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(-) Description

Title :  CRYSTAL STRUCTURE OF OXYB, A CYTOCHROME P450 IMPLICATED IN AN OXIDATIVE PHENOL COUPLING REACTION DURING VANCOMYCIN BIOSYNTHESIS
 
Authors :  O. Pylypenko, K. Zerbe, F. Vitali, W. Zhang, J. W. Vrijbloed, J. A. Robinson, I. Schlichting
Date :  11 Apr 02  (Deposition) - 11 Dec 02  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym./Biol. Unit :  A
Keywords :  Oxidative Phenol Coupling Reaction P450 Vancomycin, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. Zerbe, O. Pylypenko, F. Vitali, W. Zhang, S. Rouset, M. Heck, J. W. Vrijbloed, D. Bischoff, B. Bister, R. D. Sussmuth, S. Pelzer, W. Wohlleben, J. A. Robinson, I. Schlichting
Crystal Structure Of Oxyb, A Cytochrome P450 Implicated In An Oxidative Phenol Coupling Reaction During Vancomycin Biosynthesis.
J. Biol. Chem. V. 277 47476 2002
PubMed-ID: 12207020  |  Reference-DOI: 10.1074/JBC.M206342200
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - P450 MONOOXYGENASE
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET14B
    Expression System Taxid: 562
    Expression System Vector: PLASMID
    Organism Scientific: AMYCOLATOPSIS ORIENTALIS
    Organism Taxid: 31958
    Synonym: OXYB

 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
1HEM1Ligand/IonPROTOPORPHYRIN IX CONTAINING FE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREMET A:55 , LEU A:88 , MET A:89 , HIS A:96 , ARG A:100 , PHE A:107 , LEU A:152 , LEU A:155 , ALA A:236 , GLY A:237 , ASN A:240 , PRO A:283 , PRO A:286 , THR A:287 , ARG A:289 , ALA A:339 , PHE A:340 , GLY A:341 , HIS A:345 , CYS A:347 , HOH A:448 , HOH A:698BINDING SITE FOR RESIDUE HEM A 430

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Pro A:93 -Pro A:94
2Ser A:135 -Pro A:136

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CYTOCHROME_P450PS00086 Cytochrome P450 cysteine heme-iron ligand signature.C5B3_AMYOR340-349  1A:340-349

(-) Exons   (0, 0)

(no "Exon" information available for 1LFK)

(-) 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:375
 aligned with C5B3_AMYOR | Q8RN04 from UniProtKB/Swiss-Prot  Length:398

    Alignment length:394
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394    
           C5B3_AMYOR     5 DPRPLHIRRQGLDPADELLAAGALTRVTIGSGADAETHWMATAHAVVRQVMGDHQQFSTRRRWDPRDEIGGKGIFRPRELVGNLMDYDPPEHTRLRRKLTPGFTLRKMQRMAPYIEQIVNDRLDEMERAGSPADLIAFVADKVPGAVLCELVGVPRDDRDMFMKLCHGHLDASLSQKRRAALGDKFSRYLLAMIARERKEPGEGMIGAVVAEYGDDATDEELRGFCVQVMLAGDDNISGMIGLGVLAMLRHPEQIDAFRGDEQSAQRAVDELIRYLTVPYSPTPRIAREDLTLAGQEIKKGDSVICSLPAANRDPALAPDVDRLDVTREPIPHVAFGHGVHHCLGAALARLELRTVFTELWRRFPALRLADPAQDTEFRLTTPAYGLTELMVAW 398
               SCOP domains d1lfka_ A: p450 monoxygenase       OxyB                                                                                                                                                                                                                                                                                                                                                                    SCOP domains
               CATH domains 1lfkA00 A:5-398 Cytochrome p      450                                                                                                                                                                                                                                                                                                                                                                      CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------p450-1lfkA01 A:158-392                                                                                                                                                                                                                     ------ Pfam domains
         Sec.struct. author ...hhhh.ee..eehhhhhh...eeee.------...eeee.hhhhhhhhhhh...eee......-------------....hhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eehhhhh..hhhhhhhhhhhh.hhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh.......eee...eee..eee....eeeehhhhhh................................hhhhhhhhhhhhhhhhhhhh...ee.......eee......eeee.eee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CYTOCHROME------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1lfk A   5 DPRPLHIRRQGLDPADELLAAGALTRVT------AETHWMATAHAVVRQVMGDHQQFSTRRRWDP-------------ELVGNLMDYDPPEHTRLRRKLTPGFTLRKMQRMAPYIEQIVNDRLDEMERAGSPADLIAFVADKVPGAVLCELVGVPRDDRDMFMKLCHGHLDASLSQKRRAALGDKFSRYLLAMIARERKEPGEGMIGAVVAEYGDDATDEELRGFCVQVMLAGDDNISGMIGLGVLAMLRHPEQIDAFRGDEQSAQRAVDELIRYLTVPYSPTPRIAREDLTLAGQEIKKGDSVICSLPAANRDPALAPDVDRLDVTREPIPHVAFGHGVHHCLGAALARLELRTVFTELWRRFPALRLADPAQDTEFRLTTPAYGLTELMVAW 398
                                    14        24       | -    |   44        54        64    |    -        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394    
                                                      32     39                            69            83
   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, 1)

Asymmetric/Biological Unit
(-)
Class: All alpha proteins (14657)

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: no clan defined [family: p450] (161)

(-) Gene Ontology  (8, 8)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (C5B3_AMYOR | Q8RN04)
molecular function
    GO:0020037    heme binding    Interacting selectively and non-covalently with heme, any compound of iron complexed in a porphyrin (tetrapyrrole) ring.
    GO:0005506    iron ion binding    Interacting selectively and non-covalently with iron (Fe) ions.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0004497    monooxygenase activity    Catalysis of the incorporation of one atom from molecular oxygen into a compound and the reduction of the other atom of oxygen to water.
    GO:0016491    oxidoreductase activity    Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
    GO:0016705    oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen    Catalysis of an oxidation-reduction (redox) reaction in which hydrogen or electrons are transferred from each of two donors, and molecular oxygen is reduced or incorporated into a donor.
biological process
    GO:0055114    oxidation-reduction process    A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.
    GO:0033072    vancomycin biosynthetic process    The chemical reactions and pathways leading to the formation of vancomycin, (3S,6R,7R,11R,23S,26S,30aS,36R,38aR)-44-[2-O-(3-amino-2,3,6-trideoxy-3-C-methyl-alpha-L-lyxo-hexopyranosyl)-beta-D-glucopyranosyloxy]-3-(carbamoylmethyl)-10,19-dichloro-2,3,4,5,6,7,23,25,26,36,37,38,38a-tetradecahydro-7,22,28,30,32-pentahydroxy-6-(N-methyl-D-leucyl)-2,5,24,38,39-pentaoxo-1H,22H-23,36-(epiminomethano)-8,11:18,21-dietheno-13,16:31,35-di(metheno)[1,6,9]oxadiazacyclohexadecino[4,5-m][10,2,16]benzoxadiazacyclotetracosine-26-carboxylic acid, a complex glycopeptide from Streptomyces orientalis that inhibits a specific step in the synthesis of the peptidoglycan layer in Gram-positive bacteria.

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        C5B3_AMYOR | Q8RN04: 1lg9 1lgf

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