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(-) Description

Title :  STRUCTURE OF MAMMALIAN CYTOCHROME P450 2C5
 
Authors :  P. A. Williams, J. Cosme, V. Sridhar, E. F. Johnson, D. E. Mcree
Date :  11 Jan 00  (Deposition) - 27 Sep 00  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.00
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  A  (4x)
Keywords :  Membrane Protein, Progesterone 21-Hydroxylase, Benzo(A)Pyrene Hydroxylase, Estradiol 2-Hydroxylase, P450, Cyp2C5, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  P. A. Williams, J. Cosme, V. Sridhar, E. F. Johnson, D. E. Mcree
Mammalian Microsomal Cytochrome P450 Monooxygenase: Structural Adaptations For Membrane Binding And Functional Diversity.
Mol. Cell V. 5 121 2000
PubMed-ID: 10678174  |  Reference-DOI: 10.1016/S1097-2765(00)80408-6
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - CYTOCHROME P450 2C5
    Chains: A
    EC Number: 1.14.14.1
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PCW
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: CYP2C5 WITH MEMBRANE SPANNING RESIDUES 3-21 DELETED AND A 4 RESIDUE HISTIDINE TAG AT THE C-TERMINUS CONTAINING ADDITIONAL INTERNAL MUTATIONS
    Mutation: YES
    Organism Common: RABBIT
    Organism Scientific: ORYCTOLAGUS CUNICULUS
    Organism Taxid: 9986
    Synonym: PROGESTERONE 21-HYDROXYLASE, CYPIIC5 P450 1, P450IIC5
    Tissue: LIVER

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (1x): A
Biological Unit 2 (4x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 5)

Asymmetric Unit (3, 5)
No.NameCountTypeFull Name
1HEM1Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
2SM1Ligand/IonSAMARIUM (III) ION
3SO43Ligand/IonSULFATE ION
Biological Unit 1 (2, 4)
No.NameCountTypeFull Name
1HEM1Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
2SM-1Ligand/IonSAMARIUM (III) ION
3SO43Ligand/IonSULFATE ION
Biological Unit 2 (2, 16)
No.NameCountTypeFull Name
1HEM4Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
2SM-1Ligand/IonSAMARIUM (III) ION
3SO412Ligand/IonSULFATE ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:199 , GLU A:203BINDING SITE FOR RESIDUE SM A 502
2AC2SOFTWAREARG A:132 , ASN A:133 , LYS A:454BINDING SITE FOR RESIDUE SO4 A 503
3AC3SOFTWARELYS A:138 , ASN A:259 , ARG A:261BINDING SITE FOR RESIDUE SO4 A 504
4AC4SOFTWAREASP A:411 , GLU A:412 , LYS A:418BINDING SITE FOR RESIDUE SO4 A 505
5AC5SOFTWAREILE A:112 , ALA A:113 , TRP A:120 , ARG A:124 , ALA A:294 , GLY A:295 , THR A:298 , THR A:299 , THR A:302 , LEU A:359 , ASN A:362 , LEU A:363 , HIS A:365 , PRO A:424 , PHE A:425 , SER A:426 , ARG A:430 , CYS A:432 , VAL A:433 , ALA A:438BINDING SITE FOR RESIDUE HEM A 501

(-) SS Bonds  (1, 1)

Asymmetric Unit
No.Residues
1A:60 -A:60

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Phe A:226 -Pro A:227

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1DT6)

(-) PROSITE Motifs  (1, 1)

Asymmetric Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CYTOCHROME_P450PS00086 Cytochrome P450 cysteine heme-iron ligand signature.CP2C5_RABIT425-434  1A:425-434
Biological Unit 1 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CYTOCHROME_P450PS00086 Cytochrome P450 cysteine heme-iron ligand signature.CP2C5_RABIT425-434  1A:425-434
Biological Unit 2 (1, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CYTOCHROME_P450PS00086 Cytochrome P450 cysteine heme-iron ligand signature.CP2C5_RABIT425-434  4A:425-434

(-) Exons   (0, 0)

(no "Exon" information available for 1DT6)

(-) 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:449
 aligned with CP2C5_RABIT | P00179 from UniProtKB/Swiss-Prot  Length:487

