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(-) Description

Title :  CRYSTAL STRUCTURE OF CYP105P1 WILD-TYPE LIGAND-FREE FORM
 
Authors :  L. H. Xu, S. Fushinobu, H. Ikeda, T. Wakagi, H. Shoun
Date :  14 Aug 08  (Deposition) - 30 Dec 08  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.95
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  A  (2x)
Keywords :  P450, Oxidoreductase, Heme, Iron, Metal-Binding, Monooxygenase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. H. Xu, S. Fushinobu, H. Ikeda, T. Wakagi, H. Shoun
Crystal Structures Of Cytochrome P450 105P1 From Streptomyces Avermitilis: Conformational Flexibility And Histidine Ligation State
J. Bacteriol. V. 191 1211 2009
PubMed-ID: 19074393  |  Reference-DOI: 10.1128/JB.01276-08

(-) Compounds

Molecule 1 - CYTOCHROME P450 (CYTOCHROME P450 HYDROXYLASE)
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET-17B
    Expression System Strain: BL21 CODONPLUS (DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: PTEC, SAV413, SAV_413
    Mutation: YES
    Organism Scientific: STREPTOMYCES AVERMITILIS
    Organism Taxid: 33903
    Strain: MA-4680
    Synonym: CYP105P1

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (1x): A
Biological Unit 2 (2x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 1)

Asymmetric Unit (1, 1)
No.NameCountTypeFull Name
1HEM1Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1HEM1Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
1HEM2Ligand/IonPROTOPORPHYRIN IX CONTAINING FE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:72 , LEU A:88 , HIS A:95 , ARG A:99 , ALA A:237 , ALA A:238 , THR A:241 , THR A:242 , ILE A:283 , GLY A:288 , ARG A:290 , ALA A:340 , PHE A:341 , GLY A:342 , HIS A:346 , CYS A:348 , GLY A:350 , ALA A:354 , HOH A:1471 , HOH A:1574 , HOH A:1712BINDING SITE FOR RESIDUE HEM A 1408

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3E5J)

(-) Cis Peptide Bonds  (7, 7)

Asymmetric Unit
No.Residues
1Asp A:75 -Gly A:76
2Val A:77 -Val A:78
3Glu A:92 -Pro A:93
4Gly A:133 -Gly A:134
5Gly A:134 -Pro A:135
6Val A:175 -Asp A:176
7Pro A:218 -Asp A:219

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3E5J)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3E5J)

(-) Exons   (0, 0)

(no "Exon" information available for 3E5J)

(-) Sequences/Alignments

Asymmetric 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:390
 aligned with Q93H81_STRAX | Q93H81 from UniProtKB/TrEMBL  Length:399

    Alignment length:394
                                                                                                                                                                                                                                                                                                                                                                                                                                  399 
                                    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  | 
         Q93H81_STRAX     7 DAPTVPKARSCPFLPPDGIADIRAAAPVTRATFTSGHEAWLVTGYEEVRALLRDSSFSVQVPHALHTQDGVVTQKPGRGSLLWQDEPEHTSDRKLLAKEFTVRRMQALRPNIQRIVDEHLDAIEARGGPVDLVKTFANAVPSMVISDLFGVPVERRAEFQDIAEAMMRVDQDAAATEAAGMRLGGLLYQLVQERRANPGDDLISALITTEDPDGVVDDMFLMNAAGTLLIAAHDTTACMIGLGTALLLDSPDQLALLREDPSLVGNAVEELLRYLTIGQFGGERVATRDVELGGVRIAKGEQVVAHVLAADFDPAFVEEPERFDITRRPAPHLAFGFGAHQCIGQQLARIELQIVFETLFRRLPGLRLAKPVEELRFRHDMVFYGVHELPVTW-   -
               SCOP domains d3e5ja_ A: automated matches                                                                                                                                                                                                                                                                                                                                                                               SCOP domains
               CATH domains 3e5jA00 A:7-400 Cytochrome p450                                                                                                                                                                                                                                                                                                                                                                            CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...............hhhhhhhhhhh.eeeee.....eeeee.hhhhhhhhhhh..eeeee.hhhhh.....----..........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eehhhhh..hhhhhhhhhhh..hhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhh......eeee...eee..eee....eeeehhhhhhh...............................hhhhhhhhhhhhhhhhhhhh...ee..hhhhh.eee...eeee...eee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3e5j A   7 DAPTVPKARSCPFLPPDGIADIRAAAPVTRATFTSGHEAWLVTGYEEVRALLRDSSFSVQVPHALHTQDGVV----GRGSLLWQDEPEHTSDRKLLAKEFTVRRMQALRPNIQRIVDEHLDAIEARGGPVDLVKTFANAVPSMVISDLFGVPVERRAEFQDIAEAMMRVDQDAAATEAAGMRLGGLLYQLVQERRANPGDDLISALITTEDPDGVVDDMFLMNAAGTLLIAAHDTTACMIGLGTALLLDSPDQLALLREDPSLVGNAVEELLRYLTIGQFGGERVATRDVELGGVRIAKGEQVVAHVLAADFDPAFVEEPERFDITRRPAPHLAFGFGAHQCIGQQLARIELQIVFETLFRRLPGLRLAKPVEELRFRHDIVFYGVHELPVTWH 400
                                    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    
                                                                                                  78   83
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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  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 Unit
(-)
Class: All alpha proteins (14657)

(-) CATH Domains  (1, 1)

Asymmetric Unit
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3E5J)

(-) Gene Ontology  (7, 7)

Asymmetric Unit(hide GO term definitions)
Chain A   (Q93H81_STRAX | Q93H81)
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

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

UniProtKB/TrEMBL
        Q93H81_STRAX | Q93H81: 3aba 3e5k 3e5l

(-) Related Entries Specified in the PDB File

3e5k 3e5l