sponer J,Kypr J

    更新日期：1991-10-05 00:00:00

  • Solution structure of a phage-derived peptide antagonist in complex with vascular endothelial growth factor.

    abstract：:Vascular endothelial growth factor (VEGF) is a potent endothelial cell-specific mediator of angiogenesis and vasculogenesis. VEGF is involved pathologically in cancer, proliferative retinopathy and rheumatoid arthritis, and as such represents an important therapeutic target. Three classes of disulfide-constrained pept...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1006/jmbi.2001.5370

    authors： Pan B,Li B,Russell SJ,Tom JY,Cochran AG,Fairbrother WJ

    更新日期：2002-02-22 00:00:00

  • Structure of the intact stem and bulge of HIV-1 Psi-RNA stem-loop SL1.

    abstract：:The Psi-RNA packaging signal of the human immunodeficiency virus type-1 (HIV-1) genome contains a 35 nucleotide stem-loop, termed SL1, which is important for efficient genome packaging during virus assembly and for reverse transcription during infectivity. The predicted secondary structure of SL1 consists of an upper ...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/s0022-2836(02)01305-0

    authors： Lawrence DC,Stover CC,Noznitsky J,Wu Z,Summers MF

    更新日期：2003-02-14 00:00:00

  • Autonomous and reversible folding of a soluble amino-terminally truncated segment of the mouse prion protein.

    abstract：:Prion diseases are assumed to be caused by the infectious isoform, PrPsc, of a single cellular surface protein, PrPc. PrPsc is an insoluble form of PrPc and is believed to possess a different three-dimensional fold. It may propagate by causing PrPc to adopt its own infectious conformation by an unknown mechanism. Stud...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1006/jmbi.1996.0487

    authors： Hornemann S,Glockshuber R

    更新日期：1996-09-06 00:00:00

  • Central domain of the positive control protein NifA and its role in transcriptional activation.

    abstract：:The positive control protein NifA of Klebsiella pneumoniae activates transcription by RNA polymerase containing sigma 54 by catalysing open promoter complex formation. We show that the integrity of the putative ATP-binding pocket in the central domain of NifA is necessary for the positive control function of NifA, but...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/0022-2836(92)90921-6

    authors： Cannon W,Buck M

    更新日期：1992-05-20 00:00:00

  • Folding mechanism of indole-3-glycerol phosphate synthase from Sulfolobus solfataricus: a test of the conservation of folding mechanisms hypothesis in (beta(alpha))(8) barrels.

    abstract：:As a test of the hypothesis that folding mechanisms are better conserved than sequences in TIM barrels, the equilibrium and kinetic folding mechanisms of indole-3-glycerol phosphate synthase (sIGPS) from the thermoacidophilic archaebacterium Sulfolobus solfataricus were compared to the well-characterized models of the...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/s0022-2836(02)00557-0

    authors： Forsyth WR,Matthews CR

    更新日期：2002-07-26 00:00:00

  • Crystal structure of human bone morphogenetic protein-2 at 2.7 A resolution.

    abstract：:Homodimeric bone morphogenetic protein-2 (BMP-2) is a member of the transforming growth factor beta (TGF-beta) superfamily that induces bone formation and regeneration, and determines important steps during early stages of embryonic development in vertebrates and non-vertebrates. BMP-2 can interact with two types of r...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1006/jmbi.1999.2590

    authors： Scheufler C,Sebald W,Hülsmeyer M

    更新日期：1999-03-19 00:00:00

  • The hyaluronan synthase catalyzes the synthesis and membrane translocation of hyaluronan.

    abstract：:Hyaluronan (HA), an extracellular linear polysaccharide of alternating N-acetyl-glucosamine and glucuronic acid residues, is ubiquitously expressed in vertebrates, where it affects a broad spectrum of physiological processes, including cell adhesion, migration and differentiation. The HA polymer is synthesized on the ...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2012.01.053

    authors： Hubbard C,McNamara JT,Azumaya C,Patel MS,Zimmer J

    更新日期：2012-04-20 00:00:00

  • X-ray structure of a water-soluble analog of the membrane protein phospholamban: sequence determinants defining the topology of tetrameric and pentameric coiled coils.

