PvdD (PA2399) is a two-module nonribosomal peptide synthetase (NRPS) of Pseudomonas aeruginosa PAO1 that assembles part of the peptide chain of the siderophore pyoverdine. Each module has condensation, adenylation and peptidyl-carrier (phosphopantetheine-binding) domains, and the protein ends in a thioesterase domain, consistent with PvdD acting at the end of the NRPS assembly line. Both adenylation domains select L-threonine, and PvdD incorporates two L-threonines into pyoverdine; the first adenylation domain is highly specific for L-threonine in ATP-PPi exchange assays. PvdD is an iron-regulated cytoplasmic protein, and a pvdD mutant makes no pyoverdine.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0002049 pyoverdine biosynthetic process | IMP PMID:15271355 Characterization and genetic manipulation of peptide synthet... | ACCEPT | Summary: PseudoCAP IMP and one of the PvdD seeds of the PTN002378821 secondary metabolite biosynthetic process IBD. A pvdD mutant makes no pyoverdine and is complemented in trans. Reason: Seed verdict SOUND. PvdD does part of the work of the process: it is the NRPS that incorporates two L-threonines into the pyoverdine peptide, so the mutant phenotype reflects loss of a catalytic step, not an indirect effect. Pyoverdine biosynthetic process is_a secondary metabolite biosynthetic process, so the seed supports the node term. Supporting Evidence: PMID:15271355 PvdD, a nonribosomal peptide synthetase (NRPS) of Pseudomonas aeruginosa PAO1, incorporates two L-threonines into the siderophore pyoverdine. PMID:15271355 A pvdD mutant did not synthesize pyoverdine and lacked a high Mr iron-regulated cytoplasmic protein (IRCP). |
| GO:0002049 pyoverdine biosynthetic process | IMP PMID:12700264 Substrate specificity of the nonribosomal peptide synthetase... | ACCEPT | Summary: PseudoCAP IMP seed citing the PvdD substrate-specificity paper, which assayed the purified first module in vitro. Reason: The claim is true: the purified module activates L-threonine, a pyoverdine residue, which is a step of pyoverdine peptide synthesis carried out by PvdD itself. The abstract reports a purified-protein assay and no mutant, so the evidence is direct (IDA) rather than IMP; recorded as a source defect. Supporting Evidence: PMID:12700264 L-Threonine, one of the amino acid residues in pyoverdine(PAO), was an effective substrate for the recombinant protein in ATP-PP(i) exchange assays, showing that PvdD has peptide synthetase activity. |
| GO:0002049 pyoverdine biosynthetic process | IMP PMID:9770291 Quorum-sensing and siderophore biosynthesis in Pseudomonas a... | ACCEPT | Summary: PseudoCAP IMP seed citing a quorum-sensing paper in which pvdD appears as an expression read-out in lasR mutants. Reason: The claim is true for PvdD (see the PMID:15271355 row). The abstract, however, describes lasR and lasI mutants and pvdD expression, not a pvdD mutant, so it is unclear that this paper supports an IMP for pvdD. A pvdD mutant used as a pyoverdine-negative control in the full text would; I have not read it. Seed verdict UNVERIFIABLE; recorded as a SUSPECTED defect. Supporting Evidence: PMID:9770291 lasR mutants were not altered with respect to expression of the pvdD gene involved in the synthesis of the peptide portion of pyoverdine PMID:15271355 A pvdD mutant did not synthesize pyoverdine |
| GO:0003824 catalytic activity | IMP PMID:15271355 Characterization and genetic manipulation of peptide synthet... | MODIFY | Summary: True but uninformative; PvdD is a nonribosomal peptide synthetase. Reason: The specific activity is non-ribosomal peptide synthetase activity (GO:1904091), a descendant of catalytic activity, shown for PvdD as an NRPS that incorporates L-threonine. Proposed replacements: non-ribosomal peptide synthetase activity Supporting Evidence: PMID:15271355 PvdD, a nonribosomal peptide synthetase (NRPS) of Pseudomonas aeruginosa PAO1, incorporates two L-threonines into the siderophore pyoverdine. |
| GO:0003824 catalytic activity | IMP PMID:12700264 Substrate specificity of the nonribosomal peptide synthetase... | MODIFY | Summary: True but uninformative. The paper shows L-threonine adenylation by the purified first module. Reason: Replace by non-ribosomal peptide synthetase activity (GO:1904091). The evidence-code defect (IMP for a purified-protein assay) is recorded on the GO:0002049 row from this paper. Proposed replacements: non-ribosomal peptide synthetase activity Supporting Evidence: PMID:12700264 L-Threonine, one of the amino acid residues in pyoverdine(PAO), was an effective substrate for the recombinant protein in ATP-PP(i) exchange assays, showing that PvdD has peptide synthetase activity. |
| GO:0003824 catalytic activity | IMP PMID:9770291 Quorum-sensing and siderophore biosynthesis in Pseudomonas a... | MODIFY | Summary: True but uninformative, and the cited paper does not test PvdD activity. Reason: The claim (PvdD is catalytic) is true and better stated as non-ribosomal peptide synthetase activity. The reference problem is recorded on the GO:0002049 row from this paper. Proposed replacements: non-ribosomal peptide synthetase activity Supporting Evidence: PMID:12700264 showing that PvdD has peptide synthetase activity |
