当前位置： SCI文献检索 > JOURNAL OF MOLECULAR BIOLOGY期刊下所有文献 > A crystallographic re-investigation into the structure of Streptomyces griseus proteinase A reveals an acyl-enzyme intermediate.

A crystallographic re-investigation into the structure of Streptomyces griseus proteinase A reveals an acyl-enzyme intermediate.

Abstract：

:A molecular dynamics (MD) simulation on the contents of two asymmetric units of the crystal structure of the bacterial serine proteinase, Streptomyces griseus proteinase A (SGPA), resulted in four dihydrogen phosphate anions migrating to form a cluster in a solvent region far removed from the protein surface. In an effort to provide experimental verification for this unexpected phenomenon, native SGPA crystals were soaked in 2.0 M KH2AsO4; intensity data were collected and difference electron density maps examined for evidence of H2AsO4- ion clusters. These maps did not corroborate the cluster observed in the MD simulation. They did, however, show positive electron density features located in the active site cavity that could be interpreted as a tetrapeptide, Gly-Ala-Ser-(beta-OH)Asp, covalently bonded to O gamma of Ser195 as an acyl-enzyme intermediate. There was also a peak of electron density corresponding to an ideal position for the hydrolytic water in the deacylation reaction. This density is centred 3.1 A from His57 N epsilon 2 and 2.7 A from the carbonyl-carbon atom of the planar acyl-ester bond of the complex. The carbonyl-oxygen atom of the ester is located in the oxyanion pocket and participates in hydrogen bonds with Gly193 NH (2.6 A) and Ser195 NH (3.0 A).

journal_name

J Mol Biol

journal_title

Journal of molecular biology

authors

Blanchard H,James MN

doi

10.1006/jmbi.1994.1532

subject

Has Abstract

pub_date

1994-08-26 00:00:00

pages

574-87

issue

4

eissn

0022-2836

issn

1089-8638

pii

S0022-2836(84)71532-4

journal_volume

241

pub_type

杂志文章

相关文献

JOURNAL OF MOLECULAR BIOLOGY文献大全
  • The activity and stability of the intrinsically disordered Cip/Kip protein family are regulated by non-receptor tyrosine kinases.

    abstract：:The Cip/Kip family of cyclin-dependent kinase (Cdk) inhibitors includes p21(Cip1), p27(Kip1) and p57(Kip2). Their kinase inhibitory activities are mediated by a homologous N-terminal kinase inhibitory domain. The Cdk inhibitory activity and stability of p27 have been shown to be regulated by a two-step phosphorylation...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2014.11.011

    authors： Huang Y,Yoon MK,Otieno S,Lelli M,Kriwacki RW

    更新日期：2015-01-30 00:00:00

  • Protein titration in the crystal state.

    abstract：:Proteins are complex structures whose overall stability critically depends on a delicate balance of numerous interactions of similar strength, which are markedly influenced by their environment. Here, we present an analysis of the effect of pH on a protein structure in the crystalline state using RNase A as a model sy...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1006/jmbi.1999.3093

    authors： Berisio R,Lamzin VS,Sica F,Wilson KS,Zagari A,Mazzarella L

    更新日期：1999-10-01 00:00:00

  • Ligand-induced assembling of the type I interferon receptor on supported lipid bilayers.

    abstract：:Type I interferons (IFNs) elicit antiviral, antiproliferative and immuno-modulatory responses through binding to a shared receptor consisting of the transmembrane proteins ifnar1 and ifnar2. Differential signaling by different interferons, in particular IFNalphas and IFNbeta, suggests different modes of receptor engag...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2004.05.059

    authors： Lamken P,Lata S,Gavutis M,Piehler J

    更新日期：2004-07-30 00:00:00

  • Functionally important correlated motions in the single-stranded DNA-binding protein encoded by filamentous phage Pf3.

    abstract：:To elucidate the interplay between different parts of dimeric single-stranded DNA-binding proteins we have studied the correlated motions in the protein encoded by filamentous phage Pf3 via the combined use of 15N-NMR relaxation experiments, molecular dynamics simulations and essential dynamics calculations. These stu...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1006/jmbi.1999.2629

    authors： Horstink LM,Abseher R,Nilges M,Hilbers CW

    更新日期：1999-04-02 00:00:00

  • Rules for coupled expression of regulator and effector genes in inducible circuits.

    abstract：:The induction of effector genes that encode enzymes is often controlled by the protein product of a regulator gene that is directly involved in the control of its own expression. This coupling of elementary gene circuits can lead to three patterns of regulator and effector gene expression. As effector gene expression ...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1006/jmbi.1996.0011

    authors： Hlavacek WS,Savageau MA

    更新日期：1996-01-12 00:00:00

  • Extending the accuracy limits of prediction for side-chain conformations.

