PA3825 is a 526-aa inner-membrane c-di-GMP phosphodiesterase of Pseudomonas aeruginosa. Two predicted transmembrane helices flank a CSS-motif domain, which is probably periplasmic, and a C-terminal cytoplasmic EAL domain carries the variant EVL signature with an intact catalytic loop. The purified EAL domain hydrolyses c-di-GMP to pGpG in the presence of Mn2+, and crystal structures with substrate and product show a dimeric active site with a third metal-binding site next to the 5'-phosphate. Lysates of cells overexpressing PA3825 also degrade added c-di-GMP. Deleting the gene increases early surface attachment and biofilm biomass but leaves swimming, swarming and twitching unchanged, so PA3825 restrains biofilm formation by lowering c-di-GMP. The signal sensed by its periplasmic domain is unknown.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0005886 plasma membrane | IBA GO_REF:0000033 | ACCEPT | Summary: PM IBD at PTN002105365. PA3825 has two predicted TM helices, like the membrane-anchored E. coli seeds. Reason: Consistent with the predicted topology, and the protein is recovered in the membrane proteome. Node-level defects of PTN002105365 (degenerate EAL leaves; PM term on soluble members) are recorded once in the rocR review and not repeated here. Supporting Evidence: file:PSEAE/PA3825/PA3825-uniprot.txt FT TRANSMEM 12..35 FT /note="Helical" FT /evidence="ECO:0000256|SAM:Phobius" |
| GO:0005886 plasma membrane | IEA GO_REF:0000044 | ACCEPT | Summary: SubCell mapping (Cell membrane; multi-pass). The UniProt statement is ARBA-derived, but the two Phobius TM helices support it independently. Reason: Same claim as the IBA row and consistent with the topology. Supporting Evidence: file:PSEAE/PA3825/PA3825-uniprot.txt FT TRANSMEM 12..35 FT /note="Helical" FT /evidence="ECO:0000256|SAM:Phobius" |
| GO:0071111 cyclic-guanylate-specific phosphodiesterase activity | IBA GO_REF:0000033 | ACCEPT | Summary: IBA from the 18-seed PTN002105365 IBD. PA3825 appears among its own sources because of its own IDA row, which is expected. Reason: Correct; the purified EAL domain is an active c-di-GMP PDE. Node-level defects of PTN002105365 (degenerate EAL leaves; PM term on soluble members) are recorded once in the rocR review and not repeated here. Supporting Evidence: PMID:28186120 In vitro PA3825EAL was able to convert c-di-GMP to pGpG, with a kcat of 0.35 ± 0.1 s−1, in the presence of Mn2+ |
| GO:0071111 cyclic-guanylate-specific phosphodiesterase activity | IDA PMID:16477007 Analysis of Pseudomonas aeruginosa diguanylate cyclases and ... | ACCEPT | Summary: PseudoCAP IDA and PA3825 seeding of PTN002105365. Lysates of a PA3825-overexpressing strain degraded 27% of added c-di-GMP (Table 1, full text read on PMC). Reason: Seed verdict SOUND. The lysate assay is crude and the activity weak, but it is direct, and purified-domain kinetics and substrate-bound structures (PMID:28186120) confirm it. Supporting Evidence: file:PSEAE/PA3825/PA3825-notes.md PA3343 GGEEF +(22) PA3702 GGEEF +(445) PA3825 EVL +(27) PMID:28186120 In vitro PA3825EAL was able to convert c-di-GMP to pGpG, with a kcat of 0.35 ± 0.1 s−1, in the presence of Mn2+ |
| GO:0071111 cyclic-guanylate-specific phosphodiesterase activity | IEA GO_REF:0000003 | ACCEPT | Summary: EC 3.1.4.52 mapping; consistent with purified-domain kinetics. Reason: Correct core activity. Supporting Evidence: PMID:28186120 In vitro PA3825EAL was able to convert c-di-GMP to pGpG, with a kcat of 0.35 ± 0.1 s−1, in the presence of Mn2+ |
| GO:1900190 regulation of single-species biofilm formation | IBA GO_REF:0000033 | ACCEPT | Summary: IBA from the 4-seed PTN009140332 IBD (bifA, PA2133, E. coli PdeF, arr). PA3825 is not a seed. Its deletion increases attachment and biofilm biomass. Reason: The IBD stands on bifA (see the bifA notes), and PA3825 has its own supporting phenotype. The deletion data show negative regulation, which the general term covers. Supporting Evidence: PMID:35935233 deletion of two genes encoding EAL-harboring enzymes, PA2200 and PA3825, resulted in elevated attachment levels, as would be expected for genes encoding PDEs PMID:35935233 Only four mutants exhibited elevated biomass measurements, namely PA0847 (Zhang et al., 2019), PA1107 (roeA; Cole and Lee, 2016), PA4367 and PA3825 |
Loading supporting content…
Download this section (compressed HTML)Experiment: Measure c-di-GMP hydrolysis by full-length PA3825 in membranes or nanodiscs, with CSS-domain cysteine mutants, to test whether the periplasmic domain gates activity.
What is not known — curated, literature-grounded statements of the open unknowns (the inverse of core functions).
Gap: The signal sensed by the periplasmic CSS domain of PA3825, and how it controls the EAL domain, are unknown.
BIOLOGY
Loading supporting content…
Download this section (compressed HTML)Loading supporting content…
Download this section (compressed HTML)