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(-) Description

Title :  CRYSTAL STRUCTURE OF VIBRIO CHOLERAE PUTATIVE NTPASE EPSE
 
Authors :  M. A. Robien, B. E. Krumm, M. Sandkvist, W. G. J. Hol
Date :  12 May 03  (Deposition) - 14 Oct 03  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.70
Chains :  Asym./Biol. Unit :  A
Keywords :  Bacterial Type Ii Secretion System Cytoplasmic Protein - Gspe, Putative Atpase, Atp Binding Protein, Metalloprotein (Metal-Cys4 Site), Protein Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. A. Robien, B. E. Krumm, M. Sandkvist, W. G. J. Hol
Crystal Structure Of The Extracellular Protein Secretion Ntpase Epse Of Vibrio Cholerae
J. Mol. Biol. V. 333 657 2003
PubMed-ID: 14556751  |  Reference-DOI: 10.1016/J.JMB.2003.07.015
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - GENERAL SECRETION PATHWAY PROTEIN E
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PQE70
    Expression System Strain: M15
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: N-TERMINAL TRUNCATION OF RESIDUES 1-90
    Gene: EPSE OR VC2732
    Organism Scientific: VIBRIO CHOLERAE
    Organism Taxid: 666
    Synonym: TYPE II TRAFFIC WARDEN ATPASE, CHOLERA TOXIN SECRETION PROTEIN EPSE

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 13)

Asymmetric/Biological Unit (3, 13)
No.NameCountTypeFull Name
1ANP1Ligand/IonPHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
2MSE11Mod. Amino AcidSELENOMETHIONINE
3ZN1Ligand/IonZINC ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:397 , CYS A:400 , CYS A:430 , CYS A:433BINDING SITE FOR RESIDUE ZN A 601
2AC2SOFTWARETHR A:232 , LEU A:234 , LEU A:239 , THR A:266 , GLY A:267 , SER A:268 , GLY A:269 , LYS A:270 , SER A:271 , THR A:272 , LEU A:392 , ARG A:441BINDING SITE FOR RESIDUE ANP A 701

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1P9W)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Asp A:293 -Pro A:294

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1P9W)

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1T2SP_EPS00662 Bacterial type II secretion system protein E signature.GSPE_VIBCH323-337  1A:323-337

(-) Exons   (0, 0)

(no "Exon" information available for 1P9W)

(-) 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:384
 aligned with GSPE_VIBCH | P37093 from UniProtKB/Swiss-Prot  Length:503

