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(-) Description

Title :  STRUCTURAL BASIS FOR THE CYCLIZATION OF THE LIPOPEPTIDE ANTIBIOTIC SURFACTIN BY THE THIOESTERASE DOMAIN SRFTE
 
Authors :  S. D. Bruner, T. Weber, R. M. Kohli, D. Schwarzer, M. A. Marahiel, C. T. Walsh, M. T. Stubbs
Date :  18 Jul 01  (Deposition) - 27 Mar 02  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.71
Chains :  Asym./Biol. Unit :  C,O
Keywords :  Thioesterase, Non-Ribosomal Peptide Synthesis, Alpha-Beta Hydrolase, Cyclic Peptide (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. D. Bruner, T. Weber, R. M. Kohli, D. Schwarzer, M. A. Marahiel, C. T. Walsh, M. T. Stubbs
Structural Basis For The Cyclization Of The Lipopeptide Antibiotic Surfactin By The Thioesterase Domain Srfte.
Structure V. 10 301 2002
PubMed-ID: 12005429  |  Reference-DOI: 10.1016/S0969-2126(02)00716-5
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - SURFACTIN SYNTHETASE
    Chains: C, O
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PQE60
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: THIOESTERASE DOMAIN
    Gene: SRFA-C
    Organism Scientific: BACILLUS SUBTILIS
    Organism Taxid: 1423
    Synonym: SRFTE

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : CO

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
1SO42Ligand/IonSULFATE ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN O:36 , ARG O:40 , GLY O:213BINDING SITE FOR RESIDUE SO4 O 501
2AC2SOFTWAREILE C:12 , MET C:13 , ASN C:14 , GLN C:15 , HOH O:543BINDING SITE FOR RESIDUE SO4 C 502

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1JMK)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1JMK)

(-) Exons   (0, 0)

(no "Exon" information available for 1JMK)

(-) 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 C from PDB  Type:PROTEIN  Length:222
 aligned with SRFAC_BACSU | Q08787 from UniProtKB/Swiss-Prot  Length:1275

    Alignment length:230
                                  1051      1061      1071      1081      1091      1101      1111      1121      1131      1141      1151      1161      1171      1181      1191      1201      1211      1221      1231      1241      1251      1261      1271
         SRFAC_BACSU   1042 GGSDGLQDVTIMNQDQEQIIFAFPPVLGYGLMYQNLSSRLPSYKLCAFDFIEEEDRLDRYADLIQKLQPEGPLTLFGYSAGCSLAFEAAKKLEEQGRIVQRIIMVDSYKKQGVSDLDGRTVESDVEALMNVNRDNEALNSEAVKHGLKQKTHAFYSYYVNLISTGQVKADIDLLTSGADFDMPEWLASWEEATTGVYRVKRGFGTHAEMLQGETLDRNAEILLEFLNTQT 1271
               SCOP domains d1jmkc_ C: Surfactin synthetase, SrfA                                                                                                                                                                                                  SCOP domains
               CATH domains 1jmkC01 C:2-111,C:167-228  [code=3.40.50.1820, no name defined]                                               1jmk        C02 C:112-166 Helix hairpin bin            1jmkC01 C:2-111,C:167-228                                     --- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eeee.....eeeeee.....hhhhhhhhhhhh..eeeeee......hhhhhhhhhhhhhh....eeeeeehhhhhhhhhhhhhhhhh...eeeeeee...ee....--------.hhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhh........eeeeee..........ee.hhhh....eeeee...hhhhh.hhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1jmk C    2 GGSDGLQDVTIMNQDQEQIIFAFPPVLGYGLMYQNLSSRLPSYKLCAFDFIEEEDRLDRYADLIQKLQPEGPLTLFGYSAGCSLAFEAAKKLEGQGRIVQRIIMVDSYKKQGVS--------SDVEALMNVNRDNEALNSEAVKHGLKQKTHAFYSYYVNLISTGQVKADIDLLTSGADFDIPEWLASWEEATTGAYRMKRGFGTHAEMLQGETLDRNAGILLEFLNTQT  231
                                    11        21        31        41        51        61        71        81        91       101       111   |     -  |    131       141       151       161       171       181       191       201       211       221       231
                                                                                                                                           115      124                                                                                                           