    abstract：:Current techniques for the prediction of side-chain conformations on a fixed backbone have an accuracy limit of about 1.0-1.5 A rmsd for core residues. We have carried out a detailed and systematic analysis of the factors that influence the prediction of side-chain conformation and, on this basis, have succeeded in ex...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1006/jmbi.2001.4865

    authors： Xiang Z,Honig B

    更新日期：2001-08-10 00:00:00

  • Kinetic coupling between protein folding and prolyl isomerization. I. Theoretical models.

    abstract：:Kinetic models were developed to describe the influence of prolyl peptide bond isomerization on the kinetics of reversible protein folding for cases in which structural intermediates do not occur. In the simulations, the number of prolyl residues and the relative rates of folding and isomerization were varied. The exp...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/0022-2836(92)90585-8

    authors： Kiefhaber T,Kohler HH,Schmid FX

    更新日期：1992-03-05 00:00:00

  • Taxonomy and conformational analysis of loops in proteins.

    abstract：:We propose a general classification scheme for loops, aperiodic segments of protein structure. In an effort to avoid the geometric complexity created by non-repeating phi psi angles, a morphologic definition that focuses upon the linearity and planarity of loops is utilized. Out of 432 loops (4 to 20 residues in lengt...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/0022-2836(92)90553-v

    authors： Ring CS,Kneller DG,Langridge R,Cohen FE

    更新日期：1992-04-05 00:00:00

  • Kinetic control in protein folding for light chain amyloidosis and the differential effects of somatic mutations.

    abstract：:Light chain amyloidosis is a devastating disease where immunoglobulin light chains form amyloid fibrils, resulting in organ dysfunction and death. Previous studies have shown a direct correlation between the protein thermodynamic stability and the propensity for amyloid formation for some proteins involved in light ch...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2013.10.016

    authors： Blancas-Mejía LM,Tischer A,Thompson JR,Tai J,Wang L,Auton M,Ramirez-Alvarado M

    更新日期：2014-01-23 00:00:00

  • Structure of turnip crinkle virus. III. Identification of a unique coat protein dimer.

    abstract：:The minor structural protein (p80), found in about one copy per virion in turnip crinkle virus (TCV), is shown by amino acid analysis and peptide mapping to be a covalent dimer of the major coat protein (p40). The covalent linkage occurs near the N termini of the crosslinked chains. These data suggest that TGV and rel...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/0022-2836(86)90456-0

    authors： Stockley PG,Kirsh AL,Chow EP,Smart JE,Harrison SC

    更新日期：1986-10-20 00:00:00

  • Domain structure, stability and domain-domain interactions in recombinant factor XIII.

    abstract：:The process of heat denaturation of recombinant factor XIII (rFXIII), as well as its C-terminal 24 kDA and 12 kDa elastase-produced fragments starting at Ser514 and Thr628, respectively, was investigated in a wide range of conditions by fluorescence, CD and differential scanning calorimetry (DSC). It was found that th...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/s0022-2836(95)80060-3

    authors： Kurochkin IV,Procyk R,Bishop PD,Yee VC,Teller DC,Ingham KC,Medved LV

    更新日期：1995-04-28 00:00:00

  • Regulation of transcriptional silencing in yeast by growth temperature.

    abstract：:Increasing evidence indicates that transcriptionally silent chromatin structure is dynamic and may change its conformation in response to external or internal stimuli. We show that growth temperature affects all three forms of transcriptional silencing in Saccharomyces cerevisiae. In general, increasing the temperatur...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2004.10.002

    authors： Bi X,Yu Q,Sandmeier JJ,Elizondo S

    更新日期：2004-12-03 00:00:00

  • Consensus protein design without phylogenetic bias.

    abstract：:Consensus design is an appealing strategy for the stabilization of proteins. It exploits amino acid conservation in sets of homologous proteins to identify likely beneficial mutations. Nevertheless, its success depends on the phylogenetic diversity of the sequence set available. Here, we show that randomization of a s...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2010.04.039

    authors： Jäckel C,Bloom JD,Kast P,Arnold FH,Hilvert D

    更新日期：2010-06-18 00:00:00

  • Mechanisms of Gasdermin Family Members in Inflammasome Signaling and Cell Death.

    abstract：:The Gasdermin (GSDM) family consists of Gasdermin A (GSDMA), Gasdermin B (GSDMB), Gasdermin C (GSDMC), Gasdermin D (GSDMD), Gasdermin E (GSDME) and Pejvakin (PJVK). GSDMD is activated by inflammasome-associated inflammatory caspases. Cleavage of GSDMD by human or mouse caspase-1, human caspase-4, human caspase-5, and ...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章,评审

    doi：10.1016/j.jmb.2018.07.002

    authors： Feng S,Fox D,Man SM

    更新日期：2018-09-14 00:00:00

  • Crystallization of and preliminary X-ray data for the mouse major urinary protein and rat alpha-2u globulin.