    Alignment length:403
                                   107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437       447       457       467       477       487       497   
           GSPE_VIBCH    98 SDDFFSLAEELPQNEDLLESEDDAPIIKLINAMLGEAIKEGASDIHIETFEKTLSIRFRVDGVLREVLAPSRKLSSLLVSRVKVMAKLDIAEKRVPQDGRISLRIGGRAVDVRVSTMPSSHGERVVMRLLDKNATRLDLHSLGMTAHNHDNFRRLIKRPHGIILVTGPTGSGKSTTLYAGLQELNSSERNILTVEDPIEFDIDGIGQTQVNPRVDMTFARGLRAILRQDPDVVMVGEIRDLETAQIAVQASLTGHLVMSTLHTNTAVGAVTRLRDMGIEPFLISSSLLGVLAQRLVRTLCPDCKEPYEADKEQRKLFDSKKKEPLILYRATGCPKCNHKGYRGRTGIHELLLVDDALQELIHSEAGEQAMEKHIRATTPSIRDDGLDKVRQGITSLEEVMRVT 500
               SCOP domains d1p9wa_ A:             Extracellular secretion NTPase EpsE                                                                                                                                                                                                                                                                                                                                                          SCOP domains
               CATH domains 1p9wA01 A:9            8-228  [code=3.30.450.90, no name defined]                                                                  1p9wA02 A:229-500 P-loop containing nucleotide triphosphate hydrolases                                                                                                                                                                                                           CATH domains
               Pfam domains -----------            -------T2SE-1p9wA01 A:128-396                                                                                                                                                                                                                                                       ------------------     --------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhh..------------hhhhhhhhhhhhhhhhhh..eeeeeee..eeeeeeee..eeeeee..hhhhhhhhhhhhhhhhh.........eeeeeee...--.eeeeeeee......eeee..ee......hhhhh..hhhhhhhhhhhh....eeeeee.....hhhhhhhhhhhhhh.....eeeee..........eeee.hhhhh.hhhhhhhhhhhh...eeee....hhhhhhhhhhhhhh..eeeeee...hhhhhhhhhhhhh.hhhhhhhheeeeeeeeeeeee.....eeee.hhhhhh..-----...eeee...........eeeeeeeeeeee.hhhhhhhhhh..hhhhhhhhhhh...hhhhhhhhhhhh...hhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------T2SP_E         ------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1p9w A  98 SDDFFSLAEEL------------APIIKLINAmLGEAIKEGASDIHIETFEKTLSIRFRVDGVLREVLAPSRKLSSLLVSRVKVmAKLDIAEKRVPQDGRISLRIG--AVDVRVSTmPSSHGERVVmRLLDKNATRLDLHSLGmTAHNHDNFRRLIKRPHGIILVTGPTGSGKSTTLYAGLQELNSSERNILTVEDPIEFDIDGIGQTQVNPRVDmTFARGLRAILRQDPDVVmVGEIRDLETAQIAVQASLTGHLVmSTLHTNTAVGAVTRLRDmGIEPFLISSSLLGVLAQRLVRTLCPDCKEPYEADKEQRKLF-----EPLILYRATGCPKCNHKGYRGRTGIHELLLVDDALQELIHSEAGEQAmEKHIRATTPSIRDDGLDKVRQGITSLEEVmRGS 500
                                   107|        -   |   127  |    137       147       157       167       177    |  187       197     | 207      |217      |227       237   |   247       257       267       277       287       297       307     | 317       327   |   337       347       357       367     | 377       387       397       407      |  -  |    427       437       447       457       467       477       487       497   
                                    108          121      130-MSE                                             182-MSE              203  |     214-MSE   224-MSE          241-MSE                                                                 313-MSE           331-MSE                 355-MSE           373-MSE                                  414   420                                            467-MSE                       497-MSE
                                                                                                                                      206
   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  (1, 1)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (2, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: P-loop_NTPase (1112)
(-)
Family: T2SE (6)
(-)
Vibrio cholerae (1)
1aT2SE-1p9wA01A:128-396

(-) Gene Ontology  (8, 8)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (GSPE_VIBCH | P37093)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    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:0008565    protein transporter activity    Enables the directed movement of proteins into, out of or within a cell, or between cells.
biological process
    GO:0015628    protein secretion by the type II secretion system    The process in which proteins are secreted across the outer membrane of Gram-negative bacteria by the type II secretion system. Proteins using this pathway are first translocated across the cytoplasmic membrane via the Sec or Tat pathways.
    GO:0015031    protein transport    The directed movement of proteins into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
    GO:0006810    transport    The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0015627    type II protein secretion system complex    A large protein complex, containing 12-15 subunits, that spans the cell envelope of Gram-negative bacteria and mediates the movement of proteins into the extracellular environment. The complex includes a component in the cytoplasm, an inner membrane subcomplex that reaches into the periplasmic compartment and a secretion pore in the outer membrane. Proteins using the Type II pathway are transported across the cytoplasmic membrane by the Sec or Tat complex.

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 Related Entries

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

UniProtKB/Swiss-Prot
        GSPE_VIBCH | P37093: 1p9r 2bh1 4ksr 4kss

(-) Related Entries Specified in the PDB File

1p9r 1P9R IS THE SAME PROTEIN WITHOUT BOUND NUCLEOTIDE ANALOG