gbuA (PA1421) encodes guanidinobutyrase (EC 3.5.3.7) of Pseudomonas aeruginosa, a manganese-dependent ureohydrolase of the arginase/agmatinase family that hydrolyses 4-guanidinobutanoate to 4-aminobutanoate (GABA) and urea. The enzyme is highly specific: it has no detectable activity on arginine, agmatine, 3-guanidinopropionate or guanidinoacetate, and its substrate selectivity relative to the paralogous guanidinopropionase GpuA is set by active-site loop residues such as Met161. It binds two Mn2+ ions per subunit and was reported as a homotetramer by gel filtration and a homohexamer in the crystal structure. GbuA catalyses a late step of the arginine dehydrogenase / arginine transaminase route of arginine catabolism, in which D- or L-arginine is converted via 2-ketoarginine and 4-guanidinobutyraldehyde to 4-guanidinobutyrate and then to GABA, which feeds succinate production. gbuA is induced by 4-guanidinobutyrate through the divergently transcribed LysR-type regulator GbuR, and is required for growth on 4-guanidinobutyrate.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0006527 L-arginine catabolic process | IBA GO_REF:0000033 | ACCEPT | Summary: IBA from PTN004253691 (guanidino acid hydrolase clade of PTHR11358); the L-arginine catabolic process IBD rests solely on this gene's PseudoCAP row (34 leaf IBAs). The target in its own WITH/FROM is expected. Reason: Correct for GbuA, which catalyses a step of the arginine dehydrogenase/transaminase catabolic route; gbuA disruption abolishes growth on L-arginine when the AST pathway is blocked. The node term does not suit the rest of the clade, which is recorded as a source defect and does not affect this gene. Supporting Evidence: PMID:17416670 disruption of gbuA abolished growth on l -arginine PMID:12029055 Guanidinobutyrase (GBase; EC 3.5.3.7) catalyzes the conversion of 4-guanidinobutyrate to 4-aminobutyrate and urea in this pathway. |
| GO:0006527 L-arginine catabolic process | IDA PMID:3141581 The fourth arginine catabolic pathway of Pseudomonas aerugin... | ACCEPT | Summary: PseudoCAP row from Jann et al. 1988 (the fourth arginine catabolic pathway of P. aeruginosa); sole seed of the PTN004253691 L-arginine catabolic process IBD. Reason: Sound seed. The paper shows, by enzyme assays in P. aeruginosa extracts, that 2-ketoarginine is degraded through 4-guanidinobutyrate to 4-aminobutyrate by an inducible guanidinobutyrase, and that L-arginine is channelled into this route when the AST pathway is blocked. The activity is attributable to GbuA, whose knockout lacks GBase. The pathway was first framed as D-arginine catabolism; the L-arginine role was confirmed genetically later (aruF gbuA double mutant). Supporting Evidence: PMID:3141581 In mutants blocked in the L-arginine succinyltransferase pathway, but no in the wild-type, L-arginine was channelled partially into the D-arginine dehydrogenase pathway. PMID:17416670 disruption of gbuA abolished growth on l -arginine |
| GO:0016813 hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amidines | IEA GO_REF:0000002 | MODIFY | Summary: InterPro2GO from the ureohydrolase manganese-binding site signature. Reason: Correct but general; the specific activity, guanidinobutyrase activity (GO:0047971), is an is_a child already carried by the gene. Proposed replacements: guanidinobutyrase activity Supporting Evidence: PMID:12029055 Purified GbuA was a homotetramer of 140 kDa that catalyzed the specific hydrolysis of 4-GB |
| GO:0046872 metal ion binding | IEA GO_REF:0000002 | MODIFY | Summary: InterPro2GO metal ion binding from the ureohydrolase signatures. Reason: Correct but general. The metal is Mn2+: two Mn2+ ions per subunit are seen in the crystal structure and Mn2+ restores activity after EDTA. Proposed replacements: manganese ion binding Supporting Evidence: PMID:12029055 EDTA inhibited the activity of GbuA, and Mn 2+ ions but not Co 2+ ions restored the full activity at 0.2 mM file:PSEAE/gbuA/gbuA-uniprot.txt Binds 2 manganese ions per subunit. |
| GO:0047971 guanidinobutyrase activity | EXP PMID:12029055 Characterization and regulation of the gbuA gene, encoding g... | ACCEPT | Summary: UniProt EXP row from Nakada and Itoh 2002 (purified recombinant GbuA, kinetics). Reason: Direct assay of the purified gene product with kinetics and N-terminal sequencing. Supporting Evidence: PMID:12029055 The apparent K m and K cat values for 4-GB were 49 mM and 1,012 s −1 , respectively. |