| GO:0003824 catalytic activity | IEA GO_REF:0000002 | MODIFY | Summary: InterPro2GO from the NRPS condensation domain; true but uninformative. Reason: Replace by non-ribosomal peptide synthetase activity (GO:1904091). Proposed replacements: non-ribosomal peptide synthetase activity Supporting Evidence: file:PSEAE/pvdD/pvdD-uniprot.txt Pfam; PF00668; Condensation; 2. |
| GO:0005737 cytoplasm | IBA GO_REF:0000033 | TOO GENERAL | Summary: True but general; the cytosol row is accepted. Reason: PvdD is a soluble iron-regulated cytoplasmic protein. GO:0005829 cytosol, accepted in this review, is part_of cytoplasm. Supporting Evidence: PMID:15271355 lacked a high Mr iron-regulated cytoplasmic protein (IRCP) |
| GO:0005829 cytosol | IBA GO_REF:0000033 | ACCEPT | Summary: Cytosol IBD from E. coli EntF. PvdD was identified as a large soluble iron-regulated cytoplasmic protein. Reason: The IRCPs are defined by fractionation as cytoplasmic proteins, which agrees with the IBA. Pyoverdine NRPSs may also associate with the inner membrane, but the soluble location is supported. Supporting Evidence: PMID:15271355 A pvdD mutant did not synthesize pyoverdine and lacked a high Mr iron-regulated cytoplasmic protein (IRCP). |
| GO:0031177 phosphopantetheine binding | IBA GO_REF:0000033 | ACCEPT | Summary: PvdD has two peptidyl carrier protein domains with phosphopantetheine attachment sites. Reason: Two PP-binding (carrier) domains are present, which carry the 4'-phosphopantetheine arm that tethers the activated amino acids. Supporting Evidence: file:PSEAE/pvdD/pvdD-uniprot.txt Pfam; PF00550; PP-binding; 2. |
| GO:0031177 phosphopantetheine binding | IEA GO_REF:0000002 | ACCEPT | Summary: Same claim as the IBA row. Reason: Carrier domains are present. Supporting Evidence: file:PSEAE/pvdD/pvdD-uniprot.txt PROSITE; PS50075; CARRIER; 2. |
| GO:0043041 obsolete amino acid activation for nonribosomal peptide biosynthetic process | IBA GO_REF:0000033 | MODIFY | Summary: Obsolete term. The underlying claim, amino acid activation by the adenylation domains for nonribosomal peptide synthesis, is true of PvdD. Reason: PvdD adenylation domains activate L-threonine for pyoverdine synthesis. With the activation term obsolete, the supported process is GO:0002049 pyoverdine biosynthetic process; the activation step itself is captured by non-ribosomal peptide synthetase activity in core_functions. Propagation Review Root cause: SOURCE STALE OR MISSING Failure modes: GRANULARITY MISMATCH Sources checked: PANTHER:PTN002378821 · PTN002378821 SOURCE STALE OR MISSING The IBD term has been obsoleted; the biological claim holds for the NRPS clade. Proposed replacements: pyoverdine biosynthetic process Supporting Evidence: PMID:12700264 L-Threonine, one of the amino acid residues in pyoverdine(PAO), was an effective substrate for the recombinant protein in ATP-PP(i) exchange assays |
| GO:0043041 obsolete amino acid activation for nonribosomal peptide biosynthetic process | IEA GO_REF:0000117 | MODIFY | Summary: Obsolete term; same claim as the IBA row. Reason: Replace by GO:0002049 pyoverdine biosynthetic process, as for the IBA row. Proposed replacements: pyoverdine biosynthetic process Supporting Evidence: PMID:15271355 PvdD, a nonribosomal peptide synthetase (NRPS) of Pseudomonas aeruginosa PAO1, incorporates two L-threonines into the siderophore pyoverdine. |
| GO:0044550 secondary metabolite biosynthetic process | IBA GO_REF:0000033 | TOO GENERAL | Summary: IBD at PTN002378821, which PvdD seeds (with PvdJ and eleven other NRPSs). PvdD in its own WITH/FROM is expected, not circular. Reason: True, and a suitably generic term for a broad NRPS clade. For PvdD itself, GO:0002049 pyoverdine biosynthetic process, accepted in this review, is_a secondary metabolite biosynthetic process. Supporting Evidence: PMID:15271355 A pvdD mutant did not synthesize pyoverdine |
| GO:0044550 secondary metabolite biosynthetic process | IEA GO_REF:0000117 | TOO GENERAL | Summary: Same claim as the IBA row. Reason: Entailed by GO:0002049 pyoverdine biosynthetic process, accepted here. Supporting Evidence: PMID:15271355 A pvdD mutant did not synthesize pyoverdine |
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Download this section (compressed HTML)Q: Does the C-terminal thioesterase of PvdD release the completed ferribactin precursor peptide, and does PvdD act within a membrane-associated pyoverdine NRPS complex (siderosome)?
Experiment: In vitro reconstitution of the PvdD thioesterase with a synthetic peptidyl-thioester mimic of the ferribactin precursor, and fluorescent tagging of chromosomal PvdD to test inner-membrane association under iron limitation.
Type: biochemical reconstitution
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