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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN CYTOCHROME P450 46A1 IN COMPLEX WITH CHOLESTEROL-3-SULPHATE
 
Authors :  M. A. White, N. V. Mast, E. F. Johnson, C. D. Stout, I. A. Pikuleva
Date :  12 Jun 07  (Deposition) - 17 Jun 08  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym./Biol. Unit :  A
Keywords :  Cyp46A1, P450 46A1, P450, Monooxygenase, Cholesterol Metabolic Enzyme, Oxidoreductase, Heme, Cholesterol-3-Sulphate (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  N. Mast, M. A. White, I. Bjorkhem, E. F. Johnson, C. D. Stout, I. A. Pikuleva
Crystal Structures Of Substrate-Bound And Substrate-Free Cytochrome P450 46A1, The Principal Cholesterol Hydroxylase In The Brain.
Proc. Natl. Acad. Sci. Usa V. 105 9546 2008
PubMed-ID: 18621681  |  Reference-DOI: 10.1073/PNAS.0803717105
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - CYTOCHROME P450 46A1
    ChainsA
    EC Number1.14.13.98
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPUC18
    Expression System StrainDH5ALPHA
    Expression System Vector TypePLASMID
    FragmentRESIDUES 51-500
    GeneCYP46A1, CYP46
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    SynonymCHOLESTEROL 24-HYDROXYLASE, CH24H

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 9)

Asymmetric/Biological Unit (4, 9)
No.NameCountTypeFull Name
1C3S1Ligand/IonCHOLEST-5-EN-3-YL HYDROGEN SULFATE
2GOL6Ligand/IonGLYCEROL
3HEM1Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
4PO41Ligand/IonPHOSPHATE ION

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:198 , MET A:199 , ARG A:261 , HOH A:786BINDING SITE FOR RESIDUE PO4 A 601
2AC2SOFTWARELYS A:104 , TYR A:109 , LEU A:125 , TRP A:134 , ARG A:138 , PHE A:299 , ALA A:302 , GLY A:303 , THR A:306 , SER A:307 , ALA A:367 , THR A:370 , PRO A:429 , PHE A:430 , SER A:431 , ARG A:435 , CYS A:437 , ILE A:438 , PHE A:442 , ALA A:443 , HOH A:712 , HOH A:715 , HOH A:732BINDING SITE FOR RESIDUE HEM A 602
3AC3SOFTWAREPHE A:80 , HIS A:81 , MET A:108 , TYR A:109 , ARG A:110 , ARG A:226 , ASN A:227 , ALA A:474BINDING SITE FOR RESIDUE C3S A 600
4AC4SOFTWARESER A:92 , LYS A:94 , LYS A:95 , ASP A:381 , HOH A:763BINDING SITE FOR RESIDUE GOL A 931
5AC5SOFTWARETRP A:67 , GLU A:334 , ARG A:349 , GLN A:351BINDING SITE FOR RESIDUE GOL A 932
6AC6SOFTWAREASN A:78 , PHE A:80 , LYS A:82 , THR A:83 , SER A:338 , LYS A:339BINDING SITE FOR RESIDUE GOL A 933
7AC7SOFTWAREPRO A:423 , PHE A:425 , HOH A:737BINDING SITE FOR RESIDUE GOL A 934
8AC8SOFTWAREMET A:183 , LEU A:204 , LYS A:209BINDING SITE FOR RESIDUE GOL A 935
9AC9SOFTWARELYS A:171 , SER A:179 , ASP A:182BINDING SITE FOR RESIDUE GOL A 936

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2Q9F)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2Q9F)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2Q9F)

(-) PROSITE Motifs  (1, 1)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2Q9F)

(-) Sequences/Alignments

Asymmetric/Biological 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:433
 aligned with CP46A_HUMAN | Q9Y6A2 from UniProtKB/Swiss-Prot  Length:500

    Alignment length:433
                                    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       408       418       428       438       448       458       468       478       488   
          CP46A_HUMAN    59 VLQDVFLDWAKKYGPVVRVNVFHKTSVIVTSPESVKKFLMSTKYNKDSKMYRALQTVFGERLFGQGLVSECNYERWHKQRRVIDLAFSRSSLVSLMETFNEKAEQLVEILEAKADGQTPVSMQDMLTYTAMDILAKAAFGMETSMLLGAQKPLSQAVKLMLEGITASRNTLAKFLPGKRKQLREVRESIRFLRQVGRDWVQRRREALKRGEEVPADILTQILKAEEGAQDDEGLLDNFVTFFIAGHETSANHLAFTVMELSRQPEIVARLQAEVDEVIGSKRYLDFEDLGRLQYLSQVLKESLRLYPPAWGTFRLLEEETLIDGVRVPGNTPLLFSTYVMGRMDTYFEDPLTFNPDRFGPGAPKPRFTYFPFSLGHRSCIGQQFAQMEVKVVMAKLLQRLEFRLVPGQRFGLQEQATLKPLDPVLCTLRPRGW 491
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains p450-2q9fA01 A:59-484                                                                                                                                                                                                                                                                                                                                                                                                                     ------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhh.eeee......eeee.hhhhhhhhhh......hhhhhhhhhee..ee..........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......eehhhhhhhhhhhhhhhhhhh...hhhhh.hhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhh.....eeeee...eee..eee...eeeeehhhhhhh...........hhhhhh..............hhhhh..hhhhhhhhhhhhhhhhhhheeeee.......eee...eee....eeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CYTOCHROME---------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2q9f A  59 VLQDVFLDWAKKYGPVVRVNVFHKTSVIVTSPESVKKFLMSTKYNKDSKMYRALQTVFGERLFGQGLVSECNYERWHKQRRVIDLAFSRSSLVSLMETFNEKAEQLVEILEAKADGQTPVSMQDMLTYTAMDILAKAAFGMETSMLLGAQKPLSQAVKLMLEGITASRNTLAKFLPGKRKQLREVRESIRFLRQVGRDWVQRRREALKRGEEVPADILTQILKAEEGAQDDEGLLDNFVTFFIAGHETSANHLAFTVMELSRQPEIVARLQAEVDEVIGSKRYLDFEDLGRLQYLSQVLKESLRLYPPAWGTFRLLEEETLIDGVRVPGNTPLLFSTYVMGRMDTYFEDPLTFNPDRFGPGAPKPRFTYFPFSLGHRSCIGQQFAQMEVKVVMAKLLQRLEFRLVPGQRFGLQEQATLKPLDPVLCTLRPRGW 491
                                    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       408       418       428       438       448       458       468       478       488   

   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 2Q9F)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2Q9F)

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit

(-) Gene Ontology  (23, 23)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (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 | Q9Y6A22q9g 3mdm 3mdr 3mdt 3mdv 4enh 4fia 4j14

(-) Related Entries Specified in the PDB File

2q9g