    abstract：:Phospholamban (PLB) is a pentameric transmembrane protein that regulates the Ca(2+)-dependent ATPase SERCA2a in sarcoplasmic reticulum membranes. We previously described the computational design of a water-soluble variant of phospholamban, WSPLB, which reproduced many of the structural and functional properties of the...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2005.02.040

    authors： Slovic AM,Stayrook SE,North B,Degrado WF

    更新日期：2005-05-06 00:00:00

  • A method for helical RNA global structure determination in solution using small-angle x-ray scattering and NMR measurements.

    abstract：:We report a "top-down" method that uses mainly duplexes' global orientations and overall molecular dimension and shape restraints, which were extracted from experimental NMR and small-angle X-ray scattering data, respectively, to determine global architectures of RNA molecules consisting of mostly A-form-like duplexes...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2009.08.001

    authors： Wang J,Zuo X,Yu P,Xu H,Starich MR,Tiede DM,Shapiro BA,Schwieters CD,Wang YX

    更新日期：2009-10-30 00:00:00

  • The mathematics of SELEX against complex targets.

    abstract：:We have developed a computer model for the simulation of simultaneous SELEX against multiple targets. The model assumes equilibrium behavior for the formation of binary ligand:target complexes, and that there is no ligand:ligand or target:target interaction. Target concentrations, ligand concentrations, and affinity d...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1006/jmbi.1998.1727

    authors： Vant-Hull B,Payano-Baez A,Davis RH,Gold L

    更新日期：1998-05-08 00:00:00

  • The mechanical role of VASP in an Arp2/3-complex-based motility assay.

    abstract：:The comet motility assay, inspired by Listeria locomotion, has been used extensively as an in vitro model to study the structural and motile properties of the actin cytoskeleton. However, there are no quantitative measurements of the mechanical properties of these actin comets. In this work, we use nanoindentation bas...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2011.08.054

    authors： Suei S,Seyan R,Noguera P,Manzi J,Plastino J,Kreplak L

    更新日期：2011-10-28 00:00:00

  • Conformational aspects of an uncharged phosphate analogon built in at the branch-point of a DNA four-way junction.

    abstract：:Electrostatic interactions appear to be important in the conformation and dynamics of DNA four-way junctions. Particularly, the Coulomb repulsion between two approaching phosphate groups at the site of strand exchange is commonly supposed to have a negative influence on the thermodynamic stability of the fully stacked...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1006/jmbi.1996.0518

    authors： Pikkemaat JA,Overmars FJ,Dreef-Tromp CM,van den Elst H,van Boom JH,Altona C

    更新日期：1996-09-27 00:00:00

  • Mitochondrial respiratory chain supercomplexes are destabilized in Barth Syndrome patients.

    abstract：:Mutations in the human TAZ gene are associated with Barth Syndrome, an often fatal X-linked disorder that presents with cardiomyopathy and neutropenia. The TAZ gene encodes Tafazzin, a putative phospholipid acyltranferase that is involved in the remodeling of cardiolipin, a phospholipid unique to the inner mitochondri...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2006.06.057

    authors： McKenzie M,Lazarou M,Thorburn DR,Ryan MT

    更新日期：2006-08-18 00:00:00

  • Dissection of the promoter region of the inositol 1,4,5-trisphosphate receptor gene, itr-1, in C. elegans: a molecular basis for cell-specific expression of IP3R isoforms.

    abstract：:Inositol 1,4,5-trisphosphate receptors in Caenorhabditis elegans are encoded by a single gene, itr-1. This provides a powerful system in which to dissect the mechanisms that control the tissue-specific expression of molecules that determine the specificity of calcium signalling. We first identified the Caenorhabditis ...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1006/jmbi.2000.4388

    authors： Gower NJ,Temple GR,Schein JE,Marra M,Walker DS,Baylis HA

    更新日期：2001-02-16 00:00:00

  • Ligand-induced conformational change in penicillin acylase.

    abstract：:The enzyme penicillin acylase (penicillin amidohydrolase EC 3.5.1. 11) catalyses the cleavage of the amide bond in the benzylpenicillin (penicillin G) side-chain to produce phenylacetic acid and 6-aminopenicillanic acid (6-APA). The enzyme is of great pharmaceutical importance, as the product 6-APA is the starting poi...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1006/jmbi.1998.2180

    authors： Done SH,Brannigan JA,Moody PC,Hubbard RE

    更新日期：1998-11-27 00:00:00

  • Bile acid interactions with rabbit ileal lipid binding protein and an engineered helixless variant reveal novel ligand binding properties of a versatile beta-clam shell protein scaffold.

