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(-) Description

Title :  FERROUS DIOXYGEN COMPLEX OF THE WILD-TYPE CYTOCHROME P450ERYF
 
Authors :  S. Nagano, J. R. Cupp-Vickery, T. L. Poulos
Date :  31 Mar 05  (Deposition) - 12 Apr 05  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym./Biol. Unit :  A
Keywords :  Heme, Cyp, P450, Erythromycin, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Nagano, J. R. Cupp-Vickery, T. L. Poulos
Crystal Structures Of The Ferrous Dioxygen Complex Of Wild-Type Cytochrome P450Eryf And Its Mutants, A245S And A245T: Investigation Of The Proton Transfer System In P450Eryf.
J. Biol. Chem. V. 280 22102 2005
PubMed-ID: 15824115  |  Reference-DOI: 10.1074/JBC.M501732200
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - 6-DEOXYERYTHRONOLIDE B HYDROXYLASE
    Chains: A
    EC Number: 1.-.-.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: ERYF, CYP107A1
    Organism Scientific: SACCHAROPOLYSPORA ERYTHRAEA
    Organism Taxid: 1836
    Synonym: 6-DEB HYDROXYLASE, ERYTHOMYCIN A BIOSYNTHESIS HYDROLASE, CYTOCHROME P450 107A1, CYPCVIIA1, P450ERYF

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (3, 3)
No.NameCountTypeFull Name
1DEB1Ligand/Ion6-DEOXYERYTHRONOLIDE B
2HEM1Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
3OXY1Ligand/IonOXYGEN MOLECULE

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREMET A:90 , GLY A:91 , HIS A:98 , ARG A:102 , PHE A:109 , GLY A:242 , ALA A:245 , PRO A:288 , ARG A:293 , SER A:343 , PHE A:344 , GLY A:345 , ILE A:348 , HIS A:349 , CYS A:351 , GLY A:353 , ALA A:357 , OXY A:417 , DEB A:420 , HOH A:422 , HOH A:427 , HOH A:432 , HOH A:446BINDING SITE FOR RESIDUE HEM A 410
2AC2SOFTWAREALA A:241 , HEM A:410 , DEB A:420BINDING SITE FOR RESIDUE OXY A 417
3AC3SOFTWAREALA A:74 , GLY A:91 , THR A:92 , ILE A:174 , LEU A:175 , VAL A:237 , LEU A:392 , HEM A:410 , OXY A:417 , HOH A:423 , HOH A:428BINDING SITE FOR RESIDUE DEB A 420

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1Z8O)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Pro A:95 -Pro A:96

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1Z8O)

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CYTOCHROME_P450PS00086 Cytochrome P450 cysteine heme-iron ligand signature.CPXJ_SACEN344-353  1A:344-353

(-) Exons   (0, 0)

(no "Exon" information available for 1Z8O)

(-) 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:402
 aligned with CPXJ_SACEN | Q00441 from UniProtKB/Swiss-Prot  Length:404

    Alignment length:402
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402  
           CPXJ_SACEN     3 TVPDLESDSFHVDWYRTYAELRETAPVTPVRFLGQDAWLVTGYDEAKAALSDLRLSSDPKKKYPGVEVEFPAYLGFPEDVRNYFATNMGTSDPPTHTRLRKLVSQEFTVRRVEAMRPRVEQITAELLDEVGDSGVVDIVDRFAHPLPIKVICELLGVDEKYRGEFGRWSSEILVMDPERAEQRGQAAREVVNFILDLVERRRTEPGDDLLSALIRVQDDDDGRLSADELTSIALVLLLAGFEASVSLIGIGTYLLLTHPDQLALVRRDPSALPNAVEEILRYIAPPETTTRFAAEEVEIGGVAIPQYSTVLVANGAANRDPKQFPDPHRFDVTRDTRGHLSFGQGIHFCMGRPLAKLEGEVALRALFGRFPALSLGIDADDVVWRRSLLLRGIDHLPVRLDG 404
               SCOP domains d1z8oa_ A: Cytochrome P450-ERYF                                                                                                                                                                                                                                                                                                                                                                                    SCOP domains
               CATH domains 1z8oA00 A:3-404 Cytochrome p450                                                                                                                                                                                                                                                                                                                                                                                    CATH domains
               Pfam domains -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------p450-1z8oA01 A:272-378                                                                                     -------------------------- Pfam domains
         Sec.struct. author ......hhhhh.hhhhhhhhhhhhh.eeeeee..eeeeee.hhhhhhhhhhh..ee.............hhhhh..hhhhhhhhh.hhhhh..hhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh.....eeehhhhh.hhhhhhhhhhhh..hhhhh.hhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhee...ee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhh.....eeeee...eee..eee....eeeehhhhhh................................hhhhhhhhhhhhhhhhhhhh...ee..hhhhh..............eee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CYTOCHROME--------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1z8o A   3 TVPDLESDSFHVDWYRTYAELRETAPVTPVRFLGQDAWLVTGYDEAKAALSDLRLSSDPKKKYPGVEVEFPAYLGFPEDVRNYFATNMGTSDPPTHTRLRKLVSQEFTVRRVEAMRPRVEQITAELLDEVGDSGVVDIVDRFAHPLPIKVICELLGVDEKYRGEFGRWSSEILVMDPERAEQRGQAAREVVNFILDLVERRRTEPGDDLLSALIRVQDDDDGRLSADELTSIALVLLLAGFEASVSLIGIGTYLLLTHPDQLALVRRDPSALPNAVEEILRYIAPPETTTRFAAEEVEIGGVAIPQYSTVLVANGAANRDPKQFPDPHRFDVTRDTRGHLSFGQGIHFCMGRPLAKLEGEVALRALFGRFPALSLGIDADDVVWRRSLLLRGIDHLPVRLDG 404
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402
   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  (10, 10)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (CPXJ_SACEN | Q00441)
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:0017000    antibiotic biosynthetic process    The chemical reactions and pathways resulting in the formation of an antibiotic, a substance produced by or derived from certain fungi, bacteria, and other organisms, that can destroy or inhibit the growth of other microorganisms.
    GO:1901115    erythromycin biosynthetic process    The chemical reactions and pathways resulting in the formation of erythromycin.
    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:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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  1z8o
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  CPXJ_SACEN | Q00441
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  1.-.-.-
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 Related Entries

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

UniProtKB/Swiss-Prot
        CPXJ_SACEN | Q00441: 1egy 1eup 1jin 1jio 1jip 1oxa 1z8p 1z8q

(-) Related Entries Specified in the PDB File

1z8p 1z8q