PA5085 (dguR) encodes DguR, a LysR-type transcriptional regulator with an N-terminal helix-turn-helix DNA-binding domain and a C-terminal co-inducer-binding domain. DguR activates the divergently transcribed dguABC operon, which encodes the FAD-dependent D-amino acid dehydrogenase DguA and other proteins for D-glutamate and D-glutamine catabolism. Purified DguR binds a conserved 19 bp operator motif in the dguR-dguA intergenic region; binding does not need D-glutamate, but D-glutamate stabilises a preferred nucleoprotein complex, so DguR acts as a D-glutamate sensor. dguR mutants cannot grow on D-glutamate as sole carbon or nitrogen source.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0010628 positive regulation of gene expression | IBA GO_REF:0000033 | MODIFY | Summary: PAINT IBA from PTN001576694, seeded by E. coli LysR (P03030), not by PA5085. Reason: DguR is a transcriptional activator of dguABC (promoter-activity assays and EMSA), so positive regulation is the right direction. The mechanism is transcriptional, and the gene already carries the parent regulation-of-transcription IEA, so the specific GO:0045893 positive regulation of DNA-templated transcription is supported. Propagation Review Root cause: NO FAILURE CORE Failure modes: GRANULARITY MISMATCH Sources checked: PANTHER:PTN001576694 · PTN001576694 SUPPORTS TRANSFER Positive regulation is correct for DguR; the replacement only sharpens it to the transcriptional level, which DguR's own data show. UniProtKB:P03030 · E. coli LysR SUPPORTS TRANSFER LysR activates lysA transcription; consistent with DguR's activator role. Proposed replacements: positive regulation of DNA-templated transcription Supporting Evidence: PMID:25082951 The function of DguR as a transcriptional activator of the dguABC operon was demonstrated by promoter activity measurements in vivo and by mobility shift assays with purified His-tagged DguR in vitro. |
| GO:0043565 sequence-specific DNA binding | IBA GO_REF:0000033 | ACCEPT | Summary: PAINT IBA from PTN001576694, whose sole seed for this term is this gene's PseudoCAP IDA (PMID:25082951). The target appearing in its own WITH/FROM is expected. Reason: Directly shown for DguR, and sequence-specific operator binding through the LysR HTH is conserved across LysR-family regulators, so the node term suits the clade. Propagation Review Root cause: NO FAILURE CORE Sources checked: PANTHER:PTN001576694 · PTN001576694 SUPPORTS TRANSFER Worklist gives 11 leaf IBAs in 7 taxa; LysR-family HTH regulators. UniProtKB:Q9HU98 · PA5085 SUPPORTS TRANSFER The target's own experimental annotation is the IBD seed; expected, not circular. Supporting Evidence: PMID:25082951 binding of DguR to a highly conserved 19 bp sequence motif was further demonstrated |
| GO:0003677 DNA binding | IEA GO_REF:0000104 | MODIFY | Summary: UniRule-based IEA for LysR-family HTH proteins. Reason: Correct but general; DguR binds a specific 19 bp operator motif, so the more specific GO:0043565 sequence-specific DNA binding, which the gene already carries by IDA, is supported. Proposed replacements: sequence-specific DNA binding Supporting Evidence: PMID:25082951 binding of DguR to a highly conserved 19 bp sequence motif was further demonstrated |
| GO:0003700 DNA-binding transcription factor activity | IEA GO_REF:0000002 | ACCEPT | Summary: InterPro2GO from the LysR HTH domain (IPR000847). Reason: DguR binds its operator and activates dguABC transcription, which is the definition of a DNA-binding transcription factor; this is the core molecular function. Supporting Evidence: PMID:25082951 The function of DguR as a transcriptional activator of the dguABC operon was demonstrated by promoter activity measurements in vivo and by mobility shift assays with purified His-tagged DguR in vitro. file:PSEAE/PA5085/PA5085-uniprot.txt LysR_HTH_N |
| GO:0006351 DNA-templated transcription | IEA GO_REF:0000104 | MARK AS OVER ANNOTATED | Summary: UniRule-based IEA for LysR-family regulators. Reason: DguR regulates transcription of dguABC; it is not a component of the transcription machinery. Its process is captured by positive regulation of DNA-templated transcription. Supporting Evidence: PMID:25082951 DguR as a D-Glu sensor and transcriptional activator of the dguA promoter |
| GO:0006355 regulation of DNA-templated transcription | IEA GO_REF:0000120 | MODIFY | Summary: Combined InterPro/UniRule IEA. Reason: Correct but general; DguR is shown to be an activator, so GO:0045893 positive regulation of DNA-templated transcription is supported. Proposed replacements: positive regulation of DNA-templated transcription Supporting Evidence: PMID:25082951 DguR as a D-Glu sensor and transcriptional activator of the dguA promoter |
| GO:0043565 sequence-specific DNA binding | IDA PMID:25082951 Functional characterization of the dguRABC locus for D-Glu a... | ACCEPT | Summary: PseudoCAP IDA from EMSA with purified His-tagged DguR. Sole seed of the GO:0043565 IBD at PTN001576694. Reason: Mobility-shift assays with purified DguR, including binding to a conserved 19 bp motif, are direct evidence of sequence-specific DNA binding. Supporting Evidence: PMID:25082951 binding of DguR to a highly conserved 19 bp sequence motif was further demonstrated |
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Download this section (compressed HTML)Q: Does D-glutamate bind DguR's co-inducer domain directly, and which residues confer D- over L-glutamate selectivity?
Experiment: Measure D- and L-glutamate binding to purified DguR (ITC or thermal shift) and map the co-inducer pocket by mutagenesis.
Type: biochemical binding assay
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