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(-) Description

Title :  A COVALENT S-F HETERODIMER OF STAPHYLOCOCCAL GAMMA-HEMOLYSIN
 
Authors :  P. Roblin, V. Guillet, L. Maveyraud, L. Mourey
Date :  10 Jul 07  (Deposition) - 19 Feb 08  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Pore-Forming Toxin, Beta-Barrel, Protein-Protein Interaction, Molecular Plasticity, Covalent Complex, Cytolysis, Hemolysis, Secreted, Toxin (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  P. Roblin, V. Guillet, O. Joubert, D. Keller, M. Erard, L. Maveyraud, G. Prevost, L. Mourey
A Covalent S-F Heterodimer Of Leucotoxin Reveals Molecular Plasticity Of Beta-Barrel Pore-Forming Toxins.
Proteins V. 71 485 2008
PubMed-ID: 18214982  |  Reference-DOI: 10.1002/PROT.21900
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - GAMMA-HEMOLYSIN COMPONENT A
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21
    Expression System Plasmid: PGEX-6P-1
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Vector Type: PLASMID
    Gene: HLGA, HLG2
    Mutation: YES
    Organism Scientific: STAPHYLOCOCCUS AUREUS SUBSP. AUREUS
    Organism Taxid: 196620
    Strain: MW2
    Synonym: H-GAMMA-2, H-GAMMA-II
 
Molecule 2 - GAMMA-HEMOLYSIN COMPONENT B
    Chains: B
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21
    Expression System Plasmid: PGEX-6P-1
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Vector Type: PLASMID
    Gene: HLGB
    Mutation: YES
    Organism Scientific: STAPHYLOCOCCUS AUREUS SUBSP. AUREUS
    Organism Taxid: 196620
    Strain: MW2
    Synonym: H-GAMMA-1, H-GAMMA-I

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 2QK7)

(-) Sites  (0, 0)

(no "Site" information available for 2QK7)

(-) SS Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1A:28 -B:156

(-) Cis Peptide Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1Leu A:95 -Pro A:96
2Ala B:100 -Pro B:101
3Gly B:177 -Pro B:178

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (1, 1)

Asymmetric/Biological Unit (1, 1)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_HLGA_STAAU_001 *R246KHLGA_STAAU  ---  ---AK217K
   * ID not provided by source
  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2QK7)

(-) Exons   (0, 0)

(no "Exon" information available for 2QK7)

(-) 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:259
 aligned with HLGA_STAAU | P0A074 from UniProtKB/Swiss-Prot  Length:309

    Alignment length:268
                                    49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299        
           HLGA_STAAU    40 AEIIKRTQDITSKRLAITQNIQFDFVKDKKYNKDALVVKMQGFISSRTTYSDLKKYPYIKRMIWPFQYNISLKTKDSNVDLINYLPKNKIDSADVSQKLGYNIGGNFQSAPSIGGSGSFNYSKTISYNQKNYVTEVESQNSKGVKWGVKANSFVTPNGQVSAYDQYLFAQDPTGPAARDYFVPDNQLPPLIQSGFNPSFITTLSHERGKGDKSEFEITYGRNMDATYAYVTRHRLAVDRKHDAFKNRNVTVKYEVNWKTHEVKIKSIT 307
               SCOP domains d2qk7a_ A: automated matches                                                                                                                                                                                                                                                 SCOP domains
               CATH domains 2qk7A00 A:11-278 Leukocidin-like                                                                                                                                                                                                                                             CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeeee....eeeeeeeeeee.....eeeeeeeeeeeee...eee..-----.eeeeeeeeeeeeee......eeeeee........eeeeeeeee...eeeee..........eeeeeeee...eeeeeeee...eeeeeeee.ee...--.ee..............hhhhhh.hhhhhhhhhhhee...eeeeeeee.....eeeeeeeeeeeeeeeeee..--..eeeeeeeeeeeeeeeeeeeee....eeeeeeee Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------K------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2qk7 A  11 AEIIKRTQDITSKRLAICQNIQFDFVKDKKYNKDALVVKMQGFISSRTTYSDL-----IKRMIWPFQYNISLKTKDSNVDLINYLPKNKIDSADVSQKLGYNIGGNFQSAPSIGGSGSFNYSKTISYNQKNYVTEVESQNSKGVKWGVKANSFVTP--QVSAYDQYLFAQDPTGPAARDYFVPDNQLPPLIQSGFNPSFITTLSHEKGKGDKSEFEITYGRNMDATYAYVT--RLAVDRKHDAFKNRNVTVKYEVNWKTHEVKIKSIT 278
                                    20        30        40        50        60  |     70        80        90       100       110       120       130       140       150       160     | 170       180       190       200       210       220       230       240|  |   250       260       270        
                                                                               63    69                                                                                              166  |                                                                     241  |                                  
                                                                                                                                                                                        169                                                                        244                                  


