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(-) Description

Title :  A ROLE FOR ACTIVE SITE WATER MOLECULES AND HYDROXYL GROUPS OF SUBSTRATE FOR OXYGEN ACTIVATION IN CYTOCHROME P450 158A2
 
Authors :  B. Zhao, M. R. Waterman
Date :  30 Jul 05  (Deposition) - 25 Oct 05  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym./Biol. Unit :  A
Keywords :  Streptomyces, Cytochrome P450 Oxidoreductase, Cyp158A2, Proton Transfer, Dioxygen Activation, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  B. Zhao, F. P. Guengerich, M. Voehler, M. R. Waterman
Role Of Active Site Water Molecules And Substrate Hydroxyl Groups In Oxygen Activation By Cytochrome P450 158A2: A New Mechanism Of Proton Transfer
J. Biol. Chem. V. 280 42188 2005
PubMed-ID: 16239228  |  Reference-DOI: 10.1074/JBC.M509220200
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PUTATIVE CYTOCHROME P450
    Chains: A
    EC Number: 1.14.-.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET17B
    Expression System Strain: HMS174(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Scientific: STREPTOMYCES COELICOLOR
    Organism Taxid: 100226
    Strain: A3(2)

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 4)

Asymmetric/Biological Unit (3, 4)
No.NameCountTypeFull Name
1FLV2Ligand/IonFLAVIOLIN
2HEM1Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
3OXY1Ligand/IonOXYGEN MOLECULE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:71 , VAL A:93 , GLY A:94 , HIS A:101 , ARG A:105 , PHE A:112 , LEU A:239 , GLY A:242 , GLY A:243 , LEU A:282 , HIS A:287 , ARG A:295 , TYR A:318 , SER A:345 , PHE A:346 , HIS A:351 , CYS A:353 , PRO A:354 , ALA A:359 , FLV A:431 , OXY A:433 , HOH A:503 , HOH A:680BINDING SITE FOR RESIDUE HEM A 430
2AC2SOFTWAREARG A:71 , ARG A:288 , GLY A:292 , LEU A:293 , HEM A:430 , FLV A:432 , OXY A:433 , HOH A:503 , HOH A:529 , HOH A:537 , HOH A:545 , HOH A:564 , HOH A:664BINDING SITE FOR RESIDUE FLV A 431
3AC3SOFTWAREILE A:87 , PRO A:88 , ILE A:241 , ARG A:288 , GLY A:292 , LEU A:393 , FLV A:431 , HOH A:528 , HOH A:545 , HOH A:607 , HOH A:664 , HOH A:747BINDING SITE FOR RESIDUE FLV A 432
4AC4SOFTWAREGLY A:242 , HEM A:430 , FLV A:431 , HOH A:529BINDING SITE FOR RESIDUE OXY A 433

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2D09)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2D09)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2D09)

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CYTOCHROME_P450PS00086 Cytochrome P450 cysteine heme-iron ligand signature.C1582_STRCO346-355  1A:346-355

(-) Exons   (0, 0)

(no "Exon" information available for 2D09)

(-) 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:404
 aligned with C1582_STRCO | Q9FCA6 from UniProtKB/Swiss-Prot  Length:404

    Alignment length:404
                                                                                                                                                                                                                                                                                                                                                                                                                                          404   
                                    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|   
          C1582_STRCO     4 ETISQAVPPVRDWPAVDLPGSDFDPVLTELMREGPVTRISLPNGEGWAWLVTRHDDVRLVTNDPRFGREAVMDRQVTRLAPHFIPARGAVGFLDPPDHTRLRRSVAAAFTARGVERVRERSRGMLDELVDAMLRAGPPADLTEAVLSPFPIAVICELMGVPATDRHSMHTWTQLILSSSHGAEVSERAKNEMNAYFSDLIGLRSDSAGEDVTSLLGAAVGRDEITLSEAVGLAVLLQIGGEAVTNNSGQMFHLLLSRPELAERLRSEPEIRPRAIDELLRWIPHRNAVGLSRIALEDVEIKGVRIRAGDAVYVSYLAANRDPEVFPDPDRIDFERSPNPHVSFGFGPHYCPGGMLARLESELLVDAVLDRVPGLKLAVAPEDVPFKKGALIRGPEALPVTW---   -
               SCOP domains d2d09a_ A: automated matches                                                                                                                                                                                                                                                                                                                                                                                         SCOP domains
               CATH domains 2d09A00 A:4-407 Cytochrome p450                                                                                                                                                                                                                                                                                                                                                                                      CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........eee...........hhhhhhhhhhh.eeeee.......eeee.hhhhhhhhhh...eehhhhh................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eehhhhh.hhhhhhhhhhhhh.hhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhh.........eee...eee..eee....eeeehhhhhh................................hhhhhhhhhhhhhhhhhhh....ee..hhhhh..............eee.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CYTOCHROME---------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2d09 A   4 ETISQAVPPVRDWPAVDLPGSDFDPVLTELMREGPVTRISLPNGEGWAWLVTRHDDVRLVTNDPRFGREAVMDRQVTRLAPHFIPARGAVGFLDPPDHTRLRRSVAAAFTARGVERVRERSRGMLDELVDAMLRAGPPADLTEAVLSPFPIAVICELMGVPATDRHSMHTWTQLILSSSHGAEVSERAKNEMNAYFSDLIGLRSDSAGEDVTSLLGAAVGRDEITLSEAVGLAVLLQIGGEAVTNNSGQMFHLLLSRPELAERLRSEPEIRPRAIDELLRWIPHRNAVGLSRIALEDVEIKGVRIRAGDAVYVSYLAANRDPEVFPDPDRIDFERSPNPHVSFGFGPHYCPGGMLARLESELLVDAVLDRVPGLKLAVAPEDVPFKKGALIRGPEALPVTWAAA 407
                                    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
   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 2D09)

(-) Gene Ontology  (8, 8)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (C1582_STRCO | Q9FCA6)
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:0042440    pigment metabolic process    The chemical reactions and pathways involving pigment, any general or particular coloring matter in living organisms, e.g. melanin.

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 Related Entries

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

UniProtKB/Swiss-Prot
        C1582_STRCO | Q9FCA6: 1s1f 1se6 1t93 2d0e 3tzo 5de9

(-) Related Entries Specified in the PDB File

1s1f THE SAME PROTEIN COMPLEXED WITH 4-PHENYLIMIDAZOLE
1se6 FREE FORM OF THE SAME PROTEIN
1t93 THE SAME PROTEIN COMPLEXED WITH TWO MOLECULES OF FLAVIOLIN