psmA1 (HVO_1091, Q9V2V6) — Haloferax volcanii DS2 — review notes

Automated deep research was unavailable for this gene; these notes were compiled
manually from PubMed (NCBI E-utilities searches for "Haloferax volcanii proteasome"),
the cached publications in publications/, and the UniProt record
(psmA1-uniprot.txt). No -deep-research-*.md file was generated.

Identity

• Proteasome subunit alpha 1 (alpha1, PsmA1), 252 aa, peptidase T1A family
  (non-catalytic alpha-type subunit). InterPro IPR019982 (Proteasome alpha subunit,
  archaeal family), IPR000426 (Proteasome alpha-subunit N-terminal domain), IPR023332
  (Proteasome alpha-type). [file:HALVD/psmA1/psmA1-uniprot.txt "Belongs to the peptidase T1A family"]
• H. volcanii encodes two alpha-type subunits (alpha1 = psmA, alpha2 = psmC) and one
  beta (psmB), plus two PAN AAA+ ATPases (panA, panB).

Structure and assembly (the core of what alpha1 does)

• First purification: alpha1 + beta form a 600-kDa four-ring barrel
  PMID:10482525.
• Catalysis lies in beta: PMID:10482525 — this is the beta subunit; alpha1 has no N-terminal Thr nucleophile (UniProt has no active-site feature on alpha1).
• Activity of the alpha1-beta particle: chymotrypsin-like peptide hydrolysis, insulin
  B-chain hydrolysis, salt-dependent PMID:10482525.
• Two CP subtypes in vivo: alpha1-beta (symmetric) and alpha1-alpha2-beta (asymmetric,
  homo-oligomeric alpha rings at opposite ends)
  PMID:12486053;
  PMID:12486053.
• Cross-linking/MS modelling: PMID:22623373.
• The alpha1 N terminus forms the CP "gate"; deleting it raises CP peptidase activity
  [PMID:19376868 "unregulated opening of the CP \"gate\" impairs the ability of cells to overcome salt stress"].

Post-translational modifications of alpha1 (PTMs OF the subunit, not functions of it)

• N-terminal acetylation PMID:16950923;
  Met1-acetylated form dominant PMID:19376868.
• Phosphorylation at Ser/Thr, growth-phase dependent; Rio1p kinase homolog (HVO_0135)
  phosphorylates alpha1 in vitro PMID:20671954.
• SAMPylation: the task brief notes alpha1 is SAMPylated. I could not verify that
  alpha1 is itself a SAMP conjugate from the cached text of PMID:20054389 (Table 1, the
  conjugate list, is not in the cached text). Not used in the review.
• None of these PTM papers are cited in GOA for alpha1, and none would justify a GO
  annotation of alpha1's own function (they are annotations about alpha1 as a substrate).

Physiology / genetics

• Knockouts PMID:18931121;
  PMID:18931121;
  psmA deletion sensitizes to hypo-osmotic stress, organic N, L-canavanine, heat. Pleiotropic
  phenotypes — not used for NEW process terms.
• In vivo proteasome-dependent proteolysis of short-lived GFP reporters PMID:15574956.
• SAMP link (indirect): PMID:20054389
  Suggestive only; whether SAMP conjugation actually targets substrates to the PAN-20S
  proteasome (a "modification-dependent protein catabolic process") remains
  unestablished. H. volcanii has no ubiquitin.

GO term checks (QuickGO, 2026-10-15)

• GO:0019773 proteasome core complex, alpha-subunit complex: "The proteasome core
  subcomplex that constitutes the two outer rings of the proteasome core complex." No
  taxon constraint; the Mus musculus mention is only an example. Applies to archaea.
• GO:0006511 ubiquitin-dependent protein catabolic process: defined as initiated by
  covalent attachment of ubiquitin. Not applicable (no ubiquitin in H. volcanii).
  QuickGO: 910 archaeal GO:0006511 rows, 888 of them via InterPro:IPR000426 (alpha
  N-terminal domain) InterPro2GO mapping.
• GO:0004298 threonine-type endopeptidase activity: 786 archaeal rows via IPR019982,
  an alpha-subunit-specific entry; alpha subunits have no catalytic Thr1. These
  "enables" catalytic-activity rows are a systematic InterPro2GO error for alpha subunits.
• GO:0140756 structural constituent of proteasome — what alpha1 enables (used for the
  human PSMA1 review in this repo as well).

Calibration verdict

• 6 IDA rows from 2 papers (1999, 2003), both from the Maupin-Furlow lab and both
  biochemical characterizations of purified CPs. Coverage of the complex and the process
  is right; the MF is assigned with "enables" to a catalytic activity that belongs to
  beta. Nothing captures the structural role, gate function or the 2008 genetics.
• IEA layer adds two eukaryote/catalysis-biased errors (ubiquitin-dependent, threonine-type
  endopeptidase).