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(-) Description

Title :  CRYSTAL STRUCTURE OF EPOTHILONE D-BOUND CYTOCHROME P450EPOK
 
Authors :  S. Nagano, H. Li, H. Shimizu, C. Nishida, H. Ogura, P. R. Ortiz De Montellano, T. L. Poulos
Date :  05 Jun 03  (Deposition) - 28 Oct 03  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym./Biol. Unit :  A
Keywords :  Cytochrome P450Epok, Oxidoreductase, Heme-Enzyme (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 - CYTOCHROME P450EPOK
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Scientific: SORANGIUM CELLULOSUM
    Organism Taxid: 56

 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
1EPD1Ligand/IonEPOTHILONE D
2HEM1Ligand/IonPROTOPORPHYRIN IX CONTAINING FE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPHE A:62 , LEU A:95 , PHE A:96 , HIS A:103 , ARG A:107 , 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 , GLY A:359 , HIS A:363 , CYS A:365 , PRO A:366 , GLY A:367 , EPD A:450 , HOH A:471 , HOH A:591BINDING SITE FOR RESIDUE HEM A 440
2AC2SOFTWARELEU A:95 , PHE A:96 , ALA A:180 , LEU A:183 , GLY A:184 , VAL A:188 , THR A:258 , GLY A:304 , THR A:305 , ALA A:402 , PHE A:403 , HEM A:440 , HOH A:464 , HOH A:488 , HOH A:632BINDING SITE FOR RESIDUE EPD A 450

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1PKF)

(-) 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:403
 aligned with C167_SORCE | Q9KIZ4 from UniProtKB/Swiss-Prot  Length:419

    Alignment length:403
                                    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       413   
           C167_SORCE    14 AFDFKPFAPGYAEDPFPAIERLREATPIFYWDEGRSWVLTRYHDVSAVFRDERFAVSREEWESSAEYSSAIPELSDMKKYGLFGLPPEDHARVRKLVNPSFTSRAIDLLRAEIQRTVDQLLDARSGQEEFDVVRDYAEGIPMRAISALLKVPAECDEKFRRFGSATARALGVGLVPRVDEETKTLVASVTEGLALLHGVLDERRRNPLENDVLTMLLQAEADGSRLSTKELVALVGAIIAAGTDTTIYLIAFAVLNLLRSPEALELVKAEPGLMRNALDEVLRFDNILRIGTVRFARQDLEYCGASIKKGEMVFLLIPSALRDGTVFSRPDVFDVRRDTSASLAYGRGPHVCPGVSLARLEAEIAVGTIFRRFPEMKLKETPVFGYHPAFRNIESLNVILKPS 416
               SCOP domains d1pkfa_ A: Cytochrome P450epok                                                                                                                                                                                                                                                                                                                                                                                      SCOP domains
               CATH domains 1pkfA00 A:14-416 Cytochrome p450                                                                                                                                                                                                                                                                                                                                                                                    CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..............hhhhhhhhhhhh.eeee....eeee.hhhhhhhhhhh..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
                 1pkf A  14 AFDFKPFAPGYAEDPFPAIERLREATPIFYWDEGRSWVLTRYHDVSAVFRDERFAVSREEWESSAEYSSAIPELSDMKKYGLFGLPPEDHARVRKLVNPSFTSRAIDLLRAEIQRTVDQLLDARSGQEEFDVVRDYAEGIPMRAISALLKVPAECDEKFRRFGSATARALGVGLVPRVDEETKTLVASVTEGLALLHGVLDERRRNPLENDVLTMLLQAEADGSRLSTKELVALVGAIIAAGTDTTIYLIAFAVLNLLRSPEALELVKAEPGLMRNALDEVLRFENILRIGTVRFARQDLEYCGASIKKGEMVFLLIPSALRDGTVFSRPDVFDVRRDTSASLAYGRGPHVCPGVSLARLEAEIAVGTIFRRFPEMKLKETPVFGYHPAFRNIESLNVILKPS 416
                                    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       413
   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  (0, 0)

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

(-) 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

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UniProtKB/Swiss-Prot
        C167_SORCE | Q9KIZ4: 1q5d 1q5e

(-) Related Entries Specified in the PDB File

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