UreC (Vapar_4243) is the 572-amino-acid catalytic alpha subunit of cytoplasmic nickel-dependent urease (EC 3.5.1.5) in the plant-growth-promoting endophyte Variovorax paradoxus S110. Together with the structural subunits UreA (gamma) and UreB (beta), UreC assembles into a trimer of heterotrimers ((UreABC)3) whose active site coordinates a dinuclear Ni(2+) metallocenter bridged by a post-translationally carboxylated lysine residue (Lys222) and a hydroxide ion, ligated by His139, His141, His251, His277, and Asp365, with His325 serving as the general acid proton donor. Following chaperone-assisted metallocenter maturation by UreD, UreF, UreG, and the nickel metallochaperone UreE, UreC catalyzes the hydrolysis of urea into ammonia and carbamate (which spontaneously decomposes to a second ammonia molecule and carbonic acid/bicarbonate), supplying assimilable nitrogen and elevating local pH in the rhizosphere where carbonate generation can also promote microbially induced metal-carbonate biomineralization.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0005737 cytoplasm | IEA GO_REF:0000120 | MODIFY | Summary: Correct but broad subcellular localization; refine to GO:0005829 (cytosol) for this soluble cytoplasmic enzyme complex lacking signal peptides or transmembrane segments. Reason: UreC (572 aa) is a soluble intracellular metalloenzyme subunit lacking any signal peptide or transmembrane helices, so the more specific descendant term GO:0005829 (cytosol) is warranted over bare GO:0005737 (cytoplasm). Proposed replacements: cytosol Supporting Evidence: UniProtKB:C5CY00 SUBCELLULAR LOCATION: Cytoplasm {ECO:0000255|HAMAP-Rule:MF_01953}. |
| GO:0009039 urease activity | IEA GO_REF:0000120 | ACCEPT | Summary: Core catalytic activity (EC 3.5.1.5, RHEA:20557) of the urease alpha subunit UreC. Reason: Vapar_4243 is a reviewed Swiss-Prot entry matching HAMAP family rule MF_01953 (Urease_alpha) with complete conservation of the dinuclear Ni(2+) coordination sphere (His139, His141, carboxylated Lys222, His251, His277, Asp365) and the catalytic proton donor His325 required for urea hydrolysis. Supporting Evidence: UniProtKB:C5CY00 Reaction=urea + 2 H2O + H(+) = hydrogencarbonate + 2 NH4(+); Xref=Rhea:RHEA:20557, ChEBI:CHEBI:15377, ChEBI:CHEBI:15378, ChEBI:CHEBI:16199, ChEBI:CHEBI:17544, ChEBI:CHEBI:28938; EC=3.5.1.5; Evidence={ECO:0000255|HAMAP-Rule:MF_01953}; PMID:20046957 Urease, the first enzyme to be crystallized, contains a dinuclear nickel metallocenter that catalyzes the decomposition of urea to produce ammonia, a reaction of great agricultural and medical importance. |
| GO:0016151 nickel cation binding | IEA GO_REF:0000120 | ACCEPT | Summary: Core cofactor-binding activity; UreC binds two catalytic Ni(2+) ions per alpha subunit at its bridged dinuclear active site. Reason: UreC coordinates two Ni(2+) ions per subunit bridged by N6-carboxylysine (Lys222) and a hydroxide molecule, with Ni1 coordinated by His139 and His141 and Ni2 coordinated by His251, His277, and Asp365. Supporting Evidence: UniProtKB:C5CY00 Note=Binds 2 nickel ions per subunit. {ECO:0000255|HAMAP-Rule:MF_01953}; PMID:20046957 The active site of urease contains two nickel atoms bridged by a carboxylated lysine and a solvent molecule, as shown for the K. aerogenes enzyme (Fig. 2).19 In addition, Ni1 is coordinated by two His residues plus a terminal water molecule while Ni2 is coordinated by two His, an Asp, and a terminal solvent. |