    abstract：:The intracellular ileal lipid binding proteins (ILBPs) are involved in the transport and enterohepatic circulation of bile acids. ILBPs from different species show high sequence and structural homology and have been shown to bind multiple bile acid ligands with differing degrees of selectivity and positive co-operativ...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2007.06.024

    authors： Kouvatsos N,Thurston V,Ball K,Oldham NJ,Thomas NR,Searle MS

    更新日期：2007-08-31 00:00:00

  • Substitution of Asp114 or Arg116 in the fingers domain of moloney murine leukemia virus reverse transcriptase affects interactions with the template-primer resulting in decreased processivity.

    abstract：:Reverse transcriptase, an essential retroviral DNA polymerase, replicates the single-stranded RNA genome of the retrovirus, producing a double-stranded DNA copy, which is subsequently integrated into the host's genome. Substitution of Ala for either Asp114 or Arg116, two highly conserved residues in the fingers domain...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1006/jmbi.2000.4281

    authors： Gu J,Villanueva RA,Snyder CS,Roth MJ,Georgiadis MM

    更新日期：2001-01-12 00:00:00

  • Functional analysis of the glutathione S-transferase 3 from Onchocerca volvulus (Ov-GST-3): a parasite GST confers increased resistance to oxidative stress in Caenorhabditis elegans.

    abstract：:This study examined the genomic organisation of the coding region of the glutathione S-transferase 3 (Ov-GST-3) from the human parasitic nematode Onchocerca volvulus; alternative splicing leads to three different transcripts (Ov-GST-3/1; Ov-GST-3/2 and Ov-GST-3/3). Since the expression of Ov-GST-3 is inducible by oxid...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/s0022-2836(02)01174-9

    authors： Kampkötter A,Volkmann TE,de Castro SH,Leiers B,Klotz LO,Johnson TE,Link CD,Henkle-Dührsen K

    更新日期：2003-01-03 00:00:00

  • Refined structure of spinach glycolate oxidase at 2 A resolution.

    abstract：:The amino acid sequence of glycolate oxidase from spinach has been fitted to an electron density map of 2.0 A nominal resolution and the structure has been refined using the restrained parameter least-squares refinement of Hendrickson and Konnert. A final crystallographic R-factor of 18.9% was obtained for 32,888 inde...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/0022-2836(89)90178-2

    authors： Lindqvist Y

    更新日期：1989-09-05 00:00:00

  • The MCM Helicase Motor of the Eukaryotic Replisome.

    abstract：:The MCM motor of the CMG helicase powers ahead of the eukaryotic replication machinery to unwind DNA, in a process that requires ATP hydrolysis. The reconstitution of DNA replication in vitro has established the succession of events that lead to replication origin activation by the MCM and recent studies have started ...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章,评审

    doi：10.1016/j.jmb.2016.01.024

    authors： Abid Ali F,Costa A

    更新日期：2016-05-08 00:00:00

  • Effect of antibiotics on large ribosomal subunit assembly reveals possible function of 5 S rRNA.

    abstract：:Functional large ribosomal subunits of Thermus aquaticus can be reconstituted from ribosomal proteins and either natural or in vitro transcribed 23 S and 5 S rRNA. Omission of 5 S rRNA during subunit reconstitution results in dramatic decrease of the peptidyl transferase activity of the assembled subunits. However, th...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1006/jmbi.1999.3030

    authors： Khaitovich P,Mankin AS

    更新日期：1999-09-03 00:00:00

  • Partitioning protein structures into domains: why is it so difficult?

    abstract：:This analysis takes an in-depth look into the difficulties encountered by automatic methods for domain decomposition from three-dimensional structure. The analysis involves a multi-faceted set of criteria including the integrity of secondary structure elements, the tendency toward fragmentation of domains, domain boun...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2006.05.060

    authors： Holland TA,Veretnik S,Shindyalov IN,Bourne PE

    更新日期：2006-08-18 00:00:00