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(-) Description

Title :  CRYSTAL STRUCTURE OF OXYC A CYTOCHROME P450 IMPLICATED IN AN OXIDATIVE C-C COUPLING REACTION DURING VANCOMYCIN BIOSYNTHESIS.
 
Authors :  O. Pylypenko, F. Vitali, K. Zerbe, J. A. Robinson, I. Schlichting
Date :  11 May 03  (Deposition) - 09 Dec 03  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Cytochrome P450 Vancomycin Biosynthesis, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  O. Pylypenko, F. Vitali, K. Zerbe, J. A. Robinson, I. Schlichting
Crystal Structure Of Oxyc, A Cytochrome P450 Implicated In An Oxidative C-C Coupling Reaction During Vancomycin Biosynthesis
J. Biol. Chem. V. 278 46727 2003
PubMed-ID: 12888556  |  Reference-DOI: 10.1074/JBC.M306486200
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - P450 MONOOXYGENASE
    ChainsA, B
    EC Number1.14.-.-
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET14B
    Expression System StrainBL21(DE3)PLYSS
    Expression System Taxid562
    Expression System Vector TypePLASMID
    Organism ScientificAMYCOLATOPSIS ORIENTALIS
    Organism Taxid31958
    SynonymP450 OXYC

 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  (3, 6)

Asymmetric Unit (3, 6)
No.NameCountTypeFull Name
1HEM2Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
2PEG2Ligand/IonDI(HYDROXYETHYL)ETHER
3PG42Ligand/IonTETRAETHYLENE GLYCOL
Biological Unit 1 (3, 3)
No.NameCountTypeFull Name
1HEM1Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
2PEG1Ligand/IonDI(HYDROXYETHYL)ETHER
3PG41Ligand/IonTETRAETHYLENE GLYCOL
Biological Unit 2 (3, 3)
No.NameCountTypeFull Name
1HEM1Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
2PEG1Ligand/IonDI(HYDROXYETHYL)ETHER
3PG41Ligand/IonTETRAETHYLENE GLYCOL

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREILE A:97 , SER A:98 , HIS A:105 , ARG A:109 , PHE A:116 , GLY A:245 , GLY A:246 , THR A:249 , MET A:253 , VAL A:292 , PRO A:295 , ARG A:298 , ILE A:321 , GLY A:348 , PHE A:349 , ILE A:353 , HIS A:354 , CYS A:356 , ALA A:362 , PG4 A:4502 , HOH A:4514 , HOH A:4518 , HOH A:4606 , HOH A:4693BINDING SITE FOR RESIDUE HEM A 1430
2AC2SOFTWAREGLN A:96 , SER A:98 , THR A:99 , ALA A:241 , GLY A:245 , ASN A:296 , HEM A:1430 , HOH A:4518 , HOH A:4611 , HOH A:4635 , HOH A:4654BINDING SITE FOR RESIDUE PG4 A 4502
3AC3SOFTWAREILE B:97 , SER B:98 , HIS B:105 , ARG B:109 , PHE B:116 , LEU B:161 , GLY B:245 , GLY B:246 , THR B:249 , VAL B:250 , VAL B:292 , PRO B:295 , ARG B:298 , ILE B:321 , GLY B:348 , PHE B:349 , GLY B:350 , ILE B:353 , HIS B:354 , CYS B:356 , ALA B:362 , PG4 B:5502 , HOH B:5505 , HOH B:5608 , HOH B:5669 , HOH B:5680BINDING SITE FOR RESIDUE HEM B 2430
4AC4SOFTWAREPHE B:93 , GLN B:96 , SER B:98 , ALA B:241 , GLY B:245 , ASN B:296 , HEM B:2430 , HOH B:5622 , HOH B:5680BINDING SITE FOR RESIDUE PG4 B 5502
5AC5SOFTWAREPHE A:272 , TRP A:374BINDING SITE FOR RESIDUE PEG A 4503

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Pro A:102 -Pro A:103
2Pro B:102 -Pro B:103

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 2)

Asymmetric Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CYTOCHROME_P450PS00086 Cytochrome P450 cysteine heme-iron ligand signature.C5C4_AMYOR349-358
 
  2A:349-358
B:349-358
Biological Unit 1 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CYTOCHROME_P450PS00086 Cytochrome P450 cysteine heme-iron ligand signature.C5C4_AMYOR349-358
 
  1A:349-358
-
Biological Unit 2 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CYTOCHROME_P450PS00086 Cytochrome P450 cysteine heme-iron ligand signature.C5C4_AMYOR349-358
 
  1-
B:349-358

(-) Exons   (0, 0)

(no "Exon" information available for 1UED)

(-) 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:391
 aligned with C5C4_AMYOR | Q8RN03 from UniProtKB/Swiss-Prot  Length:406

