UreD (Vapar_3971) in Variovorax paradoxus S110 is a 276-amino-acid cytoplasmic urease accessory protein (HAMAP rule MF_01384, InterPro IPR002669, PANTHER PTHR33643:SF1, Pfam PF01774). Based on conserved bacterial urease maturation biochemistry, UreD binds the inactive (UreABC)3 apoprotein, stabilizes an activation-competent conformation, and scaffolds the recruitment of UreF and the GTPase UreG to promote carbamylation and dinickel metallocenter installation in the UreC active site.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0005737 cytoplasm | IEA GO_REF:0000120 | ACCEPT | Summary: UreD acts on the soluble UreABC apoprotein in the bacterial cytoplasm. Reason: C5CVT2 (Vapar_3971) is a soluble 276-residue cytoplasmic protein that forms the UreD-UreF-UreG activation complex on cytoplasmic apo-urease (HAMAP rule MF_01384). Supporting Evidence: UniProtKB:C5CVT2 CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000255|HAMAP-Rule:MF_01384}. |
| GO:0016151 nickel cation binding | IEA GO_REF:0000120 | KEEP AS NON CORE | Summary: Orthologous UreD binds divalent metal ions in vitro, but selective nickel delivery is mediated by UreE and UreG rather than UreD. Reason: Purified Klebsiella aerogenes MBP-UreD binds divalent metal ions including Ni(2+) and Zn(2+) (PMID:22369361), supporting retention as a non-core annotation, whereas UreD's defining core role is scaffolding the UreDFG activation complex on apo-urease (GO:0018237, GO:0044183). Supporting Evidence: PMID:22369361 MBP-UreD binds divalent metal ions |
| GO:0018237 urease activator activity | ISS PMID:7909161 In vitro activation of urease apoprotein and role of UreD as... | NEW | Summary: UreD binds apo-urease and promotes nickel incorporation into the UreC active site. Reason: Inferred from sequence and structural similarity (ISS) to Klebsiella aerogenes UreD (PMID:7909161; PANTHER PTHR33643:SF1), which binds apo-UreABC and is required to form activation-competent complexes for nickel incorporation into the active site (GO:0018237). Supporting Evidence: PMID:7909161 The UreD-urease apoprotein complexes are competent for activation by nickel, with the level of activity obtained being directly related to the number of UreD molecules bound per urease molecule. |
| GO:0044183 protein folding chaperone | ISS PMID:7909161 In vitro activation of urease apoprotein and role of UreD as... | NEW | Summary: UreD stabilizes an activation-competent conformation of the urease apoprotein. Reason: Inferred from sequence similarity (ISS) to Klebsiella aerogenes UreD (PMID:7909161), which acts as an apoprotein chaperone stabilizing a conformation of apo-UreABC competent for active-site carbamylation and nickel insertion. Supporting Evidence: PMID:7909161 We propose that UreD is a chaperone protein which stabilizes a urease apoprotein conformation that is competent for nickel incorporation. |
| GO:0043419 urea catabolic process | ISS PMID:7909161 In vitro activation of urease apoprotein and role of UreD as... | NEW | Summary: UreD is essential for maturation of the urease enzyme that catalyzes urea catabolism. Reason: Inferred from sequence similarity (ISS) to Klebsiella aerogenes UreD (PMID:7909161), where deletion of ureD abolishes formation of active urease required for urea catabolism. Supporting Evidence: PMID:7909161 extracts of cells containing a ureD deletion derivative failed to generate active urease |
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Download this section (compressed HTML)Q: Why is ureD (Vapar_3971) encoded at a separate locus from the main ureA-ureB-ureC-ureEFGD cluster (Vapar_4240-Vapar_4249) on chromosome 1 of Variovorax paradoxus S110, and is Vapar_4249 a second functional UreD paralog?
Experiment: Perform pull-down and in vitro urease activation assays with purified Vapar_3971, apo-UreABC, UreF, and UreG in the presence of Ni(2+), bicarbonate, and GTP.
Hypothesis: Vapar_3971 (UreD) forms a direct pre-activation complex with V. paradoxus S110 apo-UreABC (Vapar_4240/Vapar_4242/Vapar_4243) and recruits UreF and UreG (Vapar_4248).
Type: Protein-protein interaction pull-down and in vitro urease activation assay
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