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(-) Description

Title :  TRANYLCYPROMINE COMPLEX OF CYTOCHROME P450 46A1
 
Authors :  N. Mast, C. Charvet, I. Pikuleva, C. D. Stout
Date :  30 Mar 10  (Deposition) - 28 Jul 10  (Release) - 20 Oct 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Cyp46A1, P450 46A1, P450, Tranylcypromine, Monooxygenase, Metabolic Enzyme, Oxidoreductase, Heme, Cholesterol Metabolism, Endoplasmic Reticulum, Iron, Lipid Metabolism, Membrane, Metal-Binding, Microsome, Nadp, Steroid Metabolism, Transmembrane (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  N. Mast, C. Charvet, I. A. Pikuleva, C. D. Stout
Structural Basis Of Drug Binding To Cyp46A1, An Enzyme That Controls Cholesterol Turnover In The Brain.
J. Biol. Chem. V. 285 31783 2010
PubMed-ID: 20667828  |  Reference-DOI: 10.1074/JBC.M110.143313
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - CHOLESTEROL 24-HYDROXYLASE
    ChainsA, B
    EC Number1.14.13.98
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPUC18
    Expression System StrainDH5ALPHA
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentUNP RESIDUES 51-500
    GeneCYP46, CYP46A1
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymCH24H, CYTOCHROME P450 46A1

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit AB
Biological Unit 1 (1x)A 
Biological Unit 2 (1x) B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric Unit (2, 4)
No.NameCountTypeFull Name
1GJZ2Ligand/Ion(1R,2S)-2-PHENYLCYCLOPROPANAMINE
2HEM2Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
Biological Unit 1 (2, 2)
No.NameCountTypeFull Name
1GJZ1Ligand/Ion(1R,2S)-2-PHENYLCYCLOPROPANAMINE
2HEM1Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
Biological Unit 2 (2, 2)
No.NameCountTypeFull Name
1GJZ1Ligand/Ion(1R,2S)-2-PHENYLCYCLOPROPANAMINE
2HEM1Ligand/IonPROTOPORPHYRIN IX CONTAINING FE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHOH A:7 , LYS A:104 , TYR A:109 , LEU A:125 , VAL A:126 , TRP A:134 , ARG A:138 , GLY A:303 , THR A:306 , SER A:307 , THR A:370 , PRO A:429 , PHE A:430 , SER A:431 , ARG A:435 , SER A:436 , CYS A:437 , GLY A:439 , PHE A:442 , ALA A:443 , GJZ A:506 , HOH A:589BINDING SITE FOR RESIDUE HEM A 505
2AC2SOFTWAREILE A:301 , ALA A:302 , THR A:306 , HEM A:505BINDING SITE FOR RESIDUE GJZ A 506
3AC3SOFTWAREHOH B:3 , LYS B:104 , TYR B:109 , LEU B:125 , VAL B:126 , TRP B:134 , ARG B:138 , PHE B:299 , ALA B:302 , GLY B:303 , THR B:306 , SER B:307 , HIS B:310 , ALA B:367 , THR B:370 , PRO B:429 , PHE B:430 , ARG B:435 , SER B:436 , CYS B:437 , GLY B:439 , PHE B:442 , GJZ B:506 , HOH B:581 , HOH B:605BINDING SITE FOR RESIDUE HEM B 505
4AC4SOFTWAREPHE B:121 , ILE B:301 , ALA B:302 , THR B:306 , HEM B:505BINDING SITE FOR RESIDUE GJZ B 506

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3MDR)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 2)

Asymmetric Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CYTOCHROME_P450PS00086 Cytochrome P450 cysteine heme-iron ligand signature.CP46A_HUMAN430-439
 
  2A:430-439
B:430-439
Biological Unit 1 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CYTOCHROME_P450PS00086 Cytochrome P450 cysteine heme-iron ligand signature.CP46A_HUMAN430-439
 
  1A:430-439
-
Biological Unit 2 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CYTOCHROME_P450PS00086 Cytochrome P450 cysteine heme-iron ligand signature.CP46A_HUMAN430-439
 
  1-
B:430-439

(-) Exons   (0, 0)

(no "Exon" information available for 3MDR)

(-) 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:427
 aligned with CP46A_HUMAN | Q9Y6A2 from UniProtKB/Swiss-Prot  Length:500

