PvdH (PA2413) is the diaminobutyrate--2-oxoglutarate aminotransferase of Pseudomonas aeruginosa PAO1, a class-III pyridoxal 5'-phosphate-dependent aminotransferase (Aminotrans_3 fold, NCBIfam dat/TIGR00709). Purified from PAO1, it interconverts L-aspartate beta-semialdehyde and L-2,4-diaminobutyrate, operating physiologically in the direction that forms L-2,4-diaminobutyrate, with 2-oxoglutarate/L-glutamate as the amino-group partner and a ping-pong kinetic mechanism. L-2,4-Diaminobutyrate is one of the two non-proteinogenic precursors of the pyoverdine dihydroxyquinoline chromophore, which is formed by condensation of D-tyrosine with L-2,4-diaminobutyrate; pvdH knockout mutants cannot make pyoverdine under iron limitation unless L-2,4-diaminobutyrate is supplied in the medium. PvdH homologues lie within pyoverdine biosynthetic loci across fluorescent pseudomonads, indicating a general route to this precursor in pyoverdine producers.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0002049 pyoverdine biosynthetic process | IDA PMID:15317763 Functional characterization of an aminotransferase required ... | ACCEPT | Summary: Core biological process. PvdH supplies L-2,4-diaminobutyrate for the pyoverdine chromophore; pvdH mutants of PAO1 fail to synthesize pyoverdine under iron limitation unless the precursor is supplied exogenously, and the purified enzyme catalyses the precursor-forming transamination. Reason: Directly supported by the biochemical and genetic characterization of PAO1 PvdH in the cited paper. Supporting Evidence: PMID:15317763 Both pvdH and asd (encoding aspartate beta-semialdehyde dehydrogenase) knockout mutants of Pseudomonas aeruginosa PAO1 were unable to synthesize pyoverdine under iron-limiting conditions in the absence of l-2,4-diaminobutyrate in the culture media. PMID:15317763 The fluorescent dihydroxyquinoline chromophore of the pyoverdine siderophore in Pseudomonas is a condensation product of D-tyrosine and l-2,4-diaminobutyrate. |
| GO:0002049 pyoverdine biosynthetic process | IMP PMID:12686626 Identification and characterization of novel pyoverdine synt... | ACCEPT | Summary: The PAO1 pyoverdine gene-identification screen mutated candidate genes and scored pyoverdine production, identifying eight new pvd genes. This is independent mutant-phenotype support for the same pathway role and is consistent with the IDA row. Reason: Mutant-phenotype evidence for a requirement in PAO1 pyoverdine synthesis, consistent with the other GO:0002049 row. Supporting Evidence: PMID:12686626 The candidate genes were mutated and the effects of the mutations on pyoverdine production were determined. Eight new pvd genes were identified. PMID:15317763 These homologues were found in the DNA loci of the corresponding genomes that contain other pyoverdine synthesis genes. |
| GO:0008483 transaminase activity | IBA GO_REF:0000033 | MODIFY | Summary: The PAINT node PTN002461253 of PTHR43552 asserts transaminase activity, and Q9I168 itself is among the seeds: PvdH's own experimental transaminase annotation is part of the descendant evidence the PAINT curator used, so the gene legitimately appears in its own WITH/FROM and the IBA adds the statement that the activity is inherited rather than lineage-specific. The claim is true but is the broad family-level parent; the assayed reaction is the specific L-2,4-diaminobutyrate:2-oxoglutarate transamination, which is the term this review carries as core. Reason: Correct but less specific than the evidence supports. GO:0045303 L-2,4-diaminobutyrate:2-oxoglutarate transaminase activity is an is_a descendant of GO:0008483 and is the reaction demonstrated with purified PAO1 PvdH; UniProt and NCBIfam also classify the protein as a diaminobutyrate--2-oxoglutarate aminotransferase (dat). Propagation Review Root cause: TERM SCOPING PROBLEM Failure modes: GRANULARITY MISMATCH Sources checked: PANTHER:PTN002461253 · PTHR43552 ancestral node for diaminobutyrate--2-oxoglutarate aminotransferases SUPPORTS TRANSFER The node is seeded by Q9I168 itself, i.e. by this protein's own experimental transaminase annotation, so the propagation is sound and not circular. Only the granularity is at issue: the family-level term is the broad parent of the assayed diaminobutyrate transamination. Proposed replacements: L-2,4-diaminobutyrate:2-oxoglutarate transaminase activity Supporting Evidence: file:interpro/panther/PTHR43552/PTHR43552-paint.tsv PTHR43552 PTN002461253 GO:0008483 F IBD false PMID:15317763 PvdH was found to catalyze an aminotransferase reaction, interconverting aspartate beta-semialdehyde and l-2,4-diaminobutyrate. |
