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Crystal structure of human cytochrome P450 46A1 in complex with cholesterol-3-sulphate
Biology and Chemistry Report
2Q9F
  •   Structure Details   Hide

    Structure Keywords

    Keywords OXIDOREDUCTASE
    Text CYP46A1, P450 46A1, P450, MONOOXYGENASE, CHOLESTEROL METABOLIC ENZYME, OXIDOREDUCTASE, HEME, cholesterol-3-sulphate

    Polymeric Molecules

    Chain A
    Description Cytochrome P450 46A1 
    Fragment RESIDUES 51-500 
    Nonstandard Linkage no 
    Nonstandard Monomers no 
    Polymer Type polypeptide(L) 
    Formula Weight 52125.7 
    Source Method genetically manipulated  
    Entity Name Cholesterol 24-hydroxylase, CH24H 

    Ligands and Prosthetic Groups

    ID Name Chemical Formula Weight Ligand Structure
    C3S  CHOLEST-5-EN-3-YL HYDROGEN SULFATE  C27 H46 O4 S   466.72  View 
    GOL  GLYCEROL  C3 H8 O3   92.09  View 
    HEM  PROTOPORPHYRIN IX CONTAINING FE  C34 H32 Fe N4 O4   616.49  View 
    PO4  PHOSPHATE ION  O4 P   94.97  View 
     
  •   Protein Details   Hide

    UniProtKB Information

    Chain SWS/UNP ID SWS/UNP Accession(s)
    A CP46A_HUMAN B4DHP8     

    Keywords and Names

    Chain(s) RCSB Name UniProtKB Name UniProtKB Keywords

    EC, Associated Pathways and Catalytic Sites

    Chain(s) IUBMB KEGG BioCyc Catalytic Site(s)
    1.14.13.98        
    C: Cellular Location | F: Molecular Function | P: Biological Process
    Chain A
    GO ID   Ontology GO Term Definition
    6629   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. 
    8202   Steroid Metabolic Process  The Chemical Reactions and Pathways Involving Steroids Compounds with a 1 2 Cyclopentanoperhydrophenanthrene Nucleus. 
    8203   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. 
    55114   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. 
    5783   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). 
    5789   Endoplasmic Reticulum Membrane  The Lipid Bilayer Surrounding the Endoplasmic Reticulum. 
    16020   Membrane  Double Layer of Lipid Molecules That Encloses All Cells and in Eukaryotes Many Organelles; May Be a Single or Double Lipid Bilayer; Also Includes Associated Proteins. 
    16021   Integral Component of Membrane  The Component of a Membrane Consisting of Gene Products and Protein Complexes That Have Some Part That Penetrates At Least One Leaflet of the Membrane Bilayer. This Component Includes Gene Products That Are Buried in the Bilayer with No Exposure Outside the Bilayer. 
    31090   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. 
    43231   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. 
    4497   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. 
    16491   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. 
    46872   Metal Ion Binding  Interacting Selectively and Non Covalently with Any Metal Ion. 


     
  •   Gene Details   Hide

    Genetic Source

    Chain A
    Common Name Human
    Scientific Name Homo sapiens  
    Gene cyp46a1, cyp46
    Host Scientific Name Escherichia coli  
    Host Strain Dh5alpha
    Host Vector Type Plasmid
    Host Plasmid Name PUC18


    Genome Information

    Chromosome Locus Gene ID Gene Name Symbol
    14 14q32.1 10858     cytochrome P450, family 46, subfamily A, polypeptide 1 CYP46A1    

    Single Nucleotide Polymorphisms (from LS-SNP database)

    SNP ID LsSnp Link dbSNP Link Chain PDB position Amino acid changes Secondary structure Solvent Accessibility Chromosome Chromosome position Ligand
    rs75832974 LS-SNP   dbSNP   A 160 K - > E Helix 3% (Buried) 14 100173018
    rs74730047 LS-SNP   dbSNP   A 187 T - > P Helix 0% (Buried) 14 100173099
    rs148568536 LS-SNP   dbSNP   A 188 A - > T Helix 1% (Buried) 14 100173102
    rs142905408 LS-SNP   dbSNP   A 241 R - > Q Helix 49% (Exposed) 14 100182175
    rs151175005 LS-SNP   dbSNP   A 262 R - > Q Helix 36% (Exposed) 14 100182238
    rs78767954 LS-SNP   dbSNP   A 299 F - > S Helix 7% (Buried) 14 100182525 HEM
    rs200661407 LS-SNP   dbSNP   A 304 H - > Q Turn 2% (Buried) 14 100184395
    rs112687989 LS-SNP   dbSNP   A 323 E - > D Helix 73% (Exposed) 14 100184452
    rs146435738 LS-SNP   dbSNP   A 387 G - > S Bend 33% (Intermediate) 14 100188386
    rs201296209 LS-SNP   dbSNP   A 417 G - > R Bend 15% (Intermediate) 14 100191800
    rs200564104 LS-SNP   dbSNP   A 424 R - > W Coil 71% (Exposed) 14 100192531
    rs144915500 LS-SNP   dbSNP   A 445 M - > V Helix 9% (Buried) 14 100192894
    rs138751864 LS-SNP   dbSNP   A 459 E - > V Beta Ladder 38% (Exposed) 14 100192937
    rs148881618 LS-SNP   dbSNP   A 461 R - > W Beta Ladder 74% (Exposed) 14 100192942
    rs200877443 LS-SNP   dbSNP   A 482 V - > L Coil 1% (Buried) 14 100193005