PA5085 (Q9HU98) notes

Identity

PA5085 is dguR, the LysR-type regulator of the divergent dguR-dguABC D-glutamate/D-glutamine
utilization locus (Pseudomonas Genome Database: PA5084 dguA, PA5083 dguB, PA5082 dguC).
Domains (UniProt Q9HU98): LysR HTH (PROSITE PS50931, residues 17-74, HTH motif 34-53) and LysR
substrate-binding domain (Pfam PF03466). PANTHER PTHR30427.

PMID:25082951
PMID:25082951 —
direct sequence-specific DNA binding by the purified protein.
PMID:25082951 —
D-Glu is the co-inducer.
PMID:25082951 — DguR is required for D-Glu catabolism, but as
a regulator, not as a catalyst.
Abstract only in the cache; the abstract is detailed enough to support the DNA-binding and activator
claims.

GO:0043565 sequence-specific DNA binding (IDA PseudoCAP; IBA): ACCEPT.
GO:0003700 DNA-binding transcription factor activity (IEA InterPro): ACCEPT; core MF.
GO:0003677 DNA binding (IEA UniRule): MODIFY to GO:0043565.
GO:0006355 regulation of DNA-templated transcription (IEA): MODIFY to GO:0045893 positive regulation
of DNA-templated transcription (activator of dguABC).
GO:0010628 positive regulation of gene expression (IBA, PTN001576694, seeded by E. coli LysR P03030):
MODIFY to GO:0045893; correct direction, more specific term supported.
GO:0006351 DNA-templated transcription (IEA UniRule): MARK_AS_OVER_ANNOTATED; DguR regulates
transcription, it is not part of the transcription machinery.
Not proposed as NEW: D-glutamate catabolic process. DguR is required for it (growth phenotype) but
performs no catabolic step; DguA (PA5084) does. Per CLAUDE.md, necessity is not participation.

PTN node	node term	n_seeds	leaf IBAs	seed annotation (term, evidence, PMID)	verdict	rationale
PTN001576694	GO:0043565 sequence-specific DNA binding	1 (sole)	11 (7 taxa)	GO:0043565, IDA, PMID:25082951 (PseudoCAP)	SOUND	EMSA with purified His-DguR, including binding to a conserved 19 bp operator motif, is direct evidence. Sequence-specific DNA binding via the LysR HTH is a property of essentially every LysR-family regulator, so the term is safe for the clade (the operator sequence itself is not propagated).