CYP46A1 (Cholesterol 24-hydroxylase) — review notes

UniProt: Q9Y6A2 (CP46A_HUMAN). HGNC:2641. Gene on chromosome 14q32.1.
Source of most quotes below: file:human/CYP46A1/CYP46A1-uniprot.txt and cached publications.

Identity and core function

• RecName: "Cholesterol 24-hydroxylase"; Short "CH24H"; EC 1.14.14.25. AltNames:
  Cholesterol 24-monooxygenase, Cholesterol 24S-hydroxylase, Cytochrome P450 46A1.
  [file:human/CYP46A1/CYP46A1-uniprot.txt "RecName: Full=Cholesterol 24-hydroxylase"]
• Member of the cytochrome P450 family (heme-thiolate monooxygenase).
  [file:human/CYP46A1/CYP46A1-uniprot.txt "Belongs to the cytochrome P450 family"]
• FUNCTION: "P450 monooxygenase that plays a major role in cholesterol homeostasis in
  the brain. Primarily catalyzes the hydroxylation (with S stereochemistry) at C-24 of
  cholesterol side chain, triggering cholesterol diffusion out of neurons and its
  further degradation" (PubMed:10377398, 14640697, 18621681, 25017465).
  [file:human/CYP46A1/CYP46A1-uniprot.txt "Primarily catalyzes the hydroxylation (with S"]
• Primary catalytic activity (RHEA:22716, EC 1.14.14.25): cholesterol + reduced
  [NADPH--hemoprotein reductase] + O2 = (24S)-hydroxycholesterol + oxidized reductase
• H2O + H(+). [file:human/CYP46A1/CYP46A1-uniprot.txt "(24S)-hydroxycholesterol + oxidized [NADPH--hemoprotein reductase]"]

Biological role: CNS cholesterol elimination

• CYP46A1 is the principal, rate-limiting route for eliminating cholesterol from the
  brain. 24S-hydroxycholesterol (24S-HC), unlike cholesterol, can cross membranes and
  the blood-brain barrier, is exported to plasma/liver and enters the bile-acid pathway.
  PMID:10377398
• The reaction is also the first step in enzymatic degradation of brain cholesterol.
  PMID:14640697
• Expressed predominantly in the brain; localized to neurons.
  PMID:10377398 and PMID:10377398
• 24S-HC is exported to the liver and converted to bile acids/salts; only a minor bile
  acid source but critical for disposing of excess brain cholesterol.
  [Reactome:R-HSA-193775 "24-hydroxycholesterol is synthesized in the brain, exported to
  the liver, and converted there to bile acids and bile salts. This pathway is only a
  minor source of bile acids and bile salts, but appears to be critical for the disposal
  of excess cholesterol from the brain"]

Cellular localization

• SUBCELLULAR LOCATION: "Endoplasmic reticulum membrane ... Single-pass membrane
  protein. Microsome membrane ... Postsynapse ... Presynapse ... Cell projection,
  dendrite." All by similarity to mouse ortholog Q9WVK8.
  [file:human/CYP46A1/CYP46A1-uniprot.txt "Endoplasmic reticulum membrane"]
• One N-terminal transmembrane helix (residues 3-23), consistent with single-pass ER
  membrane anchoring. Original cloning localized both mouse and human enzymes to the ER.
  PMID:10377398
• N.B. the synaptic (pre-/postsynapse) and dendrite locations are ISS transferred from
  the mouse ortholog (Q9WVK8), not directly demonstrated for the human protein.

