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(-) Description

Title :  X-RAY STRUCTURE OF THE SUBSTRATE-BOUND CYTOCHROME P450 PIMD - A POLYENE MACROLIDE ANTIBIOTIC PIMARICIN EPOXIDASE
 
Authors :  P. M. Kells, H. Ouellet, J. Santos-Aberturas, J. F. Aparicio, L. M. Pod
Date :  12 Apr 10  (Deposition) - 04 Aug 10  (Release) - 15 Sep 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.95
Chains :  Asym./Biol. Unit :  A
Keywords :  Epoxidation, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  P. M. Kells, H. Ouellet, J. Santos-Aberturas, J. F. Aparicio, L. M. Podust
Structure Of Cytochrome P450 Pimd Suggests Epoxidation Of The Polyene Macrolide Pimaricin Occurs Via A Hydroperoxoferric Intermediate.
Chem. Biol. V. 17 841 2010
PubMed-ID: 20797613  |  Reference-DOI: 10.1016/J.CHEMBIOL.2010.05.026

(-) Compounds

Molecule 1 - PIMD PROTEIN
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PQE-30
    Expression System Strain: HMS174(DE3)
    Expression System Taxid: 562
    Fragment: RESIDUES 5-397
    Organism Scientific: STREPTOMYCES NATALENSIS
    Organism Taxid: 68242
    Other Details: RESIDUES UPSTREAM OF SER 5 INCLUDING 6XHIS TAG ARE ENGINEERED

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (2, 2)
No.NameCountTypeFull Name
1HEM1Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
2XBK1Ligand/Ion4,5-DE-EPOXYPIMARICIN

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:65 , HIS A:98 , ARG A:102 , PHE A:109 , LEU A:154 , LEU A:231 , ALA A:234 , GLY A:235 , SER A:238 , VAL A:239 , ILE A:242 , PRO A:286 , ARG A:288 , LEU A:311 , THR A:338 , PHE A:339 , GLY A:340 , ILE A:343 , TRP A:344 , CYS A:346 , ILE A:347 , GLY A:348 , ALA A:352 , XBK A:1399 , HOH A:2168 , HOH A:2268 , HOH A:2269BINDING SITE FOR RESIDUE HEM A1398
2AC2SOFTWAREARG A:65 , LEU A:178 , PHE A:233 , SER A:238 , SER A:241 , ARG A:279 , SER A:283 , VAL A:284 , SER A:387 , GLY A:388 , GLY A:389 , HEM A:1398 , HOH A:2168 , HOH A:2261 , HOH A:2270 , HOH A:2271 , HOH A:2272BINDING SITE FOR RESIDUE XBK A1399

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Pro A:137 -Pro A:138
2Thr A:332 -Pro A:333

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2XBK)

(-) 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:391
 aligned with Q9EW92_9ACTN | Q9EW92 from UniProtKB/TrEMBL  Length:397

    Alignment length:391
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396 
         Q9EW92_9ACTN     7 DLPCLNLEPPKMLKLSPLLRALQDRGPIHRVRTPAGDEAWLVTRHAELKQLLHDERIGRTHPDPPSAAQYVRSPFLDLLISDADAESGRRQHAETRRLLTPLFSARRVLEMQPKVEEAADTLLDAFIAQGPPGDLHGELTVPFALTVLCEVIGVPPQRRAELTTLLAGIAKLDDREGAVRAQDDLFGYVAGLVEHKRAEPGPDIISRLNDGELTEDRVAHLAMGLLFAGLDSVASIMDNGVVLLAAHPDQRAAALADPDVMARAVEEVLRTARAGGSVLPPRYASEDMEFGGVTIRAGDLVLFDLGLPNFDERAFTGPEEFDAARTPNPHLTFGHGIWHCIGAPLARLELRTMFTKLFTRLPELRPELPVEQLRLKEGQLSGGFAELRVVW 397
               SCOP domains d2xbka_ A: automated matches                                                                                                                                                                                                                                                                                                                                                                            SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...............hhhhhhhhhhh.eeeee.....eeeee.hhhhhhhhh....ee....hhhhh.....hhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eehhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.........eee...eee..eee....eee..hhhhhh.......................ee..ee..hhhhhhhhhhhhhhhhhhhh...ee..hhhhh..............eee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2xbk A   7 DLPCLNLEPPKMLKLSPLLRALQDRGPIHRVRTPAGDEAWLVTRHAELKQLLHDERIGRTHPDPPSAAQYVRSPFLDLLISDADAESGRRQHAETRRLLTPLFSARRVLEMQPKVEEAADTLLDAFIAQGPPGDLHGELTVPFALTVLCEVIGVPPQRRAELTTLLAGIAKLDDREGAVRAQDDLFGYVAGLVEHKRAEPGPDIISRLNDGELTEDRVAHLAMGLLFAGLDSVASIMDNGVVLLAAHPDQRAAALADPDVMARAVEEVLRTARAGGSVLPPRYASEDMEFGGVTIRAGDLVLFDLGLPNFDERAFTGPEEFDAARTPNPHLTFGHGIWHCIGAPLARLELRTMFTKLFTRLPELRPELPVEQLRLKEGQLSGGFAELRVVW 397
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396
   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  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (Q9EW92_9ACTN | Q9EW92)
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.

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 Related Entries

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UniProtKB/TrEMBL
        Q9EW92_9ACTN | Q9EW92: 2x9p

(-) Related Entries Specified in the PDB File

2x9p X-RAY STRUCTURE OF THE SUBSTRATE-FREE CYTOCHROME P450 PIMD - A POLYENE MACROLIDE ANTIBIOTIC PIMARICIN EPOXIDASE