    Alignment length:403
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403   
           C5C4_AMYOR     4 DIDQVAPLLREPANFQLRTNCDPHEDNFGLRAHGPLVRIVGESSTQLGRDFVWQAHGYEVVRRILGDHEHFTTRPQFTQSKSGAHVEAQFVGQISTYDPPEHTRLRKMLTPEFTVRRIRRMEPAIQSLIDDRLDLLEAEGPSADLQGLFADPVGAHALCELLGIPRDDQREFVRRIRRNADLSRGLKARAADSAAFNRYLDNLLARQRADPDDGLLGMIVRDHGDNVTDEELKGLCTALILGGVETVAGMIGFGVLALLDNPGQIELLFESPEKAERVVNELVRYLSPVQAPNPRLAIKDVVIDGQLIKAGDYVLCSILMANRDEALTPDPDVLDANRAAVSDVGFGHGIHYCVGAALARSMLRMAYQTLWRRFPGLRLAVPIEEVKYRSAFVDCPDQVPVTW 406
               SCOP domains d1ueda_ A: p450 monoxygenase OxyC                                                                                                                                                                                                                                                                                                                                                                                   SCOP domains
               CATH domains 1uedA00 A:4-406 Cytochrome p450                                                                                                                                                                                                                                                                                                                                                                                     CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eee.......ee..eehhhhhhhhh...eeeeehhhhhhh....eeee.hhhhhhhhhhh...ee.....---------hhhhh.hhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eehhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh.---.hhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......eee...eee..eee....eeeehhhhhh................................hhhhhhhhhhhhhhhhhhhh...ee..hhhhh.............eee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CYTOCHROME------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ued A   4 DIDQVAPLLREPANFQLRTNCDPHEDNFGLRAHGPLVRIVGESSTQLGRDFVWQAHGYEVVRRILGDHEHFTTRPQF---------EAQFVGQISTYDPPEHTRLRKMLTPEFTVRRIRRMEPAIQSLIDDRLDLLEAEGPSADLQGLFADPVGAHALCELLGIPRDDQREFVRRIRRNA---RGLKARAADSAAFNRYLDNLLARQRADPDDGLLGMIVRDHGDNVTDEELKGLCTALILGGVETVAGMIGFGVLALLDNPGQIELLFESPEKAERVVNELVRYLSPVQAPNPRLAIKDVVIDGQLIKAGDYVLCSILMANRDEALTPDPDVLDANRAAVSDVGFGHGIHYCVGAALARSMLRMAYQTLWRRFPGLRLAVPIEEVKYRSAFVDCPDQVPVTW 406
                                    13        23        33        43        53        63        73      |  -      | 93       103       113       123       133       143       153       163       173       183   |   193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403   
                                                                                                       80        90                                                                                          183 187                                                                                                                                                                                                                           

Chain B from PDB  Type:PROTEIN  Length:391
 aligned with C5C4_AMYOR | Q8RN03 from UniProtKB/Swiss-Prot  Length:406

    Alignment length:405
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401     
           C5C4_AMYOR     2 GHDIDQVAPLLREPANFQLRTNCDPHEDNFGLRAHGPLVRIVGESSTQLGRDFVWQAHGYEVVRRILGDHEHFTTRPQFTQSKSGAHVEAQFVGQISTYDPPEHTRLRKMLTPEFTVRRIRRMEPAIQSLIDDRLDLLEAEGPSADLQGLFADPVGAHALCELLGIPRDDQREFVRRIRRNADLSRGLKARAADSAAFNRYLDNLLARQRADPDDGLLGMIVRDHGDNVTDEELKGLCTALILGGVETVAGMIGFGVLALLDNPGQIELLFESPEKAERVVNELVRYLSPVQAPNPRLAIKDVVIDGQLIKAGDYVLCSILMANRDEALTPDPDVLDANRAAVSDVGFGHGIHYCVGAALARSMLRMAYQTLWRRFPGLRLAVPIEEVKYRSAFVDCPDQVPVTW 406
               SCOP domains d1uedb_ B: p450 monoxygenase OxyC                                                                                                                                                                                                                                                                                                                                                                                     SCOP domains
               CATH domains 1uedB00 B:2-406 Cytochrome p450                                                                                                                                                                                                                                                                                                                                                                                       CATH domains
           Pfam domains (1) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------p450-1uedB01 B:276-381                                                                                    ------------------------- Pfam domains (1)
           Pfam domains (2) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------p450-1uedB02 B:276-381                                                                                    ------------------------- Pfam domains (2)
         Sec.struct. author .........eee.......ee..eehhhhhhhhh...eeeeehhhhhhh....eeee.hhhhhhhhhhh...ee...------------.....hhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eehhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh--..hhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh.......eee...eee..eee....eeeehhhhhh................................hhhhhhhhhhhhhhhhhhhh...ee..hhhhh.............eee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CYTOCHROME------------------------------------------------ PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ued B   2 GHDIDQVAPLLREPANFQLRTNCDPHEDNFGLRAHGPLVRIVGESSTQLGRDFVWQAHGYEVVRRILGDHEHFTTRP------------AQFVGQISTYDPPEHTRLRKMLTPEFTVRRIRRMEPAIQSLIDDRLDLLEAEGPSADLQGLFADPVGAHALCELLGIPRDDQREFVRRIRRNA--SRGLKARAADSAAFNRYLDNLLARQRADPDDGLLGMIVRDHGDNVTDEELKGLCTALILGGVETVAGMIGFGVLALLDNPGQIELLFESPEKAERVVNELVRYLSPVQAPNPRLAIKDVVIDGQLIKAGDYVLCSILMANRDEALTPDPDVLDANRAAVSDVGFGHGIHYCVGAALARSMLRMAYQTLWRRFPGLRLAVPIEEVKYRSAFVDCPDQVPVTW 406
                                    11        21        31        41        51        61        71      |  -        91       101       111       121       131       141       151       161       171       181 |  |  191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401     
                                                                                                       78           91                                                                                         183  |                                                                                                                                                                                                                            
                                                                                                                                                                                                                  186                                                                                                                                                                                                                            

   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 Unit

(-) CATH Domains  (1, 2)

Asymmetric Unit

(-) Pfam Domains  (1, 2)

Asymmetric Unit

(-) Gene Ontology  (8, 8)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (C5C4_AMYOR | Q8RN03)
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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1lfk 1lg9 1lgf