COQ4 (YDR204W, UniProt O13525) – review notes

Function

• Cloned by complementation of a Q-deficient mutant; peripheral protein on the matrix face of the inner membrane PMID:11469793. At that time the function was unknown PMID:11469793.
• coq4 mutants make no Q and accumulate 3-hexaprenyl-4-hydroxybenzoate (HHB) PMID:9266513.
• Structural organizer of the CoQ synthome PMID:24406904.
• Catalytic role: COQ4 performs C1 decarboxylation + hydroxylation as a single oxidative decarboxylation PMID:38295803. Evidence is complementation of E. coli ubiD/ubiX-ubiH defects and activity in C. glutamicum; the abstract does not specify which COQ4 ortholog(s) were used.
• UniProt: EC 4.1.1.130 by similarity (HAMAP MF_03111); Zn2+ cofactor by similarity [UniProt:O13525 "Name=Zn(2+)"].

GO notes

• GO:0120539 (4-hydroxy-3-methoxy-5-polyprenylbenzoate decarboxylase) is the right MF; GO definition cites PMID:38295803. The companion GO:0120538 (2-methoxy-6-polyprenylphenol 4-hydroxylase, ferredoxin-dependent) is defined as a separate reaction; PomBase GO-CAM 662af8fa00000408 assigns GO:0120538 to coq6 whereas Pelosi et al. attribute both C1 reactions to COQ4.
• CC: extrinsic component of mitochondrial inner membrane (matrix side) is the most precise location; complex membership = GO:0110142 ubiquinone biosynthesis complex (definition explicitly includes COQ4).
• ND root MF from SGD is superseded by GO:0120539 IBA/IEA.

YeastPathways

• YeastPathways PWY3O-19 / PWY3O-862 have no gene for the decarboxylation (RXN3O-73) and assign C1 hydroxylation (RXN3O-12) to COQ6; COQ4 is absent from YeastCyc entirely (no COQ4 reactions in the summary file).

ND literature-search citations (2026-11-06)

• existing_annotations[0] GO:0003674 molecular_function (ND) not cited, flagged as possibly
  stale. These notes cite yeast literature that assigns Coq4 a role in this aspect: the yeast
  CoQ-synthome study PMID:24406904 (a structural/scaffolding role) and the oxidative-decarboxylase paper
  PMID:38295803, whose cached abstract does not say whether the yeast protein was among the
  COQ4 orthologs assayed. If either paper tested S. cerevisiae Coq4, the MF ND is stale; check
  the PMID:38295803 full text before re-actioning.

Audit to COMPLETE (2026-11-11)

• Deep research: no provider deep-research file is available (no API keys in this session); the review
  rests on UniProt O13525, the SGD description and the cached literature below.
• ND MF row resolved as STALE. The full text of Pelosi et al. 2024 (PMC7616408, re-fetched into the
  publications cache) shows the yeast protein itself was assayed: PMID:38295803
  and in C. glutamicum PMID:38295803. The activity is O2-dependent
  PMID:38295803. The ND row is therefore REMOVEd
  (nd_case STALE); the GO:0120539 IBA/EC rows carry the activity.
• GO:0120539 is defined as a non-oxidative decarboxylation (phenol product); the Pelosi data describe an
  oxidative decarboxylation to the C1-hydroxylated product. Kept GO:0120539 (closest term, used by the
  module and the human COQ4 review) and raised the gap as a suggested question.
• Zinc ion binding changed from KEEP_AS_NON_CORE to ACCEPT for consistency with human COQ4: the
  HDxxH(x)11E motif is conserved, and PMID:38295803.