Msed_1424 (A4YGN0, SUCD_METS5) — curation notes

Metallosphaera sedula DSM 5348. ARCHAEA project gene.

Provenance note: automated deep research was unavailable in this session; no
-deep-research-*.md file was created. Literature was searched manually (NCBI E-utilities
esearch/esummary, cached publications). PMIDs cited here were cached with just fetch-pmid.

Bottom line: UniProt's name and EC are wrong

UniProt (Swiss-Prot, entry v101) names A4YGN0 "Succinate-semialdehyde dehydrogenase
(acetylating)", EC 1.2.1.76 (RHEA:26450, succinate semialdehyde + NADP+ + CoA = succinyl-CoA
+ NADPH), with ECO:0000269 citing Berg et al. 2007 (PMID:18079405). Its FUNCTION text reads
"Catalyzes the reduction of succinate semialdehyde to succinyl-CoA", which is chemically
incoherent (going from the aldehyde to the thioester is an oxidation).

The primary literature says something different. Msed_1424 is the succinic semialdehyde
reductase (SSR), which reduces succinate semialdehyde with NADPH to 4-hydroxybutyrate
(a Zn-dependent medium-chain alcohol dehydrogenase). The succinyl-CoA reductase step
(EC 1.2.1.76) belongs to Msed_0709, the promiscuous malonyl-CoA/succinyl-CoA reductase
(see genes/METS5/Msed_0709/). So the two genes do not conflict; UniProt has given Msed_1424
the EC of the step just upstream of the one it catalyses.

• PMID:19684143
• Native enzyme purified from autotrophic cells, identified by peptide mass fingerprinting:
  PMID:19684143
• Recombinant enzyme: PMID:19684143
  PMID:19684143
• Kinetics / cofactor: PMID:19684143
• Substrate specificity: PMID:19684143
• Homodimer: PMID:19684143
• The authors assign EC 1.1.1.2: PMID:19684143
• Rhea has the exact reaction (undirected master reaction, written oxidatively; the
  enzyme works in the reductive direction): RHEA:26381, 4-hydroxybutanoate + NADP(+) = succinate
  semialdehyde + NADPH + H(+) (EC 1.1.1.n11), with no GO cross-reference (Rhea REST query,
  2026-10-31). The NAD+ reaction RHEA:23948 maps to GO:0047577 4-hydroxybutyrate dehydrogenase
  activity, which is defined with NAD+ only.

Zinc

• UniProt family: zinc-containing alcohol dehydrogenase family (MDR); InterPro IPR002328
  ADH_Zn_CS (PROSITE PS00059), IPR013154/IPR013149 ADH N/C, PANTHER PTHR43350:SF2. It is not an
  aldehyde dehydrogenase (ALDH, PF00171) family protein, which is what a CoA-acylating
  EC 1.2.1.76 enzyme would usually be. The family is itself evidence against UniProt's name.
• Zinc was measured: PMID:19684143
• Both sites: PMID:19684143
  Catalytic site GHE (58-60) with Cys38/Cys165; structural CXCXXCXXXXXXXC (Cys89, 92, 95, 103).
  These match the UniProt BINDING features (38, 59, 165 catalytic; 89, 92, 95, 103 structural).
• EDTA did not inactivate; zinc is not EDTA-accessible, probably due to thermostability.

Pathway

• 3HP/4HB autotrophic CO2-fixation cycle, second half (succinyl-CoA -> 2 acetyl-CoA).
  PMID:18079405
• Autotrophic induction: PMID:19684143
• Gene neighbourhood: PMID:19684143
• Homologs: T. neutrophilus Tneu_0419 (DC/4HB cycle) is the SSR there.
  PMID:21169482
• Used as "SSR" in the in vitro cycle reconstruction:
  PMID:27771364

Where did EC 1.2.1.76 come from?

Unverified. UniProt cites Berg et al. 2007 (PMID:18079405), which predates the gene
identification in Kockelkorn & Fuchs 2009; only the abstract is cached, and I could not read the
Science supplement. Possibly the 2007 paper's supplement listed Msed_1424 as a candidate for
the succinyl-CoA/succinate semialdehyde step, and the Swiss-Prot entry (integrated 2011) was
not updated after PMID:19684143. Whatever the origin, the 2009 and 2011 papers identify the
protein by purification and recombinant expression as SSR, and the succinyl-CoA reductase as
Msed_0709.

Annotation decisions

• GO:0008270 zinc ion binding (IEA, IPR002328) — ACCEPT: 1.9 Zn/monomer measured; the
  catalytic and structural sites are conserved.
• GO:0016491 oxidoreductase activity (IEA) — MODIFY to GO:0008106 alcohol dehydrogenase
  (NADP+) activity (EC 1.1.1.2, the EC the authors assign; 4-hydroxybutanoate is a primary
  alcohol and succinate semialdehyde an aldehyde). No GO term exists for the exact reaction
  (RHEA:26381); a new term "succinate-semialdehyde reductase (NADPH) activity" is proposed.
• NOT proposed: "succinyl-CoA reductase (NADP+) activity" (the Msed_0709 proposed term). It
  is the wrong activity for this gene.
• NEW GO:0015977 carbon fixation (IDA, PMID:19684143), consistent with Msed_0709; the enzyme
  catalyses a cycle step.

Pattern for the catalogue

A UniProt/Swiss-Prot name and EC (and Rhea catalytic activity) assigned to the wrong step of a
pathway: Msed_1424 carries EC 1.2.1.76 (succinyl-CoA reductase) but is the downstream
succinate semialdehyde reductase. No GO row derives from it yet, but a Rhea-to-GO mapping for
RHEA:26450 (for example a new succinyl-CoA reductase term) would put the wrong activity on it.
The InterPro family (MDR zinc ADH) already contradicts the name.