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(-) Description

Title :  STRUCTURAL ANALYSIS OF XANTHOMONAS XOPD PROVIDES INSIGHTS INTO SUBSTRATE SPECIFICITY OF UBIQUITIN-LIKE PROTEIN PROTEASES
 
Authors :  R. Chosed, D. R. Tomchick, C. A. Brautigam, M. Machius, K. Orth
Date :  11 Jan 07  (Deposition) - 29 May 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.95
Chains :  Asym./Biol. Unit :  A
Keywords :  Clan Ce Family 48 Cysteine Protease, Type Iii Secreted Effector, Desumoylating Enzyme, Secreted Virulence Factor, Peptidase, Isopeptidase, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  R. Chosed, D. R. Tomchick, C. A. Brautigam, S. Mukherjee, V. S. Negi, M. Machius, K. Orth
Structural Analysis Of Xanthomonas Xopd Provides Insights Into Substrate Specificity Of Ubiquitin-Like Protein Proteases.
J. Biol. Chem. V. 282 6773 2007
PubMed-ID: 17204475  |  Reference-DOI: 10.1074/JBC.M608730200
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - XANTHOMONAS OUTER PROTEIN D
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21(DE3)
    Expression System PlasmidPGEX-RTEV
    Expression System StrainBL21/DE3
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    FragmentCATALYTIC FRAGMENT (RESIDUES 335-520)
    GeneXOPD
    Organism ScientificXANTHOMONAS EUVESICATORIA
    Organism Taxid456327

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 1)

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1PO41Ligand/IonPHOSPHATE ION

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHOH A:35 , ASN A:360 , ARG A:418 , VAL A:485 , GLY A:488 , ASP A:491BINDING SITE FOR RESIDUE PO4 A 100

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2OIV)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2OIV)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2OIV)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2OIV)

(-) Exons   (0, 0)

(no "Exon" information available for 2OIV)

(-) 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    
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SAPs(SNPs) PROSITE motifs Exons
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Chain A from PDB  Type:PROTEIN  Length:170
 aligned with Q3BYJ5_XANC5 | Q3BYJ5 from UniProtKB/TrEMBL  Length:545

    Alignment length:177
                                   347       357       367       377       387       397       407       417       427       437       447       457       467       477       487       497       507       
         Q3BYJ5_XANC5   338 WLLDGHLRAYTDDLARRLRGEPNAHLLHFADSQVVTMLSSADPDQQARAQRLLAGDDIPPIVFLPINQPNAHWSLLVVDRRNKDAVAAYHYDSMAQKDPQQRYLADMAAYHLGLDYQQTHEMPIAIQSDGYSCGDHVLTGIEVLAHRVLDGTFDYAGGRDLTDIEPDRGLIRDRLAQ 514
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains Peptidase_C48-2oivA01 A:338-514                                                                                                                                                   Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhh...hhh.eee.hhhhhhhh...hhhhhhhhhhhhhh.....eeeeeeee...eeeeeeee.......eeeee...--..hhhhhhhhhhhhhh..hhhhheee....-----hhhhhhhhhhhhhhhhhhhhhhhh...........hhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2oiv A 338 WLLDGHLRAYTDDLARRLRGEPNAHLLHFADSQVVTMLSSADPDQQARAQRLLAGDDIPPIVFLPINQPNAHWSLLVVDRRNKDAVAAYHYDSM--KDPQQRYLADMAAYHLGLDYQQTHEMPIAI-----SCGDHVLTGIEVLAHRVLDGTFDYAGGRDLTDIEPDRGLIRDRLAQ 514
                                   347       357       367       377       387       397       407       417       427   |  |437       447       457     |   - |     477       487       497       507       
                                                                                                                       431  |                          463   469                                             
                                                                                                                          434                                                                                

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  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 2OIV)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2OIV)

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit

(-) Gene Ontology  (2, 2)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (Q3BYJ5_XANC5 | Q3BYJ5)
molecular function
    GO:0008234    cysteine-type peptidase activity    Catalysis of the hydrolysis of peptide bonds in a polypeptide chain by a mechanism in which the sulfhydryl group of a cysteine residue at the active center acts as a nucleophile.
biological process
    GO:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.

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  2oiv
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 Related Entries

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UniProtKB/TrEMBL
        Q3BYJ5_XANC5 | Q3BYJ52oix 5jp1 5jp3

(-) Related Entries Specified in the PDB File

2oix