Chain O from PDB  Type:PROTEIN  Length:230
 aligned with SRFAC_BACSU | Q08787 from UniProtKB/Swiss-Prot  Length:1275

    Alignment length:230
                                  1051      1061      1071      1081      1091      1101      1111      1121      1131      1141      1151      1161      1171      1181      1191      1201      1211      1221      1231      1241      1251      1261      1271
         SRFAC_BACSU   1042 GGSDGLQDVTIMNQDQEQIIFAFPPVLGYGLMYQNLSSRLPSYKLCAFDFIEEEDRLDRYADLIQKLQPEGPLTLFGYSAGCSLAFEAAKKLEEQGRIVQRIIMVDSYKKQGVSDLDGRTVESDVEALMNVNRDNEALNSEAVKHGLKQKTHAFYSYYVNLISTGQVKADIDLLTSGADFDMPEWLASWEEATTGVYRVKRGFGTHAEMLQGETLDRNAEILLEFLNTQT 1271
               SCOP domains d1jmko_ O: Surfactin synthetase, SrfA                                                                                                                                                                                                  SCOP domains
               CATH domains 1jmkO01 O:2-111,O:167-228  [code=3.40.50.1820, no name defined]                                               1jmkO02 O:112-166 Helix hairpin bin                    1jmkO01 O:2-111,O:167-228                                     --- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eeee.....eeeeee.....hhhhhhhhhhhh..eeeeee......hhhhhhhhhhhhhh....eeeeee.hhhhhhhhhhhhhhhh...eeeeeee...ee.........hhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhh........eeeeee..........ee.hhhh....eeeee...hhhhh.hhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1jmk O    2 GGSDGLQDVTIMNQDQEQIIFAFPPVLGYGLMYQNLSSRLPSYKLCAFDFIEEEDRLDRYADLIQKLQPEGPLTLFGYSAGCSLAFEAAKKLEGQGRIVQRIIMVDSYKKQGVSDLDGRTVESDVEALMNVNRDNEALNSEAVKHGLKQKTHAFYSYYVNLISTGQVKADIDLLTSGADFDIPEWLASWEEATTGAYRMKRGFGTHAEMLQGETLDRNAGILLEFLNTQT  231
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231
   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: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (2, 4)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1JMK)

(-) Gene Ontology  (8, 8)

Asymmetric/Biological Unit(hide GO term definitions)
Chain C,O   (SRFAC_BACSU | Q08787)
molecular function
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    GO:0016788    hydrolase activity, acting on ester bonds    Catalysis of the hydrolysis of any ester bond.
    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:0031177    phosphopantetheine binding    Interacting selectively and non-covalently with phosphopantetheine, the vitamin pantetheine 4'-(dihydrogen phosphate).
biological process
    GO:0017000    antibiotic biosynthetic process    The chemical reactions and pathways resulting in the formation of an antibiotic, a substance produced by or derived from certain fungi, bacteria, and other organisms, that can destroy or inhibit the growth of other microorganisms.
    GO:0009058    biosynthetic process    The chemical reactions and pathways resulting in the formation of substances; typically the energy-requiring part of metabolism in which simpler substances are transformed into more complex ones.
    GO:0008152    metabolic process    The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
    GO:0030435    sporulation resulting in formation of a cellular spore    The process in which a relatively unspecialized cell acquires the specialized features of a cellular spore, a cell form that can be used for dissemination, for survival of adverse conditions because of its heat and dessication resistance, and/or for reproduction.

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 Related Entries

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        SRFAC_BACSU | Q08787: 2vsq

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