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(-) Description

Title :  CRYSTAL STRUCTURE OF BORDETELLA PERTUSSIS BVGS PERIPLASMIC VFT2 DOMAIN
 
Authors :  J. Herrou, C. Bompard, R. Wintjens, E. Dupre, E. Willery, V. Villeret, C R. Antoine, F. Jacob-Dubuisson
Date :  27 Apr 10  (Deposition) - 06 Oct 10  (Release) - 20 Oct 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.04
Chains :  Asym./Biol. Unit :  A
Keywords :  Venus Flytrap, Sensor Domain, Signaling Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  J. Herrou, C. Bompard, R. Wintjens, E. Dupre, E. Willery, V. Villeret, C. Locht, R. Antoine, F. Jacob-Dubuisson
Periplasmic Domain Of The Sensor-Kinase Bvgs Reveals A New Paradigm For The Venus Flytrap Mechanism.
Proc. Natl. Acad. Sci. Usa V. 107 17351 2010
PubMed-ID: 20855615  |  Reference-DOI: 10.1073/PNAS.1006267107

(-) Compounds

Molecule 1 - VIRULENCE SENSOR PROTEIN BVGS
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPQE30
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    FragmentUNP RESIDUES 286-542
    GeneBP1877, BVGS
    Organism ScientificBORDETELLA PERTUSSIS
    Organism Taxid257313
    StrainTOHAMAI

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric/Biological Unit (2, 4)
No.NameCountTypeFull Name
1ACT2Ligand/IonACETATE ION
2GOL2Ligand/IonGLYCEROL

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREACT A:2 , HOH A:69 , HOH A:110 , HOH A:113 , HOH A:131 , PHE A:375 , SER A:423 , ALA A:425 , GLN A:461 , THR A:462BINDING SITE FOR RESIDUE GOL A 1
2AC2SOFTWAREHOH A:111 , HOH A:146 , LEU A:314 , PHE A:317 , LEU A:374 , PHE A:375BINDING SITE FOR RESIDUE ACT A 543
3AC3SOFTWAREGOL A:1 , HOH A:112 , HOH A:114 , PHE A:375 , VAL A:420 , PRO A:444 , GLN A:461BINDING SITE FOR RESIDUE ACT A 2
4AC4SOFTWAREHOH A:53 , HOH A:83 , HOH A:87 , HOH A:142 , HOH A:143 , VAL A:376 , ASN A:377 , SER A:378 , LEU A:428BINDING SITE FOR RESIDUE GOL A 544

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3MPK)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Ala A:318 -Pro A:319
2Thr A:325 -Asp A:326

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3MPK)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3MPK)

(-) Exons   (0, 0)

(no "Exon" information available for 3MPK)

(-) Sequences/Alignments

Asymmetric/Biological Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it)
Chain A from PDB  Type:PROTEIN  Length:235
 aligned with BVGS_BORPE | P16575 from UniProtKB/Swiss-Prot  Length:1238

    Alignment length:235
                                   301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491       501       511       521     
           BVGS_BORPE   292 HPAYSAREQQWMADHPVVKVAVLNLFAPFTLFRTDEQFGGISAAVLQLLQLRTGLDFEIIGVDTVEELIAKLRSGEADMAGALFVNSARESFLSFSRPYVRNGMVIVTRQDPDAPVDADHLDGRTVALVRNSAAIPLLQRRYPQAKVVTADNPSEAMLMVANGQADAVVQTQISASYYVNRYFAGKLRIASALDLPPAEIALATTRGQTELMSILNKALYSISNDELASIISRWR 526
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -----------------SBP_bac_3-3mpkA01 A:309-526                                                                                                                                                                                                Pfam domains
         Sec.struct. author ....hhhhhhhhhhh.eeeeeee.ee...ee........hhhhhhhhhhhhhhh.eeeeeee.hhhhhhhhhhhh...eeeeee.hhhhh..eee....eee.eeeeee.......hhhhh...eeeee...hhhhhhhhhh...eeeee.hhhhhhhhhhh....eeeeehhhhhhhhhhhh...eeeeee.....eeeeeeee..hhhhhhhhhhhhhh.hhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3mpk A 292 HPAYSAREQQWMADHPVVKVAVLNLFAPFTLFRTDEQFGGISAAVLQLLQLRTGLDFEIIGVDTVEELIAKLRSGEADMAGALFVNSARESFLSFSRPYVRNGMVIVTRQDPDAPVDADHLDGRTVALVRNSAAIPLLQRRYPQAKVVTADNPSEAMLMVANGQADAVVQTQISASYYVNRYFAGKLRIASALDLPPAEIALATTRGQTELMSILNKALYSISNDELASIISRWR 526
                                   301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491       501       511       521     

