Msed_1426 (A4YGN2, ACAR_METS5) — curation notes

Metallosphaera sedula DSM 5348. ARCHAEA project gene; grounds the acryloyl-CoA reductase
step of modules/hydroxypropionate_hydroxybutyrate_cycle.yaml.

Provenance note: automated deep research was unavailable in this session; no
-deep-research-*.md file was created. Literature was searched manually (Europe PMC REST
search for "Msed_1426" and "acryloyl-CoA reductase Sulfolobales"; NCBI E-utilities was
returning backend errors) and read from cached full texts. PMIDs 20008169 (transcriptomics)
and 40192334 (Pyrococcus 1-propanol engineering) were found but could not be cached
(just fetch-pmid failed), so they are not cited.

Identity and evidence

• Swiss-Prot, EC 1.3.1.84, RHEA:26454 (propanoyl-CoA + NADP+ = acryloyl-CoA + NADPH + H+).
  Zinc-containing alcohol dehydrogenase (MDR) family; InterPro IPR053496
  Acryloyl-CoA_Reductase_Zn-ADH; NCBIfam NF041172 AcrlCoa_red_Thmprot; PANTHER PTHR42940:SF8.
• Native enzyme enriched >200-fold from autotrophic M. sedula; the 40 kDa band was first
  matched to S. tokodaii ST0480 and, when the genome appeared, to Msed_1426:
  PMID:19429610
• Recombinant work in PMID:19429610 used the S. tokodaii ortholog (ST0480, Q975C8):
  PMID:19429610
  So kinetics, cofactor specificity, monomer state and zinc content are from ST0480; UniProt
  marks these as ECO:0000250 from Q975C8. The activity of the native M. sedula enzyme is direct
  (Msed_1426-containing fraction).
• Recombinant M. sedula Msed_1426 was later obtained by co-expression with Msed_1424
  and assayed: PMID:27771364
  PMID:27771364
• Reaction: PMID:19429610
• Cofactor specificity: no NADH activity:
  PMID:19429610
  PMID:19429610
  Not acting on crotonyl-CoA matters physiologically (crotonyl-CoA is an intermediate of the
  second half of the cycle).
• Zinc: PMID:19429610
  Catalytic GHE motif with Cys38/Cys146; structural site with Asp90 replacing the first Cys:
  PMID:19429610

Role in the 3HP/4HB cycle

• Autotrophic up-regulation: PMID:19429610
• PMID:19429610
• Three separate enzymes (HPCS Msed_1456, HPCD Msed_2001, ACR Msed_1426) replace the
  trifunctional Chloroflexus propionyl-CoA synthase, so the archaeal and Chloroflexus cycles
  evolved independently:
  PMID:19429610
• Kinetic model of the cycle uses Msed_1426 as acr:
  PMID:27771364

GO term choices

• GO:0043957 acryloyl-CoA reductase (NADPH) activity (EXP and IEA from RHEA:26454): ACCEPT;
  the definition (acryloyl-CoA + NADPH + H+ = propionyl-CoA + NADP+) is exactly the reaction.
  The module's MF term therefore fits.
• GO:0043958 acryloyl-CoA reductase (NADH) activity, IDA from PMID:19429610: the paper
  (full text cached and read) explicitly says the enzyme does not use NADH. Since the
  acryloyl-CoA reductase part is right and only the cofactor is wrong, MODIFY laterally to
  GO:0043957 rather than REMOVE. Likely a term-selection slip by the annotator (the NADH term
  is for the Clostridium propionicum fermentation enzyme, which the same paper says is
  unrelated).
• GO:0004022 alcohol dehydrogenase (NAD+) activity (TreeGrafter, PTN000191633): REMOVE. This
  is the ancestral MDR/zinc ADH activity. Msed_1426 reduces a C=C bond of an enoyl-CoA
  (EC 1.3.1), not a CH-OH group, and does not use NAD(H). Zinc-ADH-family over-annotation.
• GO:0008270 zinc ion binding: ACCEPT (Zn measured in the ortholog; ligands conserved).
• GO:0005737 cytoplasm: ACCEPT (soluble enzyme of a cytosolic pathway; no TM/signal).
• GO:0016491 oxidoreductase activity: MODIFY to GO:0043957.
• NEW GO:0015977 carbon fixation (IDA, PMID:19429610); proposed 3HP/4HB cycle term reused
  verbatim from Msed_0709. GO:0043427 (Chloroflexus cycle) not used.