clpX (E. coli K-12, P0A6H1) review notes

Deep research was unavailable for this review (no deep-research API keys in the
container), so no -deep-research-<provider>.md file exists. These notes were
compiled directly from the cached publications in publications/, the UniProt
record, and PubMed searches. The GONUTS wiki (gowiki.tamu.edu) was tried for the
CACAO papers (PMID:21317324, PMID:11278349) on 2026-10-29 but returned only a
"temporarily offline" maintenance page, so no student evidence text could be read.

Identity and activity

• ClpX is the AAA+ unfoldase / specificity subunit of the ClpXP protease. It was first
  purified as a lambda O-degrading activity together with ClpP
  PMID:8226769.
• Hexameric ring, stabilised by ATP; ClpP double heptamer docked by one or two ClpX rings
  PMID:9575205.
• ClpX binding increases ClpP peptidase activity (activator role)
  PMID:9575205.
• N-terminal C4 zinc-binding domain; Zn(II) required for oligomerisation, ClpP binding
  and proteolysis PMID:11278349.
• Mechanical unfolding: ATP consumption scales with substrate stability
  PMID:12941278;
  optical-trap observation of unfolding by ClpX alone and ClpXP
  PMID:21529717.
• Asymmetric hexamer structures, nucleotide-loadable/unloadable subunits
  [PMID:19914167; PMID:23622246; PMID:25866879].

Substrates and adaptors

• SsrA-tagged proteins degraded by ClpXP and ClpAP in vitro with purified components
  PMID:9573050.
• SspB adaptor docks via its disordered C-terminal peptide
  PMID:14536075.
• RseA(1-108) degradation releases sigma-E (extracytoplasmic stress)
  PMID:15371343.
• FtsZ is a substrate; ClpX N-domain recognises polymers PMID:19541655;
  genetic interplay with division mutants PMID:21317324.
• UvrA degraded by ClpXP after UV recovery PMID:19183285.

CACAO rows (assigned_by CACAO)

1. GO:0016887 ATP hydrolysis activity, IDA, PMID:11278349 — abstract states ClpX is an ATPase
   and dissects the single ATP site; ATPase assays presumably in full text (not cached). Term
   correct; ACCEPT.
2. GO:0004176 ATP-dependent peptidase activity, IDA, PMID:9573050 — in vitro reconstitution of
   SsrA-tagged substrate degradation by purified ClpX + ClpP + ATP. Activity of the ClpXP
   holoenzyme (ClpP holds the active sites); matches the paper; ACCEPT (complex-level activity).
3. GO:0043335 protein unfolding, IDA, PMID:21529717 — optical-trap single-molecule unfolding;
   exact match; ACCEPT.
4. GO:0051301 cell division, IGI with ftsZ, PMID:21317324 — clpX deletion suppresses ftsZ84
   filamentation and exacerbates delta-minC filamentation; the paper's own conclusion is that ClpXP
   modulates division by degrading FtsZ. Phenotype read as process: ClpX does not perform
   division, it tunes FtsZ levels. MODIFY to GO:0051302 regulation of cell division.
5. GO:0004176 ATP-dependent peptidase activity, IDA, PMID:8226769 — purification of the
   ATP-dependent lambda O-degrading ClpXP protease; matches; ACCEPT.

Other notable issues

• GO:0009376 HslUV protease complex (CAFA IDA, PMID:14536075; IBA PTN000137358 seeded only by
  P0A6H1 itself). ClpX is not a subunit of HslUV (HslU/HslV); the paper is about SspB-ClpXP
  delivery complexes. The correct complex is GO:0009368 endopeptidase Clp complex. Wrong-complex
  term — recorded as a source defect, MODIFY.