UreA (Vapar_4240) in Variovorax paradoxus S110 is the 100-amino-acid cytoplasmic gamma structural subunit (HAMAP rule MF_00739, InterPro IPR012010, Pfam PF00547) of the three-chain bacterial urease complex. Encoded at the head of the ureA-ureB-ureC-ureEFGD locus on chromosome 1, UreA assembles with UreB (beta subunit, Vapar_4242) and UreC (alpha catalytic subunit, Vapar_4243) into the (UreABC)3 trimer of heterotrimers and contributes structurally to nickel-dependent urea hydrolysis once the carbamylated dinickel active site is installed in UreC.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0005737 cytoplasm | IEA GO_REF:0000120 | ACCEPT | Summary: UreA is a cytoplasmic subunit of the soluble UreABC urease complex. Reason: C5CXZ7 (Vapar_4240) is a soluble 100-residue protein lacking signal peptides or transmembrane segments that assembles into the cytoplasmic (UreABC)3 urease complex (HAMAP rule MF_00739). Supporting Evidence: UniProtKB:C5CXZ7 CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000255|HAMAP-Rule:MF_00739}. |
| GO:0009039 urease activity | IEA GO_REF:0000120 | MARK AS OVER ANNOTATED | Summary: UreA contributes structurally to the heteromeric urease complex but does not independently catalyze urea hydrolysis. Reason: In three-chain bacterial ureases, the carbamylated dinickel active site resides exclusively in the alpha subunit UreC (Vapar_4243, C5CY00; PMID:8718850). Asserting that the gamma structural subunit UreA independently enables urease activity (GO:0009039) over-annotates a non-catalytic structural subunit; instead, UreA enables structural molecule activity (GO:0005198) and contributes_to urease activity within the assembled (UreABC)3 complex. Supporting Evidence: PMID:8718850 Urease from Klebsiella aerogenes [Jabri et al. (1995) Science 268, 998-1004] is an (alpha beta gamma)3 trimer with each alpha-subunit having an (alpha beta)8-barrel domain containing a binickel active center. |
| GO:0016151 nickel cation binding | IEA GO_REF:0000002 | REMOVE | Summary: InterPro-to-GO over-propagates nickel binding to UreA from the composite gamma/gamma-beta family entry. Reason: Structural studies of three-chain bacterial urease demonstrate that the binickel active center is coordinated solely within the (alpha beta)8 TIM-barrel of the alpha subunit (UreC), whereas the gamma subunit (UreA) contains no metal-binding site (PMID:8718850). Supporting Evidence: PMID:8718850 Urease from Klebsiella aerogenes [Jabri et al. (1995) Science 268, 998-1004] is an (alpha beta gamma)3 trimer with each alpha-subunit having an (alpha beta)8-barrel domain containing a binickel active center. |
| GO:0019627 urea metabolic process | IEA GO_REF:0000002 | TOO GENERAL | Summary: Broad parent term subsumed by urea catabolic process (GO:0043419). Reason: Urea metabolic process (GO:0019627) is true of UreA as part of the urease complex, but is strictly entailed by the more specific child term urea catabolic process (GO:0043419) already accepted on this record. Supporting Evidence: UniProtKB:C5CXZ7 CC -!- PATHWAY: Nitrogen metabolism; urea degradation; CO(2) and NH(3) from CC urea (urease route): step 1/1. {ECO:0000255|HAMAP-Rule:MF_00739}. |
| GO:0043419 urea catabolic process | IEA GO_REF:0000120 | ACCEPT | Summary: UreA is an essential structural component of the urea-hydrolyzing UreABC complex. Reason: UreA assembles with UreB and UreC into the mature (UreABC)3 urease complex that catalyzes urea hydrolysis in the urea catabolic pathway. Supporting Evidence: UniProtKB:C5CXZ7 CC -!- PATHWAY: Nitrogen metabolism; urea degradation; CO(2) and NH(3) from CC urea (urease route): step 1/1. {ECO:0000255|HAMAP-Rule:MF_00739}. |
| GO:0035550 urease complex | IC UniProtKB:C5CXZ7 | NEW | Summary: UreA is the gamma subunit of the heterotrimeric (UreABC)3 urease complex. Reason: Inferred by curator (IC) from HAMAP rule MF_00739 and conserved three-chain bacterial urease structure (PMID:8718850), where UreA (Vapar_4240) forms the gamma subunit of the cytoplasmic (UreABC)3 urease complex (GO:0035550). Supporting Evidence: UniProtKB:C5CXZ7 CC -!- SUBUNIT: Heterotrimer of UreA (gamma), UreB (beta) and UreC (alpha) CC subunits. Three heterotrimers associate to form the active enzyme. CC {ECO:0000255|HAMAP-Rule:MF_00739}. |
| GO:0005198 structural molecule activity | ISS PMID:8718850 Structures of the Klebsiella aerogenes urease apoenzyme and ... | NEW | Summary: UreA provides structural stability to the trimeric (UreABC)3 urease complex. Reason: Inferred from sequence and structural similarity (ISS) to Klebsiella aerogenes UreA (PMID:8718850), where the gamma subunit forms the trimer interface of the (alpha beta gamma)3 assembly without participating directly in active-site catalysis. Supporting Evidence: PMID:8718850 Urease from Klebsiella aerogenes [Jabri et al. (1995) Science 268, 998-1004] is an (alpha beta gamma)3 trimer with each alpha-subunit having an (alpha beta)8-barrel domain containing a binickel active center. |
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Download this section (compressed HTML)Q: What is the role of the small hypothetical ORF Vapar_4241 located between ureA (Vapar_4240) and ureB (Vapar_4242) in the Variovorax paradoxus S110 urease gene cluster?
Experiment: Construct an in-frame deletion of ureA (Vapar_4240) in V. paradoxus S110 and measure native (UreABC)3 complex assembly by blue-native PAGE and cell-extract urease activity using the phenol-hypochlorite ammonia assay.
Hypothesis: Vapar_4240 (UreA) is essential for assembly of the trimeric (UreABC)3 urease complex and urea-dependent growth in Variovorax paradoxus S110.
Type: In-frame gene deletion, native PAGE complex analysis, and enzymatic assay
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