   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 3MPK)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3MPK)

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: PBP (391)

(-) Gene Ontology  (19, 19)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (BVGS_BORPE | P16575)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0016301    kinase activity    Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    GO:0000155    phosphorelay sensor kinase activity    Catalysis of the phosphorylation of a histidine residue in response to detection of an extracellular signal such as a chemical ligand or change in environment, to initiate a change in cell state or activity. The two-component sensor is a histidine kinase that autophosphorylates a histidine residue in its active site. The phosphate is then transferred to an aspartate residue in a downstream response regulator, to trigger a response.
    GO:0004673    protein histidine kinase activity    Catalysis of the reaction: ATP + protein L-histidine = ADP + protein phospho-L-histidine.
    GO:0004871    signal transducer activity    Conveys a signal across a cell to trigger a change in cell function or state. A signal is a physical entity or change in state that is used to transfer information in order to trigger a response.
    GO:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
    GO:0016772    transferase activity, transferring phosphorus-containing groups    Catalysis of the transfer of a phosphorus-containing group from one compound (donor) to another (acceptor).
biological process
    GO:0009405    pathogenesis    The set of specific processes that generate the ability of an organism to induce an abnormal, generally detrimental state in another organism.
    GO:0018106    peptidyl-histidine phosphorylation    The phosphorylation of peptidyl-histidine to form peptidyl-1'-phospho-L-histidine (otherwise known as tau-phosphohistidine, tele-phosphohistidine) or peptidyl-3'-phospho-L-histidine (otherwise known as pi-phosphohistidine, pros-phosphohistidine).
    GO:0000160    phosphorelay signal transduction system    A conserved series of molecular signals found in prokaryotes and eukaryotes; involves autophosphorylation of a histidine kinase and the transfer of the phosphate group to an aspartate that then acts as a phospho-donor to response regulator proteins.
    GO:0016310    phosphorylation    The process of introducing a phosphate group into a molecule, usually with the formation of a phosphoric ester, a phosphoric anhydride or a phosphoric amide.
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0007165    signal transduction    The cellular process in which a signal is conveyed to trigger a change in the activity or state of a cell. Signal transduction begins with reception of a signal (e.g. a ligand binding to a receptor or receptor activation by a stimulus such as light), or for signal transduction in the absence of ligand, signal-withdrawal or the activity of a constitutively active receptor. Signal transduction ends with regulation of a downstream cellular process, e.g. regulation of transcription or regulation of a metabolic process. Signal transduction covers signaling from receptors located on the surface of the cell and signaling via molecules located within the cell. For signaling between cells, signal transduction is restricted to events at and within the receiving cell.
    GO:0023014    signal transduction by protein phosphorylation    A process in which the transfer of one or more phosphate groups to a substrate transmits a signal to the phosphorylated substrate.
cellular component
    GO:0016021    integral component of membrane    The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0005622    intracellular    The living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0005886    plasma membrane    The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        BVGS_BORPE | P165753mpl 4q0c

(-) Related Entries Specified in the PDB File

3mpl