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(-) Description

Title :  CRYSTAL STRUCTURE OF SALMONELLA EFFECTOR PROTEIN SOPA
 
Authors :  J. Diao, J. Chen
Date :  16 Aug 07  (Deposition) - 11 Dec 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.80
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
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, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PMCSG7
    Expression System Strain: B834(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: RESIDUES 165-782
    Gene: SOPA
    Organism Scientific: SALMONELLA TYPHIMURIUM
    Organism Taxid: 216597
    Strain: SL1344

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 24)

Asymmetric Unit (1, 24)
No.NameCountTypeFull Name
1MSE24Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (1, 12)
No.NameCountTypeFull Name
1MSE12Mod. Amino AcidSELENOMETHIONINE
Biological Unit 2 (1, 12)
No.NameCountTypeFull Name
1MSE12Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (0, 0)

(no "Site" information available for 2QZA)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (10, 10)

Asymmetric Unit
No.Residues
1Ser A:166 -Pro A:167
2Pro A:315 -Ser A:316
3Pro A:406 -Pro A:407
4Arg A:569 -Ala A:570
5Ala A:570 -Gly A:571
6Ser B:166 -Pro B:167
7Ser B:520 -Pro B:521
8Ser B:580 -Pro B:581
9Ser B:661 -Pro B:662
10Pro B:709 -Pro B:710

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2QZA)

(-) Sequences/Alignments

Asymmetric 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:617
 aligned with SOPA_SALTY | Q8ZNR3 from UniProtKB/Swiss-Prot  Length:782

    Alignment length:617
                                   175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       485       495       505       515       525       535       545       555       565       575       585       595       605       615       625       635       645       655       665       675       685       695       705       715       725       735       745       755       765       775       
           SOPA_SALTY   166 SPSSPADWAKKLTDAVLRQKAGETLTAADRDFSNADFRNITFSKILPPSFMERDGDIIKGFNFSNSKFTYSDISHLHFDECRFTYSTLSDVVCSNTKFSNSDMNEVFLQYSITTQQQPSFIDTTLKNTLIRHKANLSGVILNEPDNSSPPSVSGGGNFIRLGDIWLQMPLLWTENAVDGFLNHEHNNGKSILMTIDSLPDKYSQEKVQAMEDLVKSLRGGRLTEACIRPVESSLVSVLAHPPYTQSALISEWLGPVQERFFAHQCQTYNDVPLPAPDTYYQQRILPVLLDSFDRNSAAMTTHSGLFNQVILHCMTGVDCTDGTRQKAAALYEQYLAHPAVSPHIHNGLFGNYDGSPDWTTRAADNFLLLSSQDSDTAMMLSTDTLLTMLNPTPDTAWDNFYLLRAGENVSTAQISPVELFRHDFPVFLAAFNQQATQRRFGELIDIILSTEEHGELNQQFLAATNQKHSTVKLIDDASVSRLATIFDPLLPEGKLSPAHYQHILSAYHLTDATPQKQAETLFCLSTAFARYSSSAIFGTEHDSPPALRGYAEALMQKAWELSPAIFPSSEQFTEWSDRFHGLHGAFTCTSVVADSMQRHARKYFPSVLSSILPLAWA 782