| GO:0008483 transaminase activity | IDA PMID:15317763 Functional characterization of an aminotransferase required ... | MODIFY | Summary: Direct assay of the purified PAO1 enzyme. The activity is real, but the paper establishes the specific reaction (aspartate beta-semialdehyde to L-2,4-diaminobutyrate, with highest specificity for alpha-ketoglutarate), so the specific child term is the informative one. Reason: The assayed reaction is the L-2,4-diaminobutyrate:2-oxoglutarate transamination; GO:0045303 is the supported is_a descendant of the broad term annotated here. Consistent with the other GO:0008483 rows. Proposed replacements: L-2,4-diaminobutyrate:2-oxoglutarate transaminase activity Supporting Evidence: PMID:15317763 PvdH was found to catalyze an aminotransferase reaction, interconverting aspartate beta-semialdehyde and l-2,4-diaminobutyrate. PMID:15317763 Steady-state kinetic analysis with a novel coupled assay established that the enzyme adopts a ping-pong kinetic mechanism and has the highest specificity for alpha-ketoglutarate. |
| GO:0008483 transaminase activity | IEA GO_REF:0000002 | MODIFY | Summary: InterPro signature IPR004637 (Dat) maps to the broad transaminase term. The signature match is good evidence of family membership, and the family is specifically the diaminobutyrate--2-oxoglutarate aminotransferases, so the specific term is warranted here too. Reason: Same granularity refinement as the other GO:0008483 rows: IPR004637 and NCBIfam TIGR00709 both identify the protein as a diaminobutyrate--2-oxoglutarate aminotransferase. Proposed replacements: L-2,4-diaminobutyrate:2-oxoglutarate transaminase activity Supporting Evidence: file:PSEAE/pvdH/pvdH-uniprot.txt DR InterPro; IPR004637; Dat. file:PSEAE/pvdH/pvdH-uniprot.txt DR NCBIfam; TIGR00709; dat; 1. PMID:15317763 PvdH was found to catalyze an aminotransferase reaction, interconverting aspartate beta-semialdehyde and l-2,4-diaminobutyrate. |
| GO:0030170 pyridoxal phosphate binding | IEA GO_REF:0000002 | KEEP AS NON CORE | Summary: PvdH matches the Aminotrans_3 (IPR005814) and PROSITE class-III aminotransferase signatures, and the class-III PLP-dependent aminotransferase family uses PLP bound through a Schiff base to a conserved catalytic lysine. The ping-pong kinetic mechanism reported for the purified enzyme is the mechanism expected of a PLP aminotransferase. Cofactor binding is a genuine but accessory property relative to the catalytic role. Reason: Well-supported cofactor-binding annotation from curated domain signatures, retained as non-core support for the PLP-dependent transaminase mechanism. Supporting Evidence: file:PSEAE/pvdH/pvdH-uniprot.txt DR PROSITE; PS00600; AA_TRANSFER_CLASS_3; 1. file:PSEAE/pvdH/pvdH-uniprot.txt SIMILARITY: Belongs to the class-III pyridoxal-phosphate-dependent aminotransferase family. PMID:15317763 established that the enzyme adopts a ping-pong kinetic mechanism |
| GO:0045303 L-2,4-diaminobutyrate:2-oxoglutarate transaminase activity | IDA PMID:15317763 Functional characterization of an aminotransferase required ... | NEW | Summary: Proposed annotation for the specific reaction that the purified PAO1 enzyme was shown to catalyse: interconversion of aspartate beta-semialdehyde and L-2,4-diaminobutyrate with highest specificity for alpha-ketoglutarate and negligible activity on other keto acids. GOA currently carries only the broad parent GO:0008483 for this gene, although the orthologous KT2440 entry already has GO:0045303. Reason: This is the core molecular function and the replacement term proposed for the GO:0008483 rows; it is directly demonstrated for this protein rather than inferred. Supporting Evidence: PMID:15317763 PvdH was found to catalyze an aminotransferase reaction, interconverting aspartate beta-semialdehyde and l-2,4-diaminobutyrate. PMID:15317763 The specificity of the enzyme toward the smaller keto acid pyruvate is 41-fold lower. The enzyme has negligible activity toward other keto acids tested. file:PSEAE/pvdH/pvdH-uniprot.txt DR NCBIfam; TIGR00709; dat; 1. |
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Download this section (compressed HTML)Q: Is PvdH the sole route to L-2,4-diaminobutyrate in PAO1, or can the ectoine-type diaminobutyrate aminotransferases of other pseudomonads substitute when pvdH is deleted?
Suggested experts: Stephen Y. K. Seah, Iain L. Lamont
Q: What determines flux partitioning of L-aspartate 4-semialdehyde between PvdH and the aspartate-semialdehyde-consuming reactions of lysine, threonine and methionine biosynthesis under iron limitation?
Suggested experts: Iain L. Lamont
Experiment: Quantify intracellular L-2,4-diaminobutyrate by LC-MS in wild-type and pvdH-deletion PAO1 under iron limitation, with and without plasmid-borne pvdH, and test whether heterologous ectB can restore pyoverdine output.
Hypothesis: PvdH is the only enzyme supplying L-2,4-diaminobutyrate for pyoverdine in PAO1.
Type: metabolomics plus genetic complementation
Experiment: Titrate pvdH expression from an inducible chromosomal promoter and measure pyoverdine yield, intracellular L-2,4-diaminobutyrate and growth, to test for a flux-control relationship between transaminase level and siderophore output.
Hypothesis: PvdH activity is rate-limiting for pyoverdine production under strong iron limitation.
Type: expression titration and flux analysis
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