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(-) Description

Title :  CRYSTAL STRUCTURE ANALYSIS OF A 6-COORDINATED CYTOCHOROME P450 FROM THERMUS THERMOPHILUS HB8
 
Authors :  Y. Kousumi, N. Nakagawa, M. Kaneko, H. Yamamoto, R. Masui, S. Kuramitsu, N. Ueyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  28 May 04  (Deposition) - 28 Nov 04  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (2x)
Keywords :  P450, Cytochrome, Riken Structural Genomics/Proteomics Initiative, Rsgi, Structural Genomics, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Kousumi, N. Nakagawa, M. Kaneko, H. Yamamoto, R. Masui, S. Kuramitsu, N. Ueyama
Crystal Structure Analysis Of Cytochrome P450 From Thermus Thermophilus Hb8
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - CYTOCHROME P450
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET11A
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Organism Scientific: THERMUS THERMOPHILUS
    Organism Taxid: 274

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (2x): AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1HEM2Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
Biological Unit 1 (1, 4)
No.NameCountTypeFull Name
1HEM4Ligand/IonPROTOPORPHYRIN IX CONTAINING FE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS A:63 , TYR A:68 , LEU A:79 , LEU A:80 , TRP A:87 , ARG A:91 , PHE A:98 , LEU A:218 , ALA A:221 , GLY A:222 , THR A:225 , ALA A:268 , ARG A:273 , PRO A:328 , PHE A:329 , ARG A:334 , CYS A:336 , GLY A:338 , HOH A:391 , HOH A:393BINDING SITE FOR RESIDUE HEM A 390
2AC2SOFTWARELYS B:63 , TYR B:68 , LEU B:79 , LEU B:80 , TRP B:87 , ARG B:91 , PHE B:98 , LEU B:140 , LEU B:144 , ALA B:221 , GLY B:222 , THR B:225 , ARG B:273 , PRO B:328 , PHE B:329 , GLY B:330 , ARG B:334 , CYS B:336 , GLY B:338 , GLU B:345 , HOH B:392 , HOH B:397BINDING SITE FOR RESIDUE HEM B 390

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Pro A:201 -Pro A:202
2Pro B:201 -Pro B:202

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1WIY)

(-) 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:358
 aligned with Q53W59_THET8 | Q53W59 from UniProtKB/TrEMBL  Length:389

    Alignment length:385
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380     
         Q53W59_THET8     1 MKRLSLREAWPYLKDLQQDPLAVLLEWGRAHPRLFLPLPRFPLALIFDPEGVEGALLAEGTTKATFQYRALSRLTGRGLLTDWGKSWKEARKALKDPFLPKSVRGYREAMEEEAWAFFGEWRGEERDLDHEMLALSLRLLGRALFGKPLSPSLAEHALKALDRIMAQTRSPLALLDLAAEARFRKDRGALYREAEALIVHPPLSHLPRERALSEAVTLLVAGHETVASALTWSFLLLSHRPDWQKRVAESEEAALAAFQEALRLYPPAWILTRRLERPLLLGEDRLPQGTTLVLSPYVTQRLYFPEGEAFQPERFLAERGTPSGRYFPFGLGQRLCLGRDFALLEGPIVLRAFFRRFRLDPLPFPRVLAQVTLRPEGGLPARPRE 385
               SCOP domains d1wiya            _ A: Cyp175a1                                                                                                                                                                                                                                                                                                                                                                   SCOP domains
               CATH domains 1wiyA0            0 A:1-385 Cytochrom    e p450                                                                                                                                                                                                                                                                                                                                                   CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .ee...------------hhhhhhhhhhhhh.eeee.----.eeee.hhhhhhhhhhh......hhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh.....eehhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhh.-----------hhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhh.....eeee....eee..eee....eeeehhhhhhhhh.........hhhhhh...................hhhhhhhhhhhhhhhhhh...........eee...eee....ee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1wiy A   1 MKRLSL------------DPLAVLLEWGRAHPRLFLP----PLALIFDPEGVEGALLAEGTTKATFQYRALSRLTGRGLLTDWGKSWKEARKALKDPFLPKSVRGYREAMEEEAWAFFGEWRGEERDLDHEMLALSLRLLGRALFGKPLSPSLAEHALKALDRIM-----------LAAEARFRKDRGALYREAEALIVHPPLSHLPRERALSEAVTLLVAGHETVASALTWSFLLLSHRPDWQKRVAESEEAALAAFQEALRLYPPAWILTRRLERPLLLGEDRLPQGTTLVLSPYVTQRLYFPEGEAFQPERFLAERGTPSGRYFPFGLGQRLCLGRDFALLEGPIVLRAFFRRFRLDPLPFPRVLAQVTLRPEGGLPARPRE 385
                                 |   -        20        30      |  - |      50        60        70        80        90       100       110       120       130       140       150       160    |    -      |180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380     
                                 6           19                37   42                                                                                                                        165         177                                                                                                                                                                                                                


