Msed_0709 (A4YEN2, MCR_METS5) — curation notes

Metallosphaera sedula DSM 5348; malonyl-CoA/succinyl-CoA reductase (NADP+), EC 1.2.1.75
(also EC 1.2.1.76 activity). ARCHAEA project gene.

Provenance note: automated deep-research providers (falcon, openai) were unavailable
in this session (API authentication failures). No -deep-research-*.md file was created.
Literature research was done manually via NCBI E-utilities, the cached publications, and
UniProt REST. All PMIDs below were verified by E-utilities esummary and cached with
just fetch-pmid.

Identity and activity

• Partially purified from M. sedula; gene identified through the S. tokodaii ortholog.
  PMID:17041055
• Reaction: PMID:17041055
• Cofactor specificity: PMID:17041055
  (These kinetics are for the recombinant S. tokodaii enzyme.) No NAD binding/use is reported.
• Thiol/cysteine mechanism: PMID:17041055
• The enzyme is also the succinyl-CoA reductase of the cycle (promiscuous):
  PMID:19684143
  The succinyl-CoA reductase partially purified from autotrophic M. sedula was identified
  by peptide mass fingerprinting as Msed_0709:
  PMID:19684143
  PMID:19684143
  PMID:19684143
• Structure (S. tokodaii ortholog): homotetramer; NADP+ and CoA occupy the same bispecific
  site in succession. PMID:23325803
  PMID:23325803
  Covalent acyl-cysteine (thioester) intermediate by analogy with the ASD Cys-aspartyl adduct.

Pathway

• 3-hydroxypropionate/4-hydroxybutyrate (3HP/4HB) CO2-fixation cycle of autotrophic
  Sulfolobales. PMID:18079405
• MCR catalyses two reductive steps: malonyl-CoA -> malonate semialdehyde (first half) and
  succinyl-CoA -> succinate semialdehyde (second half, regenerating acetyl-CoA).
  PMID:23325803
• Heterologous use: Msed_0709 ("E2") was one of five M. sedula genes expressed in
  Pyrococcus furiosus to make 3-hydroxypropionate from CO2 + H2.
  PMID:23530213
• MCR is unrelated to the bifunctional Chloroflexus MCR (convergent evolution).
  PMID:17041055

Evolution: ASD paralog, not ASD

• PMID:17041055
• PMID:23325803
• PMID:23325803
• PMID:23325803
• PMID:19684143

Own check of the M. sedula ASD paralog (UniProt REST, 2026-10-15)

Query organism_id:399549 AND (ec:1.2.1.11 OR family:"aspartate-semialdehyde dehydrogenase")
returned two proteins: A4YEN2 (Msed_0709, this gene) and A4YHF3 (Msed_1700, unreviewed).
Msed_1700 neighbours are Msed_1698 threonine synthase and Msed_1699 aspartokinase, i.e. the
asd context described in PMID:23325803. So Msed_1700 is the genuine ASD of M. sedula.

Correction (2026-10-15, from the Msed_1700 review): an earlier version of these notes said
that Msed_1700 carries NCBIfam TIGR00978 (asd_EA) and PRK08664 and that A4YEN2 lacks them.
That was wrong: the A4YEN2 UniProt record (Msed_0709-uniprot.txt) also lists TIGR00978 and
NF006416 (PRK08664.1). The paralogs are separated by CDD models instead: Msed_1700 matches the
archaeal/fungal ASD models cd18130 and cd02315, Msed_0709 the MCR models cd23940 and cd24150
(genes/METS5/Msed_1700/Msed_1700-bioinformatics/RESULTS.md).

Both paralogs fall in PANTHER PTHR46718:SF1 and share identical InterPro signatures, so they
receive identical GO sets (ASD activity, threonine biosynthesis, NAD binding, NADP binding,
dimerization). Conversely, ARBA (ARBA00067001) names the true ASD Msed_1700 "malonyl CoA
reductase (malonate semialdehyde-forming), EC 1.2.1.75". The neofunctionalized paralog and
the ancestral enzyme are not separated by either pipeline — a paralog over-annotation in both
directions. (Not cited as a supporting_text source because it is a live database query.)

Annotation decisions (summary)

• GO:0004073 ASD activity (TreeGrafter) — REMOVE: paralog over-annotation; ASD role is
  Msed_1700's; substrate pocket remodelled around the missing ammonium group.
• GO:0009088 threonine biosynthesis (TreeGrafter) — REMOVE, same reason.
• GO:0008652 amino acid biosynthetic process (InterPro dimerization domain) — REMOVE.
• GO:0016620 aldehyde/oxo oxidoreductase, NAD(P) acceptor — ACCEPT (most specific existing
  term; GO has no term for EC 1.2.1.75 or EC 1.2.1.76 — checked ec2go and QuickGO search).
• GO:0050661 NADP binding — ACCEPT (NADPH-specific; NADP+ co-crystal structure of ortholog).
• GO:0051287 NAD binding — REMOVE: enzyme is NADPH-specific.
• GO:0046983 protein dimerization — KEEP_AS_NON_CORE (homotetramer).
• NEW GO:0015977 carbon fixation. GO:0043427 "carbon fixation by 3-hydroxypropionate cycle" is
  the Chloroflexus glyoxylate-forming cycle by definition, so it is not used; a 3HP/4HB-cycle
  term is proposed.
• Proposed new terms: malonyl-CoA reductase (NADP+) activity (EC 1.2.1.75, RHEA:26446);
  succinyl-CoA reductase (NADP+) activity (EC 1.2.1.76); carbon fixation by
  3-hydroxypropionate/4-hydroxybutyrate cycle.