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhh......hhhhh.........hhhhh.hhhhhh.....ee.................eee.................eee.......ee..........eeeeee....ee....eeeeee.................eeee..eeee.....hhhhhhhhhhhhhh...hhhhhhhh......hhhhhhhhhhhhhhhh.......hhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhh..hhhhh.....................eeee.......eeeehhhhhhhhhh..........eee....ee.....hhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhh.........hhhhhhhhhhhhhhh.....hhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhh.hhhhh.hhhhhhhhhhhh...........hhhhhhhhhhhh..........hhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2qza A 166 SPSSPADWAKKLTDAVLRQKAGETLTAADRDFSNADFRNITFSKILPPSFmERDGDIIKGFNFSNSKFTYSDISHLHFDECRFTYSTLSDVVCSNTKFSNSDmNEVFLQYSITTQQQPSFIDTTLKNTLIRHKANLSGVILNEPDNSSPPSVSGGGNFIRLGDIWLQmPLLWTENAVDGFLNHEHNNGKSILmTIDSLPDKYSQEKVQAmEDLVKSLRGGRLTEACIRPVESSLVSVLAHPPYTQSALISEWLGPVQERFFAHQCQTYNDVPLPAPDTYYQQRILPVLLDSFDRNSAAmTTHSGLFNQVILHCmTGVDCTDGTRQKAAALYEQYLAHPAVSPHIHNGLFGNYDGSPDWTTRAADNFLLLSSQDSDTAmmLSTDTLLTmLNPTPDTAWDNFYLLRAGENVSTAQISPVELFRHDFPVFLAAFNQQATQRRFGELIDIILSTEEHGELNQQFLAATNQKHSTVKLIDDASVSRLATIFDPLLPEGKLSPAHYQHILSAYHLTDATPQKQAETLFCLSTAFARYSSSAIFGTEHDSPPALRGYAEALmQKAWELSPAIFPSSEQFTEWSDRFHGLHGAFTCTSVVADSmQRHARKYFPSVLSSILPLAWA 782
                                   175       185       195       205       215|      225       235       245       255       265  |    275       285       295       305       315       325       335       345       355  |    365       375       385       395       405       415       425       435       445       455       465       475   |   485       495       505       515       525       535       545       555       565       575       585       595       605       615       625       635       645       655       665       675       685       695       705       715    |  725       735       745       755     | 765       775       
                                                                            216-MSE                                             268-MSE                                                          333-MSE                  358-MSE          375-MSE                                                                                  464-MSE        479-MSE                                                         543-MSE   553-MSE                                                                                                                                                                720-MSE                                  761-MSE                 
                                                                                                                                                                                                                                                                                                                                                                                                                    544-MSE                                                                                                                                                                                                                                          