| GO:0016787 hydrolase activity | IEA GO_REF:0000002 | TOO GENERAL | Summary: True ancestor term subsumed by the accepted specific catalytic activity GO:0009039 (urease activity). Reason: GO:0009039 (urease activity) is a specific descendant of GO:0016787 (hydrolase activity) already accepted in this review. Supporting Evidence: UniProtKB:C5CY00 Reaction=urea + 2 H2O + H(+) = hydrogencarbonate + 2 NH4(+); Xref=Rhea:RHEA:20557, ChEBI:CHEBI:15377, ChEBI:CHEBI:15378, ChEBI:CHEBI:16199, ChEBI:CHEBI:17544, ChEBI:CHEBI:28938; EC=3.5.1.5; Evidence={ECO:0000255|HAMAP-Rule:MF_01953}; |
| GO:0016810 hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds | IEA GO_REF:0000002 | TOO GENERAL | Summary: True intermediate ancestor term subsumed by the accepted specific catalytic activity GO:0009039 (urease activity). Reason: GO:0009039 (urease activity) is a direct descendant of GO:0016810 (hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds) and is already accepted as the core molecular function of UreC. Supporting Evidence: UniProtKB:C5CY00 Reaction=urea + 2 H2O + H(+) = hydrogencarbonate + 2 NH4(+); Xref=Rhea:RHEA:20557, ChEBI:CHEBI:15377, ChEBI:CHEBI:15378, ChEBI:CHEBI:16199, ChEBI:CHEBI:17544, ChEBI:CHEBI:28938; EC=3.5.1.5; Evidence={ECO:0000255|HAMAP-Rule:MF_01953}; |
| GO:0043419 urea catabolic process | IEA GO_REF:0000120 | ACCEPT | Summary: Core biological process catalyzed by UreC (UniPathway UPA00258: urea degradation to CO2/hydrogencarbonate and NH3/NH4+). Reason: UreC catalyzes the hydrolytic cleavage of urea into ammonia and carbamate (which decomposes to carbonic acid/hydrogencarbonate and a second ammonia molecule), constituting the single step of the urease pathway of urea catabolism. Supporting Evidence: UniProtKB:C5CY00 PATHWAY: Nitrogen metabolism; urea degradation; CO(2) and NH(3) from urea (urease route): step 1/1. {ECO:0000255|HAMAP-Rule:MF_01953}. PMID:20046957 The enzyme catalyzes the deceptively simple hydrolysis of urea into ammonia and carbamic acid. The latter compound spontaneously decomposes into carbonic acid and a second ammonia molecule |
| GO:0035550 urease complex | IC PMID:20046957 Interplay of metal ions and urease. | NEW | Summary: UreC (alpha) assembles with UreA (gamma) and UreB (beta) into the canonical bacterial (UreABC)3 urease holoenzyme complex. Reason: Bacterial three-subunit ureases form a trimer of UreA-UreB-UreC heterotrimers ((UreABC)3), in which UreC contributes the catalytic alpha subunit housing the dinuclear Ni(2+) active site. Supporting Evidence: UniProtKB:C5CY00 SUBUNIT: Heterotrimer of UreA (gamma), UreB (beta) and UreC (alpha) subunits. Three heterotrimers associate to form the active enzyme. {ECO:0000255|HAMAP-Rule:MF_01953}. PMID:20046957 Most bacterial ureases, exemplified by those from Klebsiella aerogenes (Fig. 1A)15 and Bacillus pasteurii,16 possess three distinct types of subunits that form a (UreABC)3 structure. |
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Download this section (compressed HTML)Q: To what extent does urease-catalyzed carbonate production and local pH elevation by Variovorax paradoxus S110 drive microbially induced carbonate precipitation (MICP) of toxic divalent heavy metals (e.g., Cd2+, Ni2+, Pb2+) and lanthanides in contaminated rhizosphere soils?
Suggested experts: Hausinger RP, Han JI, Leadbetter JR
Experiment: Compare urea-supplemented cultures of wild-type Variovorax paradoxus S110 and a ΞureC (Vapar_4243) mutant for pH elevation, dissolved carbonate production, and extracellular precipitation of CdCO3, NiCO3, and lanthanide carbonates by ICP-MS and X-ray diffraction.
Hypothesis: UreC-dependent urea hydrolysis raises extracellular pH and carbonate ion activity sufficiently to precipitate divalent heavy metals and rare earth elements out of solution, protecting host roots from metal toxicity while supplying ammonium nitrogen.
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