putA (PA0782, Q9I5F6) review notes

No deep-research API was available. These notes come from manual literature
research on 2026-11-05: the cached publications, a Europe PMC title search for
"putA AND Pseudomonas" (PubMed MCP and NCBI E-utilities returned server errors
that day), and the UniProt record.

Biology

PutA of P. aeruginosa PAO1 is a bifunctional proline dehydrogenase (PRODH) /
1-pyrroline-5-carboxylate dehydrogenase (P5CDH). The native enzyme was purified
from PAO1 and oxidises L-proline to glutamate in two steps PMID:6819140.
Kinetics: Km 45 mM for L-proline, 0.03 mM for NAD and 0.17 mM for NADP, so NAD+
is the preferred cosubstrate PMID:6819140. Single 119 kDa subunit,
native dimer/tetramer.
Domain architecture: P. aeruginosa PutA (1060 aa) has the PRODH and P5CDH
domains but lacks the N-terminal ribbon-helix-helix (RHH) DNA-binding domain of
the E. coli/Salmonella PutA PMID:29632523. The authors conclude PMID:29632523. My check of the N-terminal sequence (MFKASHVLQG...)
agrees: no RHH motif precedes the Pfam PF14850 domain at residues 74-187.
putA is activated by the AraC/XylS regulator PruR, which binds the putA
promoter; glutamate releases PruR PMID:29632523. PutA is required for virulence in a mouse acute
pneumonia model and for oxidative-stress tolerance (same paper).
Consequences for the IEA rows: GO:0003700 DNA-binding transcription factor
activity and GO:0006355 regulation of DNA-templated transcription (InterPro2GO
from IPR025703, the whole bifunctional-PutA family) are over-propagated from
RHH-containing enterobacterial PutAs. GO:0055129 L-proline biosynthetic process
(from IPR005933) is the reverse of this enzyme's physiological direction.
Membrane location: E. coli PutA associates with the inner membrane when
proline is high; PRODH reduces membrane quinone (EC 1.5.5.2). No direct
localization data exist for P. aeruginosa PutA, so the IBA/IEA
"cytoplasmic side of plasma membrane" rows are plausible but unverified.

PseudoCAP IBA-seed assessment

Other seeds read from .cache/paint/IBD.gaf (column 8) on 2026-11-05.

PTN node	node term	n_seeds	leaf IBAs	seed annotation (term, evidence, PMID)	verdict	rationale	other seeds	IBD stands without this seed?
PTN000193023	GO:0003842 L-glutamate gamma-semialdehyde dehydrogenase (NAD+) activity	5	62 (52 taxa)	GO:0003842, IDA, PMID:6819140 (PseudoCAP)	SOUND	Native PutA purified to >98% from PAO1 converts P5C to glutamate with NAD (Km 0.03 mM) or NADP; abstract states this outright.	E. coli PutA P09546, S. typhimurium PutA P10503, Q2FV67 (S. aureus RocA), yeast PUT2 SGD:S000001079	Yes

The node term (P5C/GSA dehydrogenase, NAD+) is shared by bifunctional PutAs and
monofunctional P5CDHs (RocA, Put2), so it suits the clade. No PSEUDOCAP or
GO_CENTRAL defect.

Observation outside this seed: the same node carries a GO:0009898 cytoplasmic
side of plasma membrane IBD seeded only by E. coli PutA (P09546), although yeast
PUT2 (a mitochondrial matrix enzyme) is a seed of sibling IBDs on this node.
Whether eukaryotic leaves inherit 9898 depends on NOT annotations lower in the
tree, which I did not check; flagged as a question, not a defect.

Action summary

ACCEPT: GO:0003842 (IDA, IBA, IEA), GO:0004657 (IDA, IEA), GO:0006562 (IBA, IEA).
KEEP_AS_NON_CORE: GO:0009898 (IBA, IEA). TOO_GENERAL: GO:0016491.
REMOVE: GO:0003700, GO:0006355, GO:0055129 (all IEA).
GO:0010133 (proline catabolic process to glutamate) is obsolete, so GO:0006562 is
the most specific BP available.