Chain B from PDB  Type:PROTEIN  Length:287
 aligned with HLGB_STAAU | P0A077 from UniProtKB/Swiss-Prot  Length:325

    Alignment length:297
                                    38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       
           HLGB_STAAU    29 KITPVSVKKVDDKVTLYKTTATADSDKFKISQILTFNFIKDKSYDKDTLVLKATGNINSGFVKPNPNDYDFSKLYWGAKYNVSISSQSNDSVNVVDYAPKNQNEEFQVQNTLGYTFGGDISISNGLSGGLNGNTAFSETINYKQESYRTTLSRNTNYKNVGWGVEAHKIMNNGWGPYGRDSFHPTYGNELFLAGRQSSAYAGQNFIAQHQMPLLSRSNFNPEFLSVLSHRQDGAKKSKITVTYQREMDLYQIRWNGFYWAGANYKNFKTRTFKSTYEIDWENHKVKLLDTKETENNK 325
               SCOP domains d2qk7b_ B: automated matches                                                                                                                                                                                                                                                                              SCOP domains
               CATH domains 2qk7B00 B:3-299 Leukocidin-like                                                                                                                                                                                                                                                                           CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeee....eeeeeeeeeeee....eeeeeeeeeeee....eeeeeeeeeeeee............eeeeeeeeeeeeeee......eeeeeee........eeeeeeeee...eeeeee..-------..eeeeeeee...eeeee.......eeeeeeee..eee..eeee..................---.hhhhh..hhhhhhhhhhhee...eeeeeeee.....eeeeeeeeeeeeeeeeeee....eeeeeeeeeeeeeeeeeeeee....eeeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2qk7 B   3 KITPVSVKKVDDKVTLYKTTATADSDKFKISQILTFNFIKDKSYDKDTLVLKAAGNINSGYEKPNPNDYDFSKLYWGAKYNVSISSQSNDSVNVVDYAPKNQNEEFQVQNTLGYTFGGDISISNGL-------TAFSETINYKQESYRTTLSRCTNYKNVGWGVEAHKIMNNGWGPYGRDSFHPTYGNELFLAGR---AYAGQNFIAQHQMPLLSRSNFNPEFLSVLSHRQDGAKKSKITVTYQREMDLYQIRWNGFYWAGANYKNFKTRTFKSTYEIDWENHKVKLLDTKETENNK 299
                                    12        22        32        42        52        62        72        82        92       102       112       122     |   -   |   142       152       162       172       182       192    |  202       212       222       232       242       252       262       272       282       292       
                                                                                                                                                       128     136                                                          197 201                                                                                                  


Chain B from PDB  Type:PROTEIN  Length:287
 aligned with Q57227_STAAU | Q57227 from UniProtKB/TrEMBL  Length:325