    Alignment length:434
                                    67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437       447       457       467       477       487    
          CP46A_HUMAN    58 RVLQDVFLDWAKKYGPVVRVNVFHKTSVIVTSPESVKKFLMSTKYNKDSKMYRALQTVFGERLFGQGLVSECNYERWHKQRRVIDLAFSRSSLVSLMETFNEKAEQLVEILEAKADGQTPVSMQDMLTYTAMDILAKAAFGMETSMLLGAQKPLSQAVKLMLEGITASRNTLAKFLPGKRKQLREVRESIRFLRQVGRDWVQRRREALKRGEEVPADILTQILKAEEGAQDDEGLLDNFVTFFIAGHETSANHLAFTVMELSRQPEIVARLQAEVDEVIGSKRYLDFEDLGRLQYLSQVLKESLRLYPPAWGTFRLLEEETLIDGVRVPGNTPLLFSTYVMGRMDTYFEDPLTFNPDRFGPGAPKPRFTYFPFSLGHRSCIGQQFAQMEVKVVMAKLLQRLEFRLVPGQRFGLQEQATLKPLDPVLCTLRPRGW 491
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhh.eeeeee..eeeeee.hhhhhhhhhh......hhhhhhhhhh...............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......eehhhhhhhhhhhhhhhhhhh...hhhhh.hhhhhhhhhhhhhhhhhhhh.-------.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhh....eeeeee...eee..eee...eeeeeehhhhh............hhhhhh..............hhhhh..hhhhhhhhhhhhhhhhhhheeeee.......eee...eee....eeeeee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CYTOCHROME---------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3mdr A  58 RVLQDVFLDWAKKYGPVVRVNVFHKTSVIVTSPESVKKFLMSTKYNKDSKMYRALQTVFGERLFGQGLVSECNYERWHKQRRVIDLAFSRSSLVSLMETFNEKAEQLVEILEAKADGQTPVSMQDMLTYTAMDILAKAAFGMETSMLLGAQKPLSQAVKLMLEGITASRNT-------KRKQLREVRESIRFLRQVGRDWVQRRREALKRGEEVPADILTQILKAEEGAQDDEGLLDNFVTFFIAGHETSANHLAFTVMELSRQPEIVARLQAEVDEVIGSKRYLDFEDLGRLQYLSQVLKESLRLYPPAWGTFRLLEEETLIDGVRVPGNTPLLFSTYVMGRMDTYFEDPLTFNPDRFGPGAPKPRFTYFPFSLGHRSCIGQQFAQMEVKVVMAKLLQRLEFRLVPGQRFGLQEQATLKPLDPVLCTLRPRGW 491
                                    67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227|      237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437       447       457       467       477       487    
                                                                                                                                                                                                    228     236                                                                                                                                                                                                                                                               

Chain B from PDB  Type:PROTEIN  Length:425
 aligned with CP46A_HUMAN | Q9Y6A2 from UniProtKB/Swiss-Prot  Length:500

    Alignment length:432
                                    67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437       447       457       467       477       487  
          CP46A_HUMAN    58 RVLQDVFLDWAKKYGPVVRVNVFHKTSVIVTSPESVKKFLMSTKYNKDSKMYRALQTVFGERLFGQGLVSECNYERWHKQRRVIDLAFSRSSLVSLMETFNEKAEQLVEILEAKADGQTPVSMQDMLTYTAMDILAKAAFGMETSMLLGAQKPLSQAVKLMLEGITASRNTLAKFLPGKRKQLREVRESIRFLRQVGRDWVQRRREALKRGEEVPADILTQILKAEEGAQDDEGLLDNFVTFFIAGHETSANHLAFTVMELSRQPEIVARLQAEVDEVIGSKRYLDFEDLGRLQYLSQVLKESLRLYPPAWGTFRLLEEETLIDGVRVPGNTPLLFSTYVMGRMDTYFEDPLTFNPDRFGPGAPKPRFTYFPFSLGHRSCIGQQFAQMEVKVVMAKLLQRLEFRLVPGQRFGLQEQATLKPLDPVLCTLRPR 489
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
           Pfam domains (1) p450-3mdrB01 B:58-484                                                                                                                                                                                                                                                                                                                                                                                                                      ----- Pfam domains (1)
           Pfam domains (2) p450-3mdrB02 B:58-484                                                                                                                                                                                                                                                                                                                                                                                                                      ----- Pfam domains (2)
         Sec.struct. author .hhhhhhhhhhhhhh.eeeeee..eeeeee.hhhhhhhhhh......hhhhhhhhhh...............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......eehhhhhhhhhhhhhhhhhhh...hhhhh.hhhhhhhhhhhhhhhhhhhh.-------.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhh....eeeeee...eee..eee...eeeeeehhhhhh...........hhhhhh..............hhhhh..hhhhhhhhhhhhhhhhhhheeeee.......eee...eee....eeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CYTOCHROME-------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3mdr B  58 RVLQDVFLDWAKKYGPVVRVNVFHKTSVIVTSPESVKKFLMSTKYNKDSKMYRALQTVFGERLFGQGLVSECNYERWHKQRRVIDLAFSRSSLVSLMETFNEKAEQLVEILEAKADGQTPVSMQDMLTYTAMDILAKAAFGMETSMLLGAQKPLSQAVKLMLEGITASRNT-------KRKQLREVRESIRFLRQVGRDWVQRRREALKRGEEVPADILTQILKAEEGAQDDEGLLDNFVTFFIAGHETSANHLAFTVMELSRQPEIVARLQAEVDEVIGSKRYLDFEDLGRLQYLSQVLKESLRLYPPAWGTFRLLEEETLIDGVRVPGNTPLLFSTYVMGRMDTYFEDPLTFNPDRFGPGAPKPRFTYFPFSLGHRSCIGQQFAQMEVKVVMAKLLQRLEFRLVPGQRFGLQEQATLKPLDPVLCTLRPR 489
                                    67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227|      237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437       447       457       467       477       487  
                                                                                                                                                                                                    228     236                                                                                                                                                                                                                                                             

