MMACHC (Q9Y4U1) review notes

Human MMACHC = "Cyanocobalamin reductase / alkylcobalamin dealkylase" (a.k.a. CblC).
Cytosolic vitamin-B12 (cobalamin) processing chaperone/enzyme. HGNC:24525, chr1.
282 aa. Belongs to the MMACHC family; a divergent member of the NADPH-dependent flavin
reductase / nitroreductase fold family.

Core biology (well established, multiple structural + biochemical papers)

MMACHC performs the FIRST intracellular tailoring step on incoming (dietary/circulating)
cobalamin, removing the upper axial (beta) ligand of cob(III)alamin to generate a common
cob(II)alamin intermediate that is then partitioned to the two downstream B12 enzymes:
- methylcobalamin (MeCbl) -> methionine synthase (MTR) cytosolic remethylation arm
- 5'-deoxyadenosylcobalamin (AdoCbl) -> methylmalonyl-CoA mutase (MMUT) mitochondrial arm

Two distinct chemistries on the same scaffold:
1. Reductive decyanation of cyanocobalamin (CNCbl, the dietary/supplement form):
base-off, FAD/FMN + NADPH-dependent reductive cleavage of the Co-CN bond -> cob(II)alamin
+ cyanide. EC 1.16.1.6; GO:0033787 cyanocobalamin reductase (cyanide-eliminating) (NADP+).
PMID:18779575
PMID:19700356
2. Glutathione-dependent dealkylation of alkylcobalamins (MeCbl, AdoCbl): thiolate of
GSH performs nucleophilic displacement of the alkyl group -> cob(I)alamin + S-alkyl-glutathione.
EC 2.5.1.151 (alkylcobalamin:glutathione S-alkyltransferase). GOA maps this to GO:0016765
(transferase, alkyl/aryl other than methyl). There is NO dedicated GO MF for EC 2.5.1.151.
[PMID:19801555 "catalyzes an entirely different chemical reaction with alkylcobalamins using
the thiolate of glutathione for nucleophilic displacement to generate cob(I)alamin and the
corresponding glutathione thioether"; "Biologically relevant thiols, e.g. cysteine and
homocysteine, cannot substitute for glutathione"]
PMID:21697092

Structure / mechanism

• Nitroreductase-like scaffold; uses FMN or FAD as prosthetic group. PMID:21697092
• Binds Cbl "base-off" (dimethylbenzimidazole displaced). PMID:19700356
• Arginine-rich pocket binds GSH; domain-swapped homodimer (PNRRP loop exchange) triggered by
  FMN or AdoCbl binding; monomer without substrate. [PMID:22642810 "identified an arginine-rich
  pocket close to the Cbl binding site responsible for GSH binding and dealkylation activity";
  "two Cbl-binding monomers dimerize to mediate the reciprocal exchange of a conserved 'PNRRP'
  loop"; "dimerization is triggered upon binding its substrate adenosyl-Cbl or cofactor FMN"]

Interactions

• MMADHC/CblD: heterodimer, partitions cofactor between MeCbl and AdoCbl routes.
  PMID:23415655
• MTR (methionine synthase, Q99707) and MTRR: multiprotein cytosolic Cbl-processing complex.
  PMID:27771510
  PMID:23825108
• Lysosomal exporters LMBD1 (LMBRD1, Q9NUN5) and ABCD4 (O14678): deliver Cbl from lysosome to
  cytosolic MMACHC. PMID:25535791
• HuRI/BioPlex proteome-scale two-hybrid: CCT6B (Q92526) PMID:33961781. Non-functional
  scaffolding/chaperonin contact from high-throughput interactome; not a core function.

Subcellular location

• Cytosolic. PMID:23270877. HPA reports a nucleoplasm IDA (GO:0005654) — likely antibody/localization
  signal but not supported by the well-established cytosolic biology; keep as non-core.

Disease

cblC disease (MAHCC, MIM:277400): most common inborn error of intracellular cobalamin metabolism.
Combined methylmalonic aciduria AND homocystinuria because BOTH the AdoCbl (MMUT) and MeCbl (MTR)
arms lose cofactor. PMID:18779575 PMID:19700356. Pathogenic mutations (e.g. R161Q/G, G147D) impair
Cbl binding, stability, decyanation and/or dealkylation. PMID:25809485

Curation reasoning summary

• CORE MF: GO:0033787 cyanocobalamin reductase (EXP/IDA, well supported) + GO:0016765 alkyl
  transferase (the GSH dealkylase, EXP) + GO:0031419 cobalamin binding (substrate binding; in
  UniProt DR but NOT in GOA) + GO:0071949 FAD binding (cofactor) + GO:0043295 glutathione binding.
• CORE BP: GO:0009235 cobalamin metabolic process. CORE CC: GO:0005829 cytosol.
• GO:0032451 demethylase activity / GO:0070988 demethylation: these are GO's mapping of the
  MeCbl dealkylation. Strictly MMACHC removes a methyl group FROM cobalamin (an S-alkyltransfer
  to glutathione), not classic substrate demethylation. The essence (removes methyl group) is
  sound but the terms are the wrong flavor; the alkyltransferase term (GO:0016765) is more
  accurate. Marking demethylase/demethylation as over-annotated (essence right, term imprecise).
• GO:0016491 oxidoreductase activity: correct but general parent of the reductase; keep as
  non-core (the specific GO:0033787 is the informative term).
• protein binding IPIs: MARK_AS_OVER_ANNOTATED per policy (uninformative; specific complex
  partners captured better). Do NOT REMOVE (experimental IPIs).
• Reactome TAS cytosol block (many R-HSA rows) + cobalamin metabolic process TAS: accept as
  location/process; keep cytosol duplicates as non-core to avoid redundancy inflation.

DR status

Falcon deep-research file (MMACHC-deep-research-falcon.md) not present within the 8-min poll
window; review grounded in UniProt (Q9Y4U1), seeded GOA, cached PMID abstracts, and the dismech
disorder KB. No -deep-research-*.md fabricated.