PA5089 (pldB, Tle5b) review notes

UniProt: Q9HU94 (unreviewed, 745 aa), "PLD phosphodiesterase domain-containing
protein". Locus PA5089. The literature name is PldB (also Tle5b).

Identity and genomic context

PA5089 is pldB, and PA3487 is pldA: the two loci are distinct genes, both
phospholipase D-family T6SS effectors. The strain table of
PMID:31417515
gives the locus mapping explicitly, as does its
PAO1ΔrsmAΔpldAtli5a entry ["Deletion in rsmA, pldA-tli5a (PA3487-PA3488)"].
PldB is followed by three cognate immunity proteins, tli5b1-3 (PA5088-PA5086)
PMID:24832454.
Secretion requires VgrG5, and killing of competitors is lost without it
PMID:31417515. PMID:24832454 attributed delivery
to the H3-T6SS; PMID:31417515 re-assigns it to the H2-T6SS. This disagreement
concerns the secretion system, not the enzyme family.

Family and catalytic motif

UniProt Q9HU94 carries a PROSITE PLD phosphodiesterase domain (637-664) with
predicted active-site residues 642, 644 and 649, Pfam PF00614 (PLDc) and
InterPro IPR001736.
The Tle5 family is defined by the PLD HKD motif
PMID:23552891. Note that the enzymology in that paper is on Tle5PA =
PldA (His167/His855), not on PldB. Q9HU94 shows only one PROSITE-detected HKD;
no in vitro assay of purified PldB was found.

Literature search

Europe PMC searches on aeruginosa AND (PldA OR PldB) AND "phospholipase D",
aeruginosa AND PldB and aeruginosa AND PldA AND trans-kingdom (2026-11-05)
returned PMID:24832454, PMID:23552891, PMID:31417515, PMID:32356524 (immunity
protein structures) and PMID:36216841 (PldA structure); no paper reporting a
purified-PldB phospholipase assay was found.

PseudoCAP IBA-seed assessment

PTN node	node term	n_seeds	leaf IBAs	seed annotation (term, evidence, PMID)	verdict	rationale	other seeds	IBD stands without this seed?
PTN004499769	GO:0004630 D-type glycerophospholipase activity	24	713 (91 taxa)	GO:0004630, IMP, PMID:24832454 (PseudoCAP)	SOUND	The cited paper characterises PldB, which is this gene (PA5089), as a phospholipase D effector with antibacterial activity in the prey periplasm, and the protein carries the family's HKD motif. The evidence code is IMP, so the activity itself rests on the family assignment plus the toxicity phenotype rather than on an assay visible in the cached abstract; the claim is nevertheless the family-defining activity and the node term is at exactly that level.	Human PLD1 (Q13393), yeast SPO14 (SGD:S000001739), rat Pld1/Pld2 (RGD:3349, RGD:3350), mouse (MGI:109585, MGI:892877), ten Arabidopsis PLDs, zebrafish, Dictyostelium, PomBase SPAC2F7.16c, Candida, and PA3487/pldA	Yes - comfortably. The characterised eukaryotic PLDs alone place the activity at this node.

No GO_CENTRAL defect for the GO:0004630 IBD. One node-level observation is
recorded instead on the second IBD at the same node, GO:0009395 phospholipid
catabolic process (4 eukaryotic seeds, no PAO1 seed): propagating an endogenous
lipid-turnover process term to a secreted interbacterial toxin conflates the
roles. That is handled as MARK_AS_OVER_ANNOTATED on the leaf row with a
propagation_review, not as an upstream defect, because the node term is
defensible for the eukaryotic members that seeded it.

No PSEUDOCAP defect for this gene: the seed row cites the paper about this
locus. (Contrast genes/PSEAE/pldA, where the same PseudoCAP row was copied onto
PA3487 and cites this PldB paper instead of the PldA papers.)