PA1342 (AatJ, Q9I402) review notes

Review session 2026-11-05 (PseudoCAP IBA-seed protocol, tier 2)

Fetched with just fetch-gene PSEAE Q9I402 --alias PA1342 (no gene symbol in
UniProt; locus tag used as folder name, as for PA1340/PA1341). Accession Q9I402
matches the worklist (rank 326). Reviewed Swiss-Prot entry GASBP_PSEAE
(L-glutamate/L-aspartate-binding protein), 302 aa, signal peptide 1-23.
Reviewed with PA5082 (Q9HUA1), the other PseudoCAP seed of the same node, and
checked for consistency with the existing PA1340 and PA1341 reviews (permeases
of the same operon). No deep-research provider was used.

Identity

Periplasmic solute-binding protein, SBP_bac_3 family (Pfam PF00497); PANTHER
PTHR30085:SF2 "GLUTAMATE_ASPARTATE IMPORT SOLUTE-BINDING PROTEIN". Binding
protein of the PA1342-PA1339 AatJQMP ABC importer (orthologue of P. putida
AatJ, E. coli GltI).

Literature

Fernandez et al. 2019 (PMID:31627455; full text cached): purified PA1342 by
thermal shift and ITC. PMID:31627455 D-Glu is not among the
ligands reported.
He et al. 2014 (PMID:25082951; abstract only), the PseudoCAP seed paper:
PMID:25082951. The abstract does not say which aat gene
was mutated. As for PA1340, I defer to the curator who read the full text.
Singh and Rohm 2008 (PMID:18310026; abstract only), P. putida orthologue:
PMID:18310026
Johnson et al. 2008 (PMID:18833300; full text cached): PA1339-PA1341 mutants
defective for L-Glu use; PA1342 itself was not in that mutant set.

Assessment: AatJ is a Glu/Asp-specific binding protein (direct ITC), the
substrate-capture component of an L-Glu/L-Asp importer. Its D-Glu role is a
system-level genetic finding whose substrate basis is unclear (no D-Glu binding
reported), so D-amino acid transport is kept as non-core, matching PA1340.

Clade check (cached PAINT IBD/leaf GAF; QuickGO 2026-11-05)

PTN004739212 (GO:0006865 amino acid transport): 3 seeds, Q9I402 (this gene,
PseudoCAP IMP GO:0042940 PMID:25082951), Q9HUA1 (PA5082/DguC, same paper)
and E. coli GltI P37902. GltI has EcoCyc IDA for L-glutamate transmembrane
transport (GO:0015813, PMID:1091635, PMID:236016) and IPI for glutamate and
aspartate binding. 31 leaf IBAs in 14 taxa: GltI orthologues, GlnH
glutamine-binding proteins (B. subtilis, Synechocystis, M. tuberculosis,
Yersinia), cystine-binding and other SBP_bac_3 amino acid binding proteins
(yhdW, sll/slr proteins, Bradyrhizobium bll/blr), and a few eukaryotic or
actinobacterial SBP_bac_3 proteins (Thalassiosira, Ixodes, SCO2664 "sugar
binding protein"). Amino acid transport is a suitably broad term for an
SBP_bac_3 amino acid binding protein clade; SCO2664 is the only leaf whose
name suggests another ligand class, too little to fault the node.
The IBD stands on E. coli GltI alone, without either PAO1 seed.
Node-level judgement for this node is recorded here (the gene with the most
direct evidence, the ITC ligand profile); genes/PSEAE/PA5082/PA5082-notes.md
points here.

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?
PTN004739212	GO:0006865 amino acid transport	3	31 (14 taxa)	GO:0042940 D-amino acid transport, IMP, PMID:25082951 (PseudoCAP)	SOUND	The abstract states that the AatJMQP transporter is essential for D-Glu utilisation; that supports the general node term for its binding protein, and AatJ independently binds L-Glu/L-Asp (ITC, PMID:31627455). Which aat gene was mutated is not in the abstract, so the D-Glu row is deferred to the curator and kept non-core.	PA5082 Q9HUA1 (same paper); E. coli GltI P37902 (IDA L-glutamate transport, IPI Glu/Asp binding)	Yes. E. coli GltI alone grounds amino acid transport for this SBP_bac_3 amino acid binding protein clade. No GO_CENTRAL defect.

Defects filed: none.

Decisions summary

ACCEPT: outer membrane-bounded periplasmic space (IBA).
MODIFY: amino acid transport (IBA) -> L-glutamate import across plasma
membrane, L-aspartate import across plasma membrane.
TOO_GENERAL: periplasmic space (IEA).
KEEP_AS_NON_CORE: D-amino acid transport (IMP).
NEW: glutamate binding and aspartate binding (IDA, PMID:31627455).