    abstract：:Crystals of the mouse major urinary protein (MUP) and rat alpha-2u globulin (AMG) have been grown from solutions of polyethylene glycol 3350 and CdCl2, respectively. The crystals differ both in their morphologies and space groups but have very similar unit cell sizes. AMG crystallized in P2(1) (a = 56.6 A, b = 103.8 A...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/0022-2836(91)90258-8

    authors： Böcskei Z,Findlay JB,North AC,Phillips SE,Somers WS,Wright CE,Lionetti C,Tirindelli R,Cavaggioni A

    更新日期：1991-04-20 00:00:00

  • Geometry of the flagellar motor in the cytoplasmic membrane of Salmonella typhimurium as determined by stereo-photogrammetry of quick-freeze deep-etch replica images.

    abstract：:The precise geometry of the flagellar basal structure anchored in the cytoplasmic membrane was determined by digital stereo-photogrammetry of the images captured by quick-freeze deep-etch replica electron microscopy. In order to examine the structure on the periplasmic side of the membrane, we analyzed the MS ring com...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1006/jmbi.1996.0038

    authors： Katayama E,Shiraishi T,Oosawa K,Baba N,Aizawa S

    更新日期：1996-01-26 00:00:00

  • Membrane topology of the MotA protein of Escherichia coli.

    abstract：:The MotA protein of Escherichia coli is a component of the flagella that functions together with the MotB protein in transmembrane proton conduction. It is an integral membrane protein, with four hydrophobic segments that might traverse the membrane and two short segments that are predicted to be in the periplasm. In ...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1006/jmbi.1995.0431

    authors： Zhou J,Fazzio RT,Blair DF

    更新日期：1995-08-11 00:00:00

  • Average orientation of aromatic residues in proteins determined from linear dichroism spectroscopy. A comparison of results on bovine gamma-crystallins with X-ray data.

    abstract：:The structures of the two very closely related proteins, bovine gamma II- and gamma IVa-crystallin have been studied by means of near-ultra-violet linear dichroism spectroscopy on squeezed polyacrylamide gel systems. The crystallin spectra are discussed in terms of the spectra of the aromatic chromophores present in t...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/s0022-2836(05)80069-5

    authors： Bloemendal M,Leunissen JA,van Amerongen H,van Grondelle R

    更新日期：1990-11-05 00:00:00

  • High-resolution structure of the major periplasmic domain from the cell shape-determining filament MreC.

    abstract：:Bacterial cell shape is dictated by the cell wall, a plastic structure that must adapt to growth and division whilst retaining its function as a selectively permeable barrier. The modulation of cell wall structure is achieved by a variety of enzymatic functions, all of which must be spatially regulated in a precise ma...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2007.07.022

    authors： Lovering AL,Strynadka NCJ

    更新日期：2007-09-28 00:00:00

  • 3D gene of foot-and-mouth disease virus. Conservation by convergence of average sequences.

    abstract：:The nucleotide sequence of the 3D (polymerase) gene of eight epidemiologically related isolates of foot-and-mouth disease virus of serotype C1 is reported. The genetic heterogeneity of 3D RNA is compared with that of the VP1-coding RNA of the same viruses. Regression lines of substitutions per nucleotide that distingu...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/0022-2836(88)90367-1

    authors： Villaverde A,Martínez-Salas E,Domingo E

    更新日期：1988-12-05 00:00:00

  • Regulation of the Caenorhabditis elegans gut cysteine protease gene cpr-1: requirement for GATA motifs.

    abstract：:Expression of the Caenorhabditis elegans cysteine protease gene cpr-1 is regulated both spatially and temporally. In situ hybridisation and Northern blot analysis have shown that this gene is expressed exclusively in gut cells of all developmental stages except the embryo. We now show by transgenic transformation with...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1006/jmbi.1998.2093

    authors： Britton C,McKerrow JH,Johnstone IL

    更新日期：1998-01-01 00:00:00

  • The human telomeric protein TRF1 specifically recognizes nucleosomal binding sites and alters nucleosome structure.

    abstract：:Telomeres are dynamic nucleoprotein structures that cap the ends of eukaryotic chromosomes. In humans, the long (TTAGGG)(n) double-stranded telomeric DNA repeats are bound specifically by the two related proteins TRF1 and TRF2, and are organized in nucleosomes. Whereas the role of TRF1 and TRF2 in telomeric function h...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2006.04.071

    authors： Galati A,Rossetti L,Pisano S,Chapman L,Rhodes D,Savino M,Cacchione S

    更新日期：2006-07-07 00:00:00

  • First structural evidence of a specific inhibition of phospholipase A2 by alpha-tocopherol (vitamin E) and its implications in inflammation: crystal structure of the complex formed between phospholipase A2 and alpha-tocopherol at 1.8 A resolution.

