BraC (PA1074) is the periplasmic substrate-binding protein of the LIV-I high-affinity branched-chain amino acid ABC transporter BraCDEFG of Pseudomonas aeruginosa. It is a type I periplasmic binding protein of the leucine-binding protein family, about 51% identical to Escherichia coli LivJ and LivK, made with a cleaved 26-residue signal peptide and recovered in osmotic shock fluid. BraC binds L-leucine, L-isoleucine, L-valine, L-threonine and L-alanine, and also L-homoserine, with nanomolar affinity, and delivers them to the BraDE permease and BraFG ATPases for sodium -independent uptake across the inner membrane.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0006865 amino acid transport | IEA GO_REF:0000002 | TOO GENERAL | Summary: InterPro2GO amino acid transport. Reason: Entailed by the accepted GO:1903805 and GO:1903806. |
| GO:0015803 branched-chain amino acid transport | IDA PMID:2509433 Cloning and nucleotide sequence of braC, the structural gene... | TOO GENERAL | Summary: PseudoCAP row. The braC plasmid restores LIV-I transport in the braC310 mutant (a complementation result; the abstract does not describe a direct assay with purified BraC). Reason: True, but entailed by the accepted GO:1903805 and GO:1903806, which are is_a descendants of branched-chain amino acid transport. |
| GO:0015808 L-alanine transport | IMP PMID:18833300 High-throughput phenotypic characterization of Pseudomonas a... | MODIFY | Summary: PseudoCAP row; the PA1074 Tn5 mutant fails to grow on L-alanine as carbon source. Reason: Sound, and backed by direct nanomolar L-alanine binding. The precise term is L-alanine import across plasma membrane (GO:1904273, is_a descendant), as on the braG review. Proposed replacements: L-alanine import across plasma membrane Supporting Evidence: PMID:18833300 In this work, mutants for each of these genes were found to be defective in Alanine metabolism PMID:31627455 ITC experiments revealed binding with nanomolar affinities for the five ligands identified in the study by Hoshino et al. [58] (Figure 6A), whereas no binding was detected for l-Met and d-Ala. |
| GO:0015818 isoleucine transport | IBA GO_REF:0000033 | TOO GENERAL | Summary: IBA from PTN002524712, seeded by E. coli LivJ (P0AD96, EcoCyc IMP) and this gene's own PseudoCAP IMP (expected self-appearance). Reason: Entailed by the accepted GO:1903806 L-isoleucine import across plasma membrane (is_a GO:0015818). |
| GO:0015820 L-leucine transport | IBA GO_REF:0000033 | MODIFY | Summary: IBA from PTN002524712, seeded by E. coli LivJ and LivK (P04816). Reason: Correct; BraC binds L-leucine with nanomolar affinity and LIV-I imports it. The specific term is L-leucine import across plasma membrane, as for the other LIV substrates on this gene. Propagation Review Root cause: NO FAILURE CORE Failure modes: GRANULARITY MISMATCH Sources checked: PANTHER:PTN002524712 · PTN002524712 SUPPORTS TRANSFER LivJ/LivK/BraC binding-protein clade; transfer sound, term general. UniProtKB:P0AD96 · E. coli LivJ SUPPORTS TRANSFER EcoCyc IMP leucine transport. UniProtKB:P04816 · E. coli LivK SUPPORTS TRANSFER EcoCyc EXP/IMP leucine transport, IPI L-leucine binding. Proposed replacements: L-leucine import across plasma membrane Supporting Evidence: PMID:31627455 ITC experiments revealed binding with nanomolar affinities for the five ligands identified in the study by Hoshino et al. [58] (Figure 6A), whereas no binding was detected for l-Met and d-Ala. |
| GO:0015829 valine transport | IBA GO_REF:0000033 | TOO GENERAL | Summary: IBA from PTN002524712, seeded by E. coli LivJ and this gene's own PseudoCAP IMP (expected self-appearance). Reason: Entailed by the accepted GO:1903805 L-valine import across plasma membrane. |
| GO:0030288 outer membrane-bounded periplasmic space | IBA GO_REF:0000033 | ACCEPT | Summary: IBA from PTN002524712, seeded by E. coli LivJ and LivK (IDA). Reason: BraC has a cleaved signal peptide and was purified from shock fluid. Supporting Evidence: PMID:2509433 Determination of the N-terminal amino acid sequence of the LIVAT-BP purified from P. aeruginosa shock fluid suggested that the N-terminal 26 residues of the gene product are cleaved off posttranslationally |
| GO:0042597 periplasmic space | IEA GO_REF:0000044 | TOO GENERAL | Summary: UniProt subcellular location mapping (periplasm). Reason: Entailed by the accepted GO:0030288 outer membrane-bounded periplasmic space. |
| GO:0042941 D-alanine transmembrane transport | IMP PMID:18833300 High-throughput phenotypic characterization of Pseudomonas a... | REMOVE | Summary: PseudoCAP row; partial (+/-) growth defect of the PA1074 Tn5 mutant on D-alanine as carbon source. Reason: Contradicted by direct binding data: purified BraC shows no binding of D-alanine by ITC. The weak growth phenotype of a possibly polar insertion is not evidence that BraC delivers D-alanine. Supporting Evidence: PMID:31627455 ITC experiments revealed binding with nanomolar affinities for the five ligands identified in the study by Hoshino et al. [58] (Figure 6A), whereas no binding was detected for l-Met and d-Ala. |
| GO:1903805 L-valine import across plasma membrane | IMP PMID:18833300 High-throughput phenotypic characterization of Pseudomonas a... | ACCEPT | Summary: PseudoCAP seed row for PTN002524712 (valine transport). Full text: the PA1074 mutant fails to use L-valine as nitrogen source. Seed verdict SOUND. Reason: A growth read-out, but consistent with direct nanomolar valine binding and with restoration of LIV-I transport by braC. Supporting Evidence: PMID:18833300 In this work, mutants for each of these genes were found to be defective in Alanine metabolism, while utilization of L-Valine and L-