Chain B from PDB  Type:PROTEIN  Length:362
 aligned with Q53W59_THET8 | Q53W59 from UniProtKB/TrEMBL  Length:389

    Alignment length:385
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380     
         Q53W59_THET8     1 MKRLSLREAWPYLKDLQQDPLAVLLEWGRAHPRLFLPLPRFPLALIFDPEGVEGALLAEGTTKATFQYRALSRLTGRGLLTDWGKSWKEARKALKDPFLPKSVRGYREAMEEEAWAFFGEWRGEERDLDHEMLALSLRLLGRALFGKPLSPSLAEHALKALDRIMAQTRSPLALLDLAAEARFRKDRGALYREAEALIVHPPLSHLPRERALSEAVTLLVAGHETVASALTWSFLLLSHRPDWQKRVAESEEAALAAFQEALRLYPPAWILTRRLERPLLLGEDRLPQGTTLVLSPYVTQRLYFPEGEAFQPERFLAERGTPSGRYFPFGLGQRLCLGRDFALLEGPIVLRAFFRRFRLDPLPFPRVLAQVTLRPEGGLPARPRE 385
               SCOP domains d1wiy             b_ B: Cyp175a1                                                                                                                                                                                                                                                                                                                                                                  SCOP domains
               CATH domains 1wiyB             00 B:1-385 Cytochrome  p450                                                                                                                                                                                                                                                                                                                                                     CATH domains
           Pfam domains (1) -----             --------------------- --------------------------------------------------------------------------------------------------------------------------------       --------p450-1wiyB01 B:184-379                                                                                                                                                                              ------ Pfam domains (1)
           Pfam domains (2) -----             --------------------- --------------------------------------------------------------------------------------------------------------------------------       --------p450-1wiyB02 B:184-379                                                                                                                                                                              ------ Pfam domains (2)
         Sec.struct. author .ee..-------------hhhhhhhhhhhhh.eeeee..-.eeeee.hhhhhhhhhhh......hhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....eehhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhh-------hhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhh.....eeee....eee..eee....eeeehhhhhhhhh.......hhhhhh--...................hhhhhhhhhhhhhhhhhhhh.........eee...eee....ee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1wiy B   1 MKRLS-------------DPLAVLLEWGRAHPRLFLPLP-FPLALIFDPEGVEGALLAEGTTKATFQYRALSRLTGRGLLTDWGKSWKEARKALKDPFLPKSVRGYREAMEEEAWAFFGEWRGEERDLDHEMLALSLRLLGRALFGKPLSPSLAEHALKALDRIMAQT-------DLAAEARFRKDRGALYREAEALIVHPPLSHLPRERALSEAVTLLVAGHETVASALTWSFLLLSHRPDWQKRVAESEEAALAAFQEALRLYPPAWILTRRLERPLLLGEDRLPQGTTLVLSPYVTQRLYFPEGEAFQPERFL--RGTPSGRYFPFGLGQRLCLGRDFALLEGPIVLRAFFRRFRLDPLPFPRVLAQVTLRPEGGLPARPRE 385
                                |    -        20        30        |-|       50        60        70        80        90       100       110       120       130       140       150       160       | -     | 180       190       200       210       220       230       240       250       260       270       280       290       300       310     | 320       330       340       350       360       370       380     
                                5            19                  39 |                                                                                                                            168     176                                                                                                                                         316  |                                                                  
                                                                   41                                                                                                                                                                                                                                                                                   319
   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, 2)

Asymmetric Unit
(-)
Class: All alpha proteins (14657)

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: no clan defined [family: p450] (161)

(-) Gene Ontology  (7, 7)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (Q53W59_THET8 | Q53W59)
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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