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(-) Description

Title :  CRYSTAL STRUCTURE OF CYP105P1 WILD-TYPE 4-PHENYLIMIDAZOLE COMPLEX
 
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 :  2.60
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  (2, 2)

Asymmetric Unit (2, 2)
No.NameCountTypeFull Name
1HEM1Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
2PIM1Ligand/Ion4-PHENYL-1H-IMIDAZOLE
Biological Unit 1 (2, 2)
No.NameCountTypeFull Name
1HEM1Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
2PIM1Ligand/Ion4-PHENYL-1H-IMIDAZOLE
Biological Unit 2 (2, 4)
No.NameCountTypeFull Name
1HEM2Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
2PIM2Ligand/Ion4-PHENYL-1H-IMIDAZOLE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELEU A:87 , LEU A:88 , HIS A:95 , ARG A:99 , ALA A:237 , THR A:241 , THR A:242 , THR A:282 , PHE A:286 , GLY A:287 , 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:1411BINDING SITE FOR RESIDUE HEM A 1408
2AC2SOFTWARELEU A:88 , THR A:241 , PHE A:286BINDING SITE FOR RESIDUE PIM A 501

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3E5K)

(-) Cis Peptide Bonds  (5, 5)

Asymmetric Unit
No.Residues
1Gly A:42 -His A:43
2Pro A:82 -Gly A:83
3Glu A:92 -Pro A:93
4Gly A:134 -Pro A:135
5Lys A:305 -Gly A:306

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3E5K)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3E5K)

(-) Exons   (0, 0)

(no "Exon" information available for 3E5K)

(-) 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:382
 aligned with Q93H81_STRAX | Q93H81 from UniProtKB/TrEMBL  Length:399

    Alignment length:393
                                                                                                                                                                                                                                                                                                                                                                                                                                399  
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398|  
         Q93H81_STRAX     9 PTVPKARSCPFLPPDGIADIRAAAPVTRATFTSGHEAWLVTGYEEVRALLRDSSFSVQVPHALHTQDGVVTQKPGRGSLLWQDEPEHTSDRKLLAKEFTVRRMQALRPNIQRIVDEHLDAIEARGGPVDLVKTFANAVPSMVISDLFGVPVERRAEFQDIAEAMMRVDQDAAATEAAGMRLGGLLYQLVQERRANPGDDLISALITTEDPDGVVDDMFLMNAAGTLLIAAHDTTACMIGLGTALLLDSPDQLALLREDPSLVGNAVEELLRYLTIGQFGGERVATRDVELGGVRIAKGEQVVAHVLAADFDPAFVEEPERFDITRRPAPHLAFGFGAHQCIGQQLARIELQIVFETLFRRLPGLRLAKPVEELRFRHDMVFYGVHELPVTW--   -
               SCOP domains d3e5ka_ A: automated matches                                                                                                                                                                                                                                                                                                                                                                              SCOP domains
               CATH domains 3e5kA00 A:9-401 Cytochrome p450                                                                                                                                                                                                                                                                                                                                                                           CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...............hhhhhhhhh.eeeee.....eeeee.hhhhhhhhhhh..eeee...-----------............hhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhh..eehhhhh.hhhhhhhhhhhh..hhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhh..hhhhhhhhhhhhhh......eeee...eee..eee....eeeehhhhhhh........................hhhhh..hhhhhhhhhhhhhhhhhhhh...ee..hhhhh.eee....eee...eee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3e5k A   9 PTVPKARSCPFLPPDGIADIRAAAPVTRATFTSGHEAWLVTGYEEVRALLRDSSFSVQVPH-----------KPGRGSLLWQDEPEHTSDRKLLAKEFTVRRMQALRPNIQRIVDEHLDAIEARGGPVDLVKTFANAVPSMVISDLFGVPVERRAEFQDIAEAMMRVDQDAAATEAAGMRLGGLLYQLVQERRANPGDDLISALITTEDPDGVVDDMFLMNAAGTLLIAAHDTTACMIGLGTALLLDSPDQLALLREDPSLVGNAVEELLRYLTIGQFGGERVATRDVELGGVRIAKGEQVVAHVLAADFDPAFVEEPERFDITRRPAPHLAFGFGAHQCIGQQLARIELQIVFETLFRRLPGLRLAKPVEELRFRHDIVFYGVHELPVTWHH 401
                                    18        28        38        48        58        68|        -  |     88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398   
                                                                                       69          81
   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 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 3E5K)

(-) 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

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        Q93H81_STRAX | Q93H81: 3aba 3e5j 3e5l

(-) Related Entries Specified in the PDB File

3e5j 3e5l