   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  (0, 0)

(no "SCOP Domain" information available for 3MDR)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3MDR)

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Family: p450 (161)

(-) Gene Ontology  (23, 23)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (CP46A_HUMAN | Q9Y6A2)
molecular function
    GO:0033781    cholesterol 24-hydroxylase activity    Catalysis of the reaction: cholesterol + H(+) + NADPH + O(2) = (24S)-24-hydroxycholesterol + H(2)O + NADP(+).
    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.
    GO:0008395    steroid hydroxylase activity    Catalysis of the formation of a hydroxyl group on a steroid by incorporation of oxygen from O2.
biological process
    GO:0006699    bile acid biosynthetic process    The chemical reactions and pathways resulting in the formation of bile acids, any of a group of steroid carboxylic acids occurring in bile.
    GO:0006707    cholesterol catabolic process    The chemical reactions and pathways resulting in the breakdown of cholesterol, cholest-5-en-3 beta-ol, the principal sterol of vertebrates and the precursor of many steroids, including bile acids and steroid hormones.
    GO:0008203    cholesterol metabolic process    The chemical reactions and pathways involving cholesterol, cholest-5-en-3 beta-ol, the principal sterol of vertebrates and the precursor of many steroids, including bile acids and steroid hormones. It is a component of the plasma membrane lipid bilayer and of plasma lipoproteins and can be found in all animal tissues.
    GO:0006629    lipid metabolic process    The chemical reactions and pathways involving lipids, compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent. Includes fatty acids; neutral fats, other fatty-acid esters, and soaps; long-chain (fatty) alcohols and waxes; sphingoids and other long-chain bases; glycolipids, phospholipids and sphingolipids; and carotenes, polyprenols, sterols, terpenes and other isoprenoids.
    GO:0007399    nervous system development    The process whose specific outcome is the progression of nervous tissue over time, from its formation to its mature state.
    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.
    GO:0008202    steroid metabolic process    The chemical reactions and pathways involving steroids, compounds with a 1,2,cyclopentanoperhydrophenanthrene nucleus.
    GO:0016125    sterol metabolic process    The chemical reactions and pathways involving sterols, steroids with one or more hydroxyl groups and a hydrocarbon side-chain in the molecule.
    GO:0006805    xenobiotic metabolic process    The chemical reactions and pathways involving a xenobiotic compound, a compound foreign to living organisms. Used of chemical compounds, e.g. a xenobiotic chemical, such as a pesticide.
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:0016021    integral component of membrane    The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    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
        CP46A_HUMAN | Q9Y6A22q9f 2q9g 3mdm 3mdt 3mdv 4enh 4fia 4j14

(-) Related Entries Specified in the PDB File

2q9f CHOLESTEROL 3-SULFATE COMPLEX OF CYTOCHROME P450 46A1
2q9g APO FORM OF CYTOCHROME P450 46A1
3mdm
3mdt
3mdv