    Alignment length:297
                                    38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       
         Q57227_STAAU    29 KITPVSVKKVDDKVTLYKTTATADSDKFKISQILTFNFIKDKSYDKDTLVLKAAGNINSGYERPNPKDYDFSKIYWGAKYNVSISSQSNDSVNVVDYAPKNQNEEFQVQNTLGYTFGGDISISNGLSGGLNGNTAFSETINYKQESYRTTLSRNTNYKNVGWGVEAHKIMNNGWGPYGRDSFHPTYGNELFLAGRQSSAYAGQNFIAQHQMPLLSRSNFNPEFLSVLSHRQDGAKKSKITVTYQREMDLYQIRWNGFYWAGANYKNFKTRTFKSTYEIDWENHKVKLLDTKETENNK 325
               SCOP domains d2qk7b_ B: automated matches                                                                                                                                                                                                                                                                              SCOP domains
               CATH domains 2qk7B00 B:3-299 Leukocidin-like                                                                                                                                                                                                                                                                           CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeee....eeeeeeeeeeee....eeeeeeeeeeee....eeeeeeeeeeeee............eeeeeeeeeeeeeee......eeeeeee........eeeeeeeee...eeeeee..-------..eeeeeeee...eeeee.......eeeeeeee..eee..eeee..................---.hhhhh..hhhhhhhhhhhee...eeeeeeee.....eeeeeeeeeeeeeeeeeee....eeeeeeeeeeeeeeeeeeeee....eeeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2qk7 B   3 KITPVSVKKVDDKVTLYKTTATADSDKFKISQILTFNFIKDKSYDKDTLVLKAAGNINSGYEKPNPNDYDFSKLYWGAKYNVSISSQSNDSVNVVDYAPKNQNEEFQVQNTLGYTFGGDISISNGL-------TAFSETINYKQESYRTTLSRCTNYKNVGWGVEAHKIMNNGWGPYGRDSFHPTYGNELFLAGR---AYAGQNFIAQHQMPLLSRSNFNPEFLSVLSHRQDGAKKSKITVTYQREMDLYQIRWNGFYWAGANYKNFKTRTFKSTYEIDWENHKVKLLDTKETENNK 299
                                    12        22        32        42        52        62        72        82        92       102       112       122     |   -   |   142       152       162       172       182       192    |  202       212       222       232       242       252       262       272       282       292       
                                                                                                                                                       128     136                                                          197 201
   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, 2)

Asymmetric/Biological Unit
(-)
Class: Membrane and cell surface proteins and peptides (2046)

(-) CATH Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2QK7)

(-) Gene Ontology  (5, 13)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (HLGA_STAAU | P0A074)
biological process
    GO:0019835    cytolysis    The rupture of cell membranes and the loss of cytoplasm.
    GO:0051715    cytolysis in other organism    The killing by an organism of a cell in another organism by means of the rupture of cell membranes and the loss of cytoplasm.
    GO:0044179    hemolysis in other organism    The cytolytic destruction of red blood cells, with the release of intracellular hemoglobin, in one organism by another.
    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.
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.

Chain B   (Q57227_STAAU | Q57227)
biological process
    GO:0051715    cytolysis in other organism    The killing by an organism of a cell in another organism by means of the rupture of cell membranes and the loss of cytoplasm.
    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.
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.

Chain B   (HLGB_STAAU | P0A077)
biological process
    GO:0019835    cytolysis    The rupture of cell membranes and the loss of cytoplasm.
    GO:0051715    cytolysis in other organism    The killing by an organism of a cell in another organism by means of the rupture of cell membranes and the loss of cytoplasm.
    GO:0044179    hemolysis in other organism    The cytolytic destruction of red blood cells, with the release of intracellular hemoglobin, in one organism by another.
    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.
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.

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  Cis Peptide Bonds
    Ala B:100 - Pro B:101   [ RasMol ]  
    Gly B:177 - Pro B:178   [ RasMol ]  
    Leu A:95 - Pro A:96   [ RasMol ]  
 

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 Related Entries

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

UniProtKB/Swiss-Prot
        HLGB_STAAU | P0A077: 1lkf 2lkf 3lkf

(-) Related Entries Specified in the PDB File

1lkf LEUKOCIDIN F (HLGB) FROM STAPHYLOCOCCUS AUREUS 1.9A
1pvl STRUCTURE OF THE PANTON-VALENTINE LEUCOCIDIN F COMPONENT FROM STAPHYLOCOCCUS AUREUS
1t5r STRUCTURE OF THE PANTON-VALENTINE LEUCOCIDIN S COMPONENT FROM STAPHYLOCOCCUS AUREUS
2lkf LEUKOCIDIN F (HLGB) FROM STAPHYLOCOCCUS AUREUS 2.5A
3lkf LEUKOCIDIN F (HLGB) FROM STAPHYLOCOCCUS AUREUS WITH 2 PHOSPHOCHOLINE BOUND