    Alignment length:460
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   487  
                                    39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439       449       459       469       479       | -
          CP2C5_RABIT    30 PPGPTPFPIIGNILQIDAKDISKSLTKFSECYGPVFTVYLGMKPTVVLHGYEAVKEALVDLGEEFAGRGSVPILEKVSKGLGIAFSNAKTWKEMRRFSLMTLRNFGMGKRSIEDRIQEEARCLVEELRKTNASPCDPTFILGCAPCNVICSVIFHNRFDYKDEEFLKLMESLNENVRILSSPWLQVYNNFPALLDYFPGIHKTLLKNADYIKNFIMEKVKEHQKLLDVNNPRDFIDCFLIKMEQENNLEFTLESLVIAVSDLFGAGTETTSTTLRYSLLLLLKHPEVAARVQEEIERVIGRHRSPCMQDRSRMPYTDAVIHEIQRFIDLLPTNLPHAVTRDVRFRNYFIPKGTDIITSLTSVLHDEKAFPNPKVFDPGHFLDESGNFKKSDYFMPFSAGKRMCVGEGLARMELFLFLTSILQNFKLQSLVEPKDLDITAVVNGFVSVPPSYQLCFIPI--   -
               SCOP domains d1dt6a_ A: Mammalian cytochrome p450 2c5                                                                                                                                                                                                                                                                                                                                                                                                                                     SCOP domains
               CATH domains 1dt6A00 A:30-489 Cytochrome p450                                                                                                                                                                                                                                                                                                                                                                                                                                             CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............hhhhh..hhhhhhhhhhhhhh.eeeee....eeeee.hhhhhhhhhh..............................hhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhh....-----------....hhhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhh..........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhh.......ee................eeeehhhhhhh...........hhhhhh.......................hhhhhhhhhhhhhhhhhhheeee...hhhhh..................eeee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CYTOCHROME------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1dt6 A  30 PPGPTPFPIIGNILQIDAKDISKSLTKFSECYGPVFTVYLGMKPTVVLHGYEAVKEALVDLGEEFAGRGSVPILEKVSKGLGIAFSNAKTWKEMRRFSLMTLRNFGMGKRSIEDRIQEEARCLVEELRKTNASPCDPTFILGCAPCNVICSVIFHNRFDYKDEEFLKLMESLHENVELLGTP-----------LDYFPGIHKTLLKNADYIKNFIMEKVKEHQKLLDVNNPRDFIDCFLIKMEQENNLEFTLESLVIAVSDLFGAGTETTSTTLRYSLLLLLKHPEVAARVQEEIERVIGRHRSPCMQDRSRMPYTDAVIHEIQRFIDLLPTNLPHAVTRDVRFRNYFIPKGTDIITSLTSVLHDEKAFPNPKVFDPGHFLDESGNFKKSDYFMPFSAGKRMCVGEGLARMELFLFLTSILQNFKLQSLVEPKDLDITAVVNGFVSVPPSYQLCFIPIHH 489
                                    39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209 |       -   |   229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439       449       459       469       479       489
                                                                                                                                                                                                               211         223
   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 1DT6)

(-) Gene Ontology  (13, 13)

Asymmetric Unit(hide GO term definitions)
Chain A   (CP2C5_RABIT | P00179)
molecular function
    GO:0070330    aromatase activity    Catalysis of the reduction of an aliphatic ring to yield an aromatic ring.
    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.
cellular component
    GO:0005783    endoplasmic reticulum    The irregular network of unit membranes, visible only by electron microscopy, that occurs in the cytoplasm of many eukaryotic cells. The membranes form a complex meshwork of tubular channels, which are often expanded into slitlike cavities called cisternae. The ER takes two forms, rough (or granular), with ribosomes adhering to the outer surface, and smooth (with no ribosomes attached).
    GO:0005789    endoplasmic reticulum membrane    The lipid bilayer surrounding the endoplasmic reticulum.
    GO:0043231    intracellular membrane-bounded organelle    Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane and occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0031090    organelle membrane    A membrane that is one of the two lipid bilayers of an organelle envelope or the outermost membrane of single membrane bound organelle.

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 Related Entries

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

UniProtKB/Swiss-Prot
        CP2C5_RABIT | P00179: 1n6b 1nr6

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