    abstract：:This is the first structural evidence of alpha-tocopherol (alpha-TP) as a possible candidate against inflammation, as it inhibits phospholipase A2 specifically and effectively. The crystal structure of the complex formed between Vipera russelli phospholipase A2 and alpha-tocopherol has been determined and refined to a...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/S0022-2836(02)00473-4

    authors： Chandra V,Jasti J,Kaur P,Betzel Ch,Srinivasan A,Singh TP

    更新日期：2002-07-05 00:00:00

  • Facioscapulohumeral muscular dystrophy region gene 1 is a dynamic RNA-associated and actin-bundling protein.

    abstract：:FSHD region gene 1 (FRG1) is a dynamic nuclear and cytoplasmic protein that, in skeletal muscle, shows additional localization to the sarcomere. Maintaining appropriate levels of FRG1 protein is critical for muscular and vascular development in vertebrates; however, its precise molecular function is unknown. This stud...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2011.06.014

    authors： Sun CY,van Koningsbruggen S,Long SW,Straasheijm K,Klooster R,Jones TI,Bellini M,Levesque L,Brieher WM,van der Maarel SM,Jones PL

    更新日期：2011-08-12 00:00:00

  • Epitopes fused to F-pilin are incorporated into functional recombinant pili.

    abstract：:In order to develop a system which allows infection by an epitope-specific phage-antibody via an F-pilus expressing that epitope, a study on the expression of foreign sequences on F-pilin was undertaken. Initially, a plasmid library was constructed with random sequences encoding one to five amino acid residues fused t...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1006/jmbi.1998.1773

    authors： Rondot S,Anthony KG,Dübel S,Ida N,Wiemann S,Beyreuther K,Frost LS,Little M,Breitling F

    更新日期：1998-06-12 00:00:00

  • The Changing Face of Aging: Highly Sulfated Glycosaminoglycans Induce Amyloid Formation in a Lattice Corneal Dystrophy Model Protein.

    abstract：:Glycosaminoglycans (GAGs) are related to multiple biological functions and diseases. There is growing evidence that GAG concentration and sulfate content increase with age. The destabilizing mutation A546T in the corneal protein TGFBIp leads to lattice-type corneal dystrophy, but symptoms only appear in the fourth dec...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2017.07.014

    authors： Malmos KG,Stenvang M,Sahin C,Christiansen G,Otzen DE

    更新日期：2017-09-01 00:00:00

  • Replication of mini RK2 plasmid in extracts of Escherichia coli requires plasmid-encoded protein TrfA and host-encoded proteins DnaA, B, G DNA gyrase and DNA polymerase III.

    abstract：:Soluble extracts of Escherichia coli capable of carrying out replication of the mini-RK2 derivative pCT461 have been prepared from cells carrying this plasmid or from plasmid-free bacteria. The latter are dependent upon exogenously added plasmid-encoded replication protein (TrfA) and require additional DnaA protein fo...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/0022-2836(88)90118-0

    authors： Pinkney M,Diaz R,Lanka E,Thomas CM

    更新日期：1988-10-20 00:00:00

  • Msh2 separation of function mutations confer defects in the initiation steps of mismatch repair.

    abstract：:In eukaryotes the MSH2-MSH3 and MSH2-MSH6 heterodimers initiate mismatch repair (MMR) by recognizing and binding to DNA mismatches. The MLH1-PMS1 heterodimer then interacts with the MSH proteins at or near the mismatch site and is thought to act as a mediator to recruit downstream repair proteins. Here we analyzed fiv...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/s0022-2836(03)00694-6

    authors： Kijas AW,Studamire B,Alani E

    更新日期：2003-08-01 00:00:00

  • S4-16 S ribosomal RNA complex. Binding constant measurements and specific recognition of a 460-nucleotide region.

    abstract：:The region of the Escherichia coli 16 S ribosomal RNA recognized by the ribosomal protein S4 has been defined by assaying a set of 13 16 S rRNA fragments for S4 binding. The fragments were prepared by transcription in vitro, and binding constants were measured in three ways: retention of labeled RNA fragments on nitro...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/0022-2836(89)90274-x

    authors： Vartikar JV,Draper DE

    更新日期：1989-09-20 00:00:00

  • Structures of the TetR-like simocyclinone efflux pump repressor, SimR, and the mechanism of ligand-mediated derepression.

    abstract：:Simocyclinone D8 (SD8), a potent DNA gyrase inhibitor made by Streptomyces antibioticus, is exported from the producing organism by the SimX efflux pump. The expression of simX is under the control of SimR, a member of the TetR family of transcriptional regulators. SimR represses simX transcription by binding to opera...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2011.02.035

    authors： Le TB,Stevenson CE,Fiedler HP,Maxwell A,Lawson DM,Buttner MJ

    更新日期：2011-04-22 00:00:00