Chain B from PDB  Type:PROTEIN  Length:612
 aligned with SOPA_SALTY | Q8ZNR3 from UniProtKB/Swiss-Prot  Length:782

    Alignment length:618
                                   174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484       494       504       514       524       534       544       554       564       574       584       594       604       614       624       634       644       654       664       674       684       694       704       714       724       734       744       754       764       774        
           SOPA_SALTY   165 SSPSSPADWAKKLTDAVLRQKAGETLTAADRDFSNADFRNITFSKILPPSFMERDGDIIKGFNFSNSKFTYSDISHLHFDECRFTYSTLSDVVCSNTKFSNSDMNEVFLQYSITTQQQPSFIDTTLKNTLIRHKANLSGVILNEPDNSSPPSVSGGGNFIRLGDIWLQMPLLWTENAVDGFLNHEHNNGKSILMTIDSLPDKYSQEKVQAMEDLVKSLRGGRLTEACIRPVESSLVSVLAHPPYTQSALISEWLGPVQERFFAHQCQTYNDVPLPAPDTYYQQRILPVLLDSFDRNSAAMTTHSGLFNQVILHCMTGVDCTDGTRQKAAALYEQYLAHPAVSPHIHNGLFGNYDGSPDWTTRAADNFLLLSSQDSDTAMMLSTDTLLTMLNPTPDTAWDNFYLLRAGENVSTAQISPVELFRHDFPVFLAAFNQQATQRRFGELIDIILSTEEHGELNQQFLAATNQKHSTVKLIDDASVSRLATIFDPLLPEGKLSPAHYQHILSAYHLTDATPQKQAETLFCLSTAFARYSSSAIFGTEHDSPPALRGYAEALMQKAWELSPAIFPSSEQFTEWSDRFHGLHGAFTCTSVVADSMQRHARKYFPSVLSSILPLAWA 782
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
           Pfam domains (1) ---------------------------------------------------------Pentapeptide_4-2qzaB01 B:222-304                                                   ---------------------------------------------------------------SopA-2qzaB03 B:368-513                                                                                                                            --------------------------------------------------------------------------------------------------------SopA_C-2qzaB05 B:618-782                                                                                                                                              Pfam domains (1)
           Pfam domains (2) ---------------------------------------------------------Pentapeptide_4-2qzaB02 B:222-304                                                   ---------------------------------------------------------------SopA-2qzaB04 B:368-513                                                                                                                            --------------------------------------------------------------------------------------------------------SopA_C-2qzaB06 B:618-782                                                                                                                                              Pfam domains (2)
         Sec.struct. author ....hhhhhhhhhhhhhhhhhh....................................ee.................eeeeee..............eeeeee....ee..........eee.......ee...........................eeee..eeee.....hhhhhhhhhh.......hhhhhh...hhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhh...hhhhh.....................ee...........ee...................................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.------..hhhhhhhhhh.................................hhhhhhhhhh.....hhhhhhhhhhhhhhhh................hhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhh........ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2qza B 165 SSPSSPADWAKKLTDAVLRQKAGETLTAADRDFSNADFRNITFSKILPPSFmERDGDIIKGFNFSNSKFTYSDISHLHFDECRFTYSTLSDVVCSNTKFSNSDmNEVFLQYSITTQQQPSFIDTTLKNTLIRHKANLSGVILNEPDNSSPPSVSGGGNFIRLGDIWLQmPLLWTENAVDGFLNHEHNNGKSILmTIDSLPDKYSQEKVQAmEDLVKSLRGGRLTEACIRPVESSLVSVLAHPPYTQSALISEWLGPVQERFFAHQCQTYNDVPLPAPDTYYQQRILPVLLDSFDRNSAAmTTHSGLFNQVILHCmTGVDCTDGTRQKAAALYEQYLAHPAVSPHIHNGLFGNYDGSPDWTTRAADNFLLLSSQDSDTAmmLSTDTLLTmLNPTPDTAWDNFYLLRAGENVSTAQISPVELFRHDFPVFLAAFNQQATQRRFGELIDI------HGELNQQFLAATNQKHSTVKLIDDASVSRLATIFDPLLPEGKLSPAHYQHILSAYHLTDATPQKQAETLFCLSTAFARYSSSAIFGTEHDSPPALRGYAEALmQKAWELSPAIFPSSEQFTEWSDRFHGLHGAFTCTSVVADSmQRHARKYFPSVLSSILPLAWA 782
                                   174       184       194       204       214 |     224       234       244       254       264   |   274       284       294       304       314       324       334       344       354   |   364       374|      384       394       404       414       424       434       444       454       464       474    |  484       494       504       514       524       534       544       554       564       574       584       594       604      |  -   |   624       634       644       654       664       674       684       694       704       714     | 724       734       744       754      |764       774        
                                                                             216-MSE                                             268-MSE                                                          333-MSE                  358-MSE          375-MSE                                                                                  464-MSE        479-MSE                                                         543-MSE   553-MSE                                                   611    618                                                                                                   720-MSE                                  761-MSE                 
                                                                                                                                                                                                                                                                                                                                                                                                                     544-MSE
   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 2QZA)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (3, 6)

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

(-) Gene Ontology  (6, 6)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (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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  Cis Peptide Bonds
    Ala A:570 - Gly A:571   [ RasMol ]  
    Arg A:569 - Ala A:570   [ RasMol ]  
    Pro A:315 - Ser A:316   [ RasMol ]  
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    Ser B:166 - Pro B:167   [ RasMol ]  
    Ser B:520 - Pro B:521   [ RasMol ]  
    Ser B:580 - Pro B:581   [ RasMol ]  
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 Related Entries

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

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

(-) Related Entries Specified in the PDB File

2qyu