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(-) Description

Title :  CRYSTAL STRUCTURE OF SALMONELLA EFFECTOR PROTEIN SOPA
 
Authors :  J. Diao, J. Chen
Date :  15 Aug 07  (Deposition) - 11 Dec 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym./Biol. Unit :  A
Keywords :  Ubiquitin E3 Ligase, Ligase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Diao, Y. Zhang, J. M. Huibregtse, D. Zhou, J. Chen
Crystal Structure Of Sopa, A Salmonella Effector Protein Mimicking A Eukaryotic Ubiquitin Ligase.
Nat. Struct. Mol. Biol. V. 15 65 2008
PubMed-ID: 18066077  |  Reference-DOI: 10.1038/NSMB1346
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - SECRETED EFFECTOR PROTEIN
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET30B
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: RESIDUES 163-782
    Gene: SOPA
    Organism Scientific: SALMONELLA TYPHIMURIUM
    Organism Taxid: 216597
    Strain: SL1344

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (2, 2)
No.NameCountTypeFull Name
1B3P1Ligand/Ion2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
2PO41Ligand/IonPHOSPHATE ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHOH A:14 , TYR A:275 , ILE A:277 , THR A:279 , ARG A:296 , LYS A:298 , LYS A:354BINDING SITE FOR RESIDUE PO4 A 2
2AC2SOFTWAREHOH A:11 , HOH A:47 , HOH A:60 , HOH A:63 , HOH A:95 , HOH A:115 , ASP A:255 , GLN A:274 , GLY A:320 , GLY A:321 , GLN A:332 , MET A:333 , PRO A:334 , GLU A:620 , GLN A:624 , ASP A:640BINDING SITE FOR RESIDUE B3P A 1

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Pro A:406 -Pro A:407

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2QYU)

(-) 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:620
 aligned with SOPA_SALTY | Q8ZNR3 from UniProtKB/Swiss-Prot  Length:782

    Alignment length:620
                                   172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472       482       492       502       512       522       532       542       552       562       572       582       592       602       612       622       632       642       652       662       672       682       692       702       712       722       732       742       752       762       772       782
           SOPA_SALTY   163 ATSSPSSPADWAKKLTDAVLRQKAGETLTAADRDFSNADFRNITFSKILPPSFMERDGDIIKGFNFSNSKFTYSDISHLHFDECRFTYSTLSDVVCSNTKFSNSDMNEVFLQYSITTQQQPSFIDTTLKNTLIRHKANLSGVILNEPDNSSPPSVSGGGNFIRLGDIWLQMPLLWTENAVDGFLNHEHNNGKSILMTIDSLPDKYSQEKVQAMEDLVKSLRGGRLTEACIRPVESSLVSVLAHPPYTQSALISEWLGPVQERFFAHQCQTYNDVPLPAPDTYYQQRILPVLLDSFDRNSAAMTTHSGLFNQVILHCMTGVDCTDGTRQKAAALYEQYLAHPAVSPHIHNGLFGNYDGSPDWTTRAADNFLLLSSQDSDTAMMLSTDTLLTMLNPTPDTAWDNFYLLRAGENVSTAQISPVELFRHDFPVFLAAFNQQATQRRFGELIDIILSTEEHGELNQQFLAATNQKHSTVKLIDDASVSRLATIFDPLLPEGKLSPAHYQHILSAYHLTDATPQKQAETLFCLSTAFARYSSSAIFGTEHDSPPALRGYAEALMQKAWELSPAIFPSSEQFTEWSDRFHGLHGAFTCTSVVADSMQRHARKYFPSVLSSILPLAWA 782
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -----------------------------------------------------------Pentapeptide_4-2qyuA01 A:222-304                                                   ---------------------------------------------------------------SopA-2qyuA02 A:368-513                                                                                                                            ------------------------------------------------------------------------------------------------------SopA_C-2qyuA03 A:616-782                                                                                                                                                Pfam domains
         Sec.struct. author ......hhhhhhhhhhhhhhhhhh...................hhhhh.hhhhhh.....ee.................eee.................eee.......ee..........eeeeee....ee....eeeeee.................eeee..eeee.....hhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhh.hhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhh..hhhhh.....................eeee......eeeeehhhhhhhhhh..........eeee..eee.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2qyu A 163 ATSSPSSPADWAKKLTDAVLRQKAGETLTAADRDFSNADFRNITFSKILPPSFMERDGDIIKGFNFSNSKFTYSDISHLHFDECRFTYSTLSDVVCSNTKFSNSDMNEVFLQYSITTQQQPSFIDTTLKNTLIRHKANLSGVILNEPDNSSPPSVSGGGNFIRLGDIWLQMPLLWTENAVDGFLNHEHNNGKSILMTIDSLPDKYSQEKVQAMEDLVKSLRGGRLTEACIRPVESSLVSVLAHPPYTQSALISEWLGPVQERFFAHQCQTYNDVPLPAPDTYYQQRILPVLLDSFDRNSAAMTTHSGLFNQVILHCMTGVDCTDGTRQKAAALYEQYLAHPAVSPHIHNGLFGNYDGSPDWTTRAADNFLLLSSQDSDTAMMLSTDTLLTMLNPTPDTAWDNFYLLRAGENVSTAQISPVELFRHDFPVFLAAFNQQATQRRFGELIDIILSTEEHGELNQQFLAATNQKHSTVKLIDDASVSRLATIFDPLLPEGKLSPAHYQHILSAYHLTDATPQKQAETLFCLSTAFARYSSSAIFGTEHDSPPALRGYAEALMQKAWELSPAIFPSSEQFTEWSDRFHGLHGAFTCTSVVADSMQRHARKYFPSVLSSILPLAWA 782
                                   172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472       482       492       502       512       522       532       542       552       562       572       582       592       602       612       622       632       642       652       662       672       682       692       702       712       722       732       742       752       762       772       782
   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 2QYU)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (3, 3)

Asymmetric/Biological Unit
(-)
Clan: Pentapeptide (11)
(-)
Clan: no clan defined [family: SopA] (2)
(-)
Clan: no clan defined [family: SopA_C] (2)

(-) Gene Ontology  (6, 6)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (SOPA_SALTY | Q8ZNR3)
molecular function
    GO:0016874    ligase activity    Catalysis of the joining of two substances, or two groups within a single molecule, with the concomitant hydrolysis of the diphosphate bond in ATP or a similar triphosphate.
    GO:0004842    ubiquitin-protein transferase activity    Catalysis of the transfer of ubiquitin from one protein to another via the reaction X-Ub + Y --> Y-Ub + X, where both X-Ub and Y-Ub are covalent linkages.
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:0016567    protein ubiquitination    The process in which one or more ubiquitin groups are added to a protein.
cellular component
    GO:0005576    extracellular region    The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.
    GO:0043657    host cell    A cell within a host organism. Includes the host plasma membrane and any external encapsulating structures such as the host cell wall and cell envelope.

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 Related Entries

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

UniProtKB/Swiss-Prot
        SOPA_SALTY | Q8ZNR3: 2qza 3sy2 5jw7

(-) Related Entries Specified in the PDB File

2qza