Msed_1993 (A4YI81) — curation notes

Metallosphaera sedula DSM 5348. ARCHAEA project gene; grounds the malonic semialdehyde
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_1993" and "malonic semialdehyde reductase Metallosphaera"; NCBI E-utilities
was returning backend errors) and read from the cached publications. PMIDs 25548047
(Nitrosopumilus malonic semialdehyde reductase) and 20008169 (M. sedula transcriptomics)
were found but could not be cached (just fetch-pmid failed), so they are not cited.

Identity and activity

• UniProt TrEMBL entry, unreviewed; SubName "3-hydroxypropionate dehydrogenase (NADP(+))";
  BRENDA 1.1.1.298; family "3-hydroxyacyl-CoA dehydrogenase family" (ARBA); Pfam PF02737
  3HCDH_N + PF00725 3HCDH; PANTHER PTHR48075:SF1 "lambda-crystallin homolog".
• Native enzyme partially purified from autotrophic cells and identified by peptide mass
  fingerprinting: PMID:19684143
• Recombinant enzyme: PMID:19684143
  Specific activity 200 U/mg at 65 C; homotrimer:
  PMID:19684143
• Kinetics: PMID:19684143
• Cofactor: NADPH preferred, NADH partial: PMID:19684143
• Substrate specificity: PMID:19684143
• No metal requirement; not classifiable from sequence:
  PMID:19684143
• Summary sentence: PMID:19684143

Physiological role

• Activity in extracts is about five-fold higher in autotrophic cells:
  PMID:19684143
• NADPH preference argues for the reductive (anabolic) direction:
  PMID:19684143
• Gene neighbourhood: PMID:19684143
• In vivo function in a heterologous host: Msed_1993 was the "E3" enzyme in the
  three-enzyme module (with ACC/PCC and MCR) that let engineered Pyrococcus furiosus make
  3-hydroxypropionate from CO2. PMID:23530213
  PMID:23530213
• Not in the 2016 kinetic reconstruction (PMID:27771364), which started from 3-hydroxypropionate.

GO term choices

• GO:0035527 3-hydroxypropionate dehydrogenase (NADP+) activity — OLS definition:
  "3-hydroxypropanoate + NADP+ = 3-oxopropanoate + H+ + NADPH". 3-Oxopropanoate is malonate
  semialdehyde, so this is exactly the reaction (written in the oxidative direction, as GO
  does for reversible dehydrogenases). Ancestors: GO:0016616 -> GO:0016614 -> GO:0016491.
  So the module's MF term fits. The NAD+ sibling GO:0047565 describes the minor (20%) NADH
  activity and is not needed.
• GO:0050104 L-gulonate 3-dehydrogenase activity (TreeGrafter, PTN000592773): this is the
  lambda-crystallin/CRYL1 activity of the PANTHER subfamily name. No one has tested
  L-gulonate with Msed_1993; the protein's substrate is a C3 oxo acid, not a hexonate, and
  there is no glucuronate/uronate pathway context in this archaeon. Over-propagation from the
  family -> REMOVE.
• GO:0006631 fatty acid metabolic process (InterPro2GO from the 3HCDH signatures): the family
  mapping assumes 3-hydroxyacyl-CoA dehydrogenase in beta-oxidation. Msed_1993 acts on a free
  aldehyde, not an acyl-CoA, in CO2 fixation. Marked as over-annotation (same treatment as
  fatty acid beta-oxidation on the sibling Msed_2001).
• GO:0070403 NAD+ binding (IPR006176): the Rossmann domain binds the nicotinamide cofactor,
  but the physiological cofactor is NADPH; MODIFY to GO:0050661 NADP binding.
• GO:0016491 / GO:0016616: correct but general -> MODIFY to GO:0035527.
• NEW GO:0015977 carbon fixation (IDA, PMID:19684143), following the sibling reviews; GO:0043427
  (Chloroflexus cycle) not used. The proposed "carbon fixation by
  3-hydroxypropionate/4-hydroxybutyrate cycle" term is reused verbatim from Msed_0709.

Open questions

• Does Msed_1993 have any L-gulonate 3-dehydrogenase or 3-hydroxyacyl-CoA dehydrogenase
  activity (never tested)?
• Structural basis for the switch from acyl-CoA to free semialdehyde substrate in this
  3HCDH-family member.