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(-) Description

Title :  EPOTHILONE B-BOUND CYTOCHROME P450EPOK
 
Authors :  S. Nagano, H. Li, H. Shimizu, C. Nishida, H. Ogura, P. R. Ortiz De Montellano, T. L. Poulos
Date :  06 Aug 03  (Deposition) - 28 Oct 03  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.93
Chains :  Asym./Biol. Unit :  A
Keywords :  Cytochrome P450, Epothilone, Oxydoreductase, Heme-Enzyme, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Nagano, H. Li, H. Shimizu, C. Nishida, H. Ogura, P. R. Ortiz De Montellano, T. L. Poulos
Crystal Structures Of Epothilone D-Bound, Epothilone B-Bound, And Substrate-Free Forms Of Cytochrome P450Epok
J. Biol. Chem. V. 278 44886 2003
PubMed-ID: 12933799  |  Reference-DOI: 10.1074/JBC.M308115200
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - P450 EPOXIDASE
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: EPOK
    Organism Scientific: SORANGIUM CELLULOSUM
    Organism Taxid: 56
    Synonym: EPOK, CYTOCHROME P450EPOK

 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
1EPB1Ligand/Ion7,11-DIHYDROXY-8,8,10,12,16-PENTAMETHYL-3-[1-METHYL-2-(2-METHYL-THIAZOL-4-YL)VINYL]-4,17-DIOXABICYCLO[14.1.0]HEPTADECANE-5,9-DIONE
2HEM1Ligand/IonPROTOPORPHYRIN IX CONTAINING FE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELEU A:95 , PHE A:96 , HIS A:103 , ARG A:107 , PHE A:114 , ILE A:251 , ALA A:254 , GLY A:255 , THR A:258 , THR A:259 , THR A:305 , ARG A:307 , ALA A:357 , TYR A:358 , HIS A:363 , CYS A:365 , PRO A:366 , GLY A:367 , ALA A:371 , EPB A:450 , HOH A:451 , HOH A:453BINDING SITE FOR RESIDUE HEM A 440
2AC2SOFTWAREARG A:71 , PHE A:96 , ALA A:180 , LEU A:183 , GLY A:184 , THR A:258 , LEU A:301 , GLY A:304 , THR A:305 , ALA A:402 , PHE A:403 , HEM A:440 , HOH A:451 , HOH A:460 , HOH A:466 , HOH A:680BINDING SITE FOR RESIDUE EPB A 450

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1Q5D)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1Q5D)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1Q5D)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1Q5D)

(-) Exons   (0, 0)

(no "Exon" information available for 1Q5D)

(-) 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:401
 aligned with C167_SORCE | Q9KIZ4 from UniProtKB/Swiss-Prot  Length:419

    Alignment length:401
                                    25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415 
           C167_SORCE    16 DFKPFAPGYAEDPFPAIERLREATPIFYWDEGRSWVLTRYHDVSAVFRDERFAVSREEWESSAEYSSAIPELSDMKKYGLFGLPPEDHARVRKLVNPSFTSRAIDLLRAEIQRTVDQLLDARSGQEEFDVVRDYAEGIPMRAISALLKVPAECDEKFRRFGSATARALGVGLVPRVDEETKTLVASVTEGLALLHGVLDERRRNPLENDVLTMLLQAEADGSRLSTKELVALVGAIIAAGTDTTIYLIAFAVLNLLRSPEALELVKAEPGLMRNALDEVLRFDNILRIGTVRFARQDLEYCGASIKKGEMVFLLIPSALRDGTVFSRPDVFDVRRDTSASLAYGRGPHVCPGVSLARLEAEIAVGTIFRRFPEMKLKETPVFGYHPAFRNIESLNVILKPS 416
               SCOP domains d1q5da_ A: Cytochrome P450epok                                                                                                                                                                                                                                                                                                                                                                                    SCOP domains
               CATH domains 1q5dA00 A:16-416 Cytochrome p450                                                                                                                                                                                                                                                                                                                                                                                  CATH domains
               Pfam domains -------------p450-1q5dA01 A:29-397                                                                                                                                                                                                                                                                                                                                                            ------------------- Pfam domains
         Sec.struct. author ............hhhhhhhhhhhh.eeee....eeee.hhhhhhhhhh...ee.hhhhh.hhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh....ee....hhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhh.....eeeeee...eee..eee....eeeeehhhhh.........................hhhhh..hhhhhhhhhhhhhhhhhhhh...ee....ee........eee.eee.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1q5d A  16 DFKPFAPGYAEDPFPAIERLREATPIFYWDEGRSWVLTRYHDVSAVFRDERFAVSREEWESSAEYSSAIPELSDMKKYGLFGLPPEDHARVRKLVNPSFTSRAIDLLRAEIQRTVDQLLDARSGQEEFDVVRDYAEGIPMRAISALLKVPAECDEKFRRFGSATARALGVGLVPRVDEETKTLVASVTEGLALLHGVLDERRRNPLENDVLTMLLQAEADGSRLSTKELVALVGAIIAAGTDTTIYLIAFAVLNLLRSPEALELVKAEPGLMRNALDEVLRFDNILRIGTVRFARQDLEYCGASIKKGEMVFLLIPSALRDGTVFSRPDVFDVRRDTSASLAYGRGPHVCPGVSLARLEAEIAVGTIFRRFPEMKLKETPVFGYHPAFRNIESLNVILKPS 416
                                    25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415
   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  (9, 9)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (C167_SORCE | Q9KIZ4)
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:0050814    epothilone biosynthetic process    The chemical reactions and pathways resulting in the formation of epothilone, a drug obtained from the myxobacteria Sporangium cellulosum that interferes with cell division. Some epothilones are being studied as treatments for cancer.
    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.
cellular component
    GO:0005575    cellular_component    The part of a cell, extracellular environment or virus in which a gene product is located. A gene product may be located in one or more parts of a cell and its location may be as specific as a particular macromolecular complex, that is, a stable, persistent association of macromolecules that function together.

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 Related Entries

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

UniProtKB/Swiss-Prot
        C167_SORCE | Q9KIZ4: 1pkf 1q5e

(-) Related Entries Specified in the PDB File

1pkf EPOTHILONE D-BOUND CYTOCHROME P450EPOK
1q5e SUBSTRATE-FREE CYTOCHROME P450EPOK