nbdA (PA3311, Q9HYT3) review notes

Summary of the literature

NbdA ("NO-induced biofilm dispersion locus A") is a 783-aa inner-membrane protein
with an N-terminal MHYT domain (seven predicted TM helices), a degenerate GGDEF
domain (AGDEF) and an EAL domain.

Li et al. 2013 (PMID:23729646; cached abstract only, full text not read; the PMC
page could not be retrieved). nbdA inactivation impairs NO-induced but not
glutamate-induced dispersion PMID:23729646. NO raises PDE activity and lowers
c-di-GMP in nbdA-expressing biofilms, but not in the deletion strain
PMID:23729646. This is mainly through transcriptional induction by NO. A
recombinant protein lacking the MHYT domain is an active PDE PMID:23729646. UniProt adds
that the protein has no DGC activity and is stimulated by GTP.
NbdA, together with DipA and RbdA, inhibits flagellar motor switching through
MapZ PMID:31350333.
Kulesekara et al. 2006 (PMID:16477007; full text read on PMC, see rocR-notes.md):
a PA3311 insertion formed a pellicle (hyperbiofilm), and the lysate PDE assay gave
no detectable activity for PA3311 ("PA3311 AGDEF EAL — —"). The authors note that
activity was not detected for any GGDEF-EAL hybrid in that assay. This does not
contradict the later purified-protein result.

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?
PTN002105365	GO:0071111 cyclic-guanylate-specific phosphodiesterase activity	18	162 (24 taxa)	GO:0071111, IDA, PMID:23729646 (PseudoCAP)	SOUND	The abstract states outright that recombinant NbdA lacking the MHYT domain is an active PDE, and UniProt curators cite the same paper for EC 3.1.4.52. Full text not read; the decisive fact is stated in the abstract.	E. coli PdeA/B/C/F/H/I/K/L/N, DosP; Mtb P9WM13; P. aeruginosa bifA, rocR, PA2133, PA2200, PA2567, PA3825	Yes. Node-level defects are recorded once in rocR-ai-review.yaml.

nbdA is not a seed of PTN009140332 but inherits GO:1900190; NbdA's own data (NO-induced
dispersion) fit that regulation term.

Annotation decisions

GO:0071111 (IBA, IEA, IDA): ACCEPT; core function.
GO:0005886 (IBA, IEA): ACCEPT; MHYT domain with seven TM helices.
GO:1900190 IBA: ACCEPT; regulates biofilm dispersal in response to NO. GO has no
biofilm-dispersal term.
GO:0071732 cellular response to nitric oxide (IMP, IEA): ACCEPT. nbdA is induced
by NO and required for the NO dispersal response.