Msed_0656 (A4YEH9) notes

Automated deep research was unavailable for this review. These notes come from my own
reading of the cached full texts (PMID:24532060, PMID:21169482, PMID:32218776), the
UniProt record and the GO term definitions in OLS. No -deep-research-*.md file was
created.

Identity

• 395 aa, unreviewed TrEMBL entry, named "Acetyl-CoA acetyltransferase" (EC 2.3.1.9).
• Thiolase family (Pfam Thiolase_N PF00108 and Thiolase_C PF02803, PROSITE PS00737
  THIOLASE_2, NCBIfam TIGR01930 AcCoA-C-Actrans, CDD cd00751). PANTHER PTHR18919:SF107.
• UniProt keywords from ARBA: Acyltransferase, Isoprene biosynthesis. UniProt also
  carries an ARBA lipid metabolic process (GO:0006629) line that is not in the GOA file.
• M. sedula has several thiolase homologs (Msed_1647, Msed_1290, Msed_0396, Msed_0386,
  Msed_0271, Msed_0270) [PMID:32218776 table 1]. Msed_0386 and Msed_0396 sit in a
  crotonase/dehydrogenase gene cluster PMID:32218776.

Identification (Ramos-Vera et al. 2011, PMID:21169482)

• Msed_0656 was assigned by similarity to the bacterial enzyme and by co-regulation, and
  the experiment was done on the Thermoproteus ortholog PMID:21169482. PMID:21169482 That sentence refers to Tneu_0249.
• PMID:21169482

Biochemistry (Hawkins et al. 2014, PMID:24532060)

• Recombinant His-tagged Msed_0656 was produced aerobically in E. coli and assayed by the
  substrate-dependent loss of CoA (DTNB) at 70 C PMID:24532060
• Km for acetoacetyl-CoA PMID:24532060. It is
  the fastest enzyme of the branch PMID:24532060.
• It is one of the four enzymes used to reconstitute 4HB to acetyl-CoA in vitro
  PMID:24532060.
• Liu et al. 2020 call it the characterized beta-ketothiolase, and note that a paralog
  (Msed_0386) may also contribute PMID:32218776.

Assessment

• GO:0003985 acetyl-CoA C-acetyltransferase activity (2 acetyl-CoA = CoA +
  acetoacetyl-CoA; OLS-verified) is the core MF. It is supported experimentally for
  Msed_0656 itself (PMID:24532060), and the IEA row is accepted. The direct evidence is
  for the thiolytic direction, which is the physiological direction in the cycle.
• GO:0016746 and GO:0016747 are ancestors of GO:0003985 (OLS). They are correct but
  general, so both rows are MODIFIED to GO:0003985.
• Process: NEW GO:0015977 carbon fixation. It catalyses the last step of the cycle,
  which regenerates the acetyl-CoA acceptor.
• Open question: archaea make isoprenoids by the mevalonate pathway, which starts from
  acetoacetyl-CoA. Msed_0656, or a paralog, may also supply acetoacetyl-CoA for
  isoprenoid synthesis, as the ARBA keyword hints, but no evidence for this was found.