Cofactor / structure

• Cofactor: heme (ChEBI:30413), experimentally established by crystallography
  (PubMed:18621681, 20667828, 23288837). Axial Fe ligand is Cys437 (heme-thiolate).
  [file:human/CYP46A1/CYP46A1-uniprot.txt "Name=heme; Xref=ChEBI:CHEBI:30413"]
• Multiple X-ray structures determined (2Q9F substrate-bound with cholesterol 3-sulfate;
  substrate-free 2Q9G; plus many drug/inhibitor co-complexes).
  PMID:18621681

Broad / secondary substrate specificity (in vitro; mostly non-core)

• Broad substrate specificity beyond cholesterol: further metabolizes
  24(S)-hydroxycholesterol to 24,25- and 24,27-dihydroxycholesterols; side-chain
  hydroxylation of 7alpha-hydroxycholesterol and cholestanol; ring hydroxylation of the
  C21-steroid hormones progesterone and testosterone; and xenobiotic metabolism.
  PMID:14640697
  PMID:14640697
• Progesterone metabolism (progesterone -> 17alpha-hydroxyprogesterone; underlies the
  GO:0004508 steroid 17-alpha-monooxygenase RHEA IEA and GO:0042448 progesterone
  metabolic process IDA). [file:human/CYP46A1/CYP46A1-uniprot.txt "Reaction=progesterone
• reduced [NADPH--hemoprotein reductase] + O2 ="]
• Testosterone hydroxylations at 6beta, 16beta, and 2-positions (underlie GO:0050649 and
  GO:0062184 RHEA/EXP). [file:human/CYP46A1/CYP46A1-uniprot.txt "16beta,17beta-dihydroxyandrost-4-en-3-one"]
• Oxidizes cholesterol precursors 7-dehydrocholesterol (to 24- and 25-hydroxy products)
  and desmosterol (epoxidation to (24S),25-epoxycholesterol and 27-hydroxylation);
  potentially relevant to Smith-Lemli-Opitz syndrome and desmosterolosis.
  PMID:25017465
  PMID:25017465
• Metabolizes 4beta-hydroxycholesterol (further 24S-hydroxylation). The cited paper
  PMID:12077124 is primarily about CYP3A4-derived 4beta-hydroxycholesterol turnover; the
  CYP46A1 4beta-OH-cholesterol activity is captured in the UniProt catalytic-activity
  block (RHEA:46392, ECO:0000269|PubMed:12077124).
  [file:human/CYP46A1/CYP46A1-uniprot.txt "Reaction=4beta-hydroxycholesterol + reduced"]
• Clotrimazole is a substrate (basis of GO:0006805 xenobiotic metabolic process IDA
  from PMID:20667828). PMID:20667828

Drug target / disease relevance (context; supports "non-core" framing of synaptic/LTP)

• CYP46A1 controls brain cholesterol turnover and is a drug target; several marketed
  drugs (voriconazole, tranylcypromine, etc.) inhibit it, and its structures underpin
  drug design. PMID:20667828
• Loss of Cyp46a1 in mice reduces cerebral cholesterol turnover and impairs learning /
  hippocampal LTP (basis of the ISS/IEA regulation-of-LTP annotation, transferred from
  the mouse ortholog). PMID:20667828

Review reasoning summary

• Core MF: cholesterol 24-hydroxylase activity (GO:0033781) — multiple EXP/IDA lines;
  the defining activity. heme binding (GO:0020037) and iron ion binding (GO:0005506) are
  core cofactor functions of this P450.
• Core BP: cholesterol catabolic process (GO:0006707) — IDA-supported "first step in
  cholesterol degradation in the brain".
• Core CC: endoplasmic reticulum membrane (GO:0005789) — single-pass ER membrane P450.
• steroid hydroxylase activity (GO:0008395, IDA) is a correct but broader parent of the
  physiological activity; retained but noted as a generalization.
• Promiscuous/in-vitro activities (testosterone 6beta/16beta-hydroxylase, steroid
  17-alpha-monooxygenase, progesterone/xenobiotic/C21-steroid processes) are real but
  non-core / over-annotations of a promiscuous P450 relative to its physiological role.
• Synaptic component (pre-/postsynapse, dendrite) and regulation-of-LTP annotations are
  ISS/IEA transferred from the mouse ortholog and kept as non-core.
• protein localization to membrane raft (GO:1903044, acts_upstream_of_negative_effect,
  ISS): indirect downstream effect of altered membrane cholesterol; kept as non-core.