Msed_1423 (A4YGM9) notes

Metallosphaera sedula DSM 5348, unreviewed UniProt entry A4YGM9, "3-hydroxyacyl-CoA
dehydrogenase" (EC 1.1.1.35), 391 aa.

Automated deep research was unavailable for this review, so no -deep-research-*.md file
exists. Literature was found by a Europe PMC full-text search for "Msed_1423" (4 hits:
PMID:32218776, PMID:34290692, PMID:33472982, PMID:25939834) and by reading the cached
papers directly.

Domain architecture (UniProt)

• Pfam PF02737 3HCDH_N (NAD-binding Rossmann domain) at 3-177; two PF00725 3HCDH
  C-terminal domains at 183-277 and 298-388. No crotonase domain, unlike the bifunctional
  paralog Msed_0399. PANTHER PTHR48075:SF5 "3-hydroxybutyryl-CoA dehydrogenase"; FunFam
  "Fatty oxidation complex, alpha subunit". [file:METS5/Msed_1423/Msed_1423-uniprot.txt]

Biochemistry (Liu, Huber & Berg 2020)

• Recombinant His-tagged enzyme purified from E. coli. PMID:32218776
• Activity and substrate affinity: PMID:32218776
• Table 3 (Msed_1423, extrapolated to 75 °C): (S)-3-hydroxybutyryl-CoA Vmax 96 U/mg,
  Km 0.005 mM, kcat/Km 14,947; NAD Km 0.03 mM, kcat/Km 2,128; NADP Vmax 86 U/mg,
  Km 5.1 mM, kcat/Km 13. So NADP+ is a very poor cosubstrate: about 170-fold higher Km and
  160-fold lower efficiency. This justifies GO:0003857 (NAD+) over GO:0008691 (defined by
  GO with NADP+, EC 1.1.1.157).
• Substrate range: PMID:32218776 Stereospecificity versus (R)-3-hydroxybutyryl-CoA is not
  reported for Msed_1423 (the (R)-isomer test in Table 4 concerns the crotonases).
• Efficiency vs Msed_0399: PMID:32218776

Physiological role

• Gene context: PMID:32218776
• Distribution: PMID:32218776; absent only from S. acidocaldarius, which cannot grow autotrophically.
• Conclusion: PMID:32218776 Estimated 1.7% of cellular protein.
  The conclusion is inferential (kinetics, gene context, distribution, transcriptomics);
  no mutant exists.
• Restated in PMID:33472982.
• Thaumarchaeal comparison: Nmar_1028 is homologous (42% identity) but proposed to be
  recruited independently PMID:34290692
• PMID:25939834 (HhcR regulon, comparative genomics) mentions Msed_1423 in its full text
  per Europe PMC, but only the abstract is cached, so it is not cited in the review.

Annotation decisions

• GO:0003857 ACCEPT (core). GO:0016491, GO:0016616 MODIFY -> GO:0003857.
• GO:0070403 NAD+ binding KEEP_AS_NON_CORE (correct cofactor, unlike Msed_0709).
• GO:0006631 fatty acid metabolic process MARK_AS_OVER_ANNOTATED: InterPro2GO family
  transfer; enzyme inactive on C8, gene in the CO2-fixation cluster. (Msed_0399, which acts
  on C8 and clusters with beta-oxidation genes, keeps this term as non-core.)
• NEW GO:0015977 carbon fixation (IDA, PMID:32218776), with the proposed
  "carbon fixation by 3-hydroxypropionate/4-hydroxybutyrate cycle" child, as in the
  Msed_0709 and Msed_2001 reviews. GO:0043427 (Chloroflexus cycle) not used.
• The module hbdh step (GO:0003857, Msed_1423 main representative) is consistent with
  this review.