| GO:0047971 guanidinobutyrase activity | EXP PMID:21600989 Crystal structures of Pseudomonas aeruginosa guanidinobutyra... | ACCEPT | Summary: UniProt EXP row from Lee et al. 2011 (crystal structure, kinetics, Met161 mutagenesis). Reason: Independent characterisation of the purified enzyme and its active site; UniProt records the kinetics (Km 10.7 mM) from this paper. Supporting Evidence: PMID:21600989 Pseudomonas aeruginosa guanidinobutyrase (GbuA) and guanidinopropionase (GpuA) catalyze the hydrolysis of 4-guanidinobutyrate and 3-guanidinopropionate, respectively. |
| GO:0047971 guanidinobutyrase activity | IBA GO_REF:0000033 | ACCEPT | Summary: IBA from PTN004253691, seeded by human AGMAT (Q9BSE5) and this gene. Reason: GbuA is the defining guanidinobutyrase of the clade, with its own experimental evidence; human AGMAT also hydrolyses 4-guanidinobutyrate efficiently. Supporting Evidence: PMID:12029055 Purified GbuA was a homotetramer of 140 kDa that catalyzed the specific hydrolysis of 4-GB |
| GO:0047971 guanidinobutyrase activity | IDA PMID:3141581 The fourth arginine catabolic pathway of Pseudomonas aerugin... | ACCEPT | Summary: PseudoCAP row from Jann et al. 1988; one of two seeds of the PTN004253691 guanidinobutyrase IBD. Guanidinobutyrase was assayed in P. aeruginosa extracts. Reason: Sound. The paper measured inducible guanidinobutyrase activity in P. aeruginosa; GbuA is the enzyme responsible (a PA1421 knockout forms no GBase). Supporting Evidence: PMID:3141581 Two enzymes involved, 4-guanidinobutyraldehyde dehydrogenase and guanidinobutyrase, were inducible by 2-ketoarginine PMID:12029055 a knockout mutant (PAO4518) having an insertion of a Gm r cassette on PA1421 (at the Bbs I site on nucleotide 532) (Fig. 2A ) did not grow on 4-GB and failed to form GBase |
| GO:0047971 guanidinobutyrase activity | IEA GO_REF:0000120 | ACCEPT | Summary: EC/Rhea-based guanidinobutyrase activity. Reason: Same correct claim as the experimental rows. Supporting Evidence: file:PSEAE/gbuA/gbuA-uniprot.txt Reaction=4-guanidinobutanoate + H2O = urea + 4-aminobutanoate |
| GO:0047972 guanidinopropionase activity | IBA GO_REF:0000033 | REMOVE | Summary: IBA from PTN004253691, seeded by human AGMAT and the P. aeruginosa paralog GpuA (Q9I6K2), not by this gene. Reason: Contradicted by direct assay of GbuA: the purified enzyme has no detectable activity with 3-guanidinopropionate, and its substrate specificity differs from GpuA's through active-site loop residues. The function was propagated from a paralog that diverged within PAO1; the node needs a NOT at the GbuA leaf (PTN002260452), the only fix the tree allows. Propagation Review Root cause: PROPAGATION BAD Failure modes: FUNCTIONAL DIVERGENCE Sources checked: PANTHER:PTN004253691 · PTN004253691 SUPPORTS SOURCE BUT NOT TARGET Guanidinopropionase IBD seeded by GpuA (Q9I6K2) and human AGMAT (Q9BSE5), both with guanidinopropionase activity; GbuA has none. Supporting Evidence: PMID:12029055 No enzyme activity was detected with other guanidino compounds, including arginine, agmatine, 3-guanidinopropionate, and guanidinoacetate. file:PSEAE/gbuA/gbuA-uniprot.txt Has no activity against arginine, agmatine, 3-guanidinopropionate and guanidinoacetate. |
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Download this section (compressed HTML)Q: The PTN004253691 L-arginine catabolic process IBD (sole seed GbuA) has no bacterial guanidinobutyrase subnode to move to: the tree places GpuA as sister to all other leaves and GbuA inside the animal clade. Should the clade-level IBD be withdrawn in favour of a leaf annotation on PTN002260452, or negated at PTN002260450, PTN000144490 and PTN000888144?
Q: Is a more specific GO process term warranted for 4-guanidinobutanoate catabolism (the GbuA step), shared by the arginine catabolic route and exogenous 4-guanidinobutyrate utilisation?
Experiment: Measure 13C-arginine flux through 4-guanidinobutyrate in wild type, aruF and aruF gbuA strains of PAO1 to quantify the share of L-arginine catabolism routed through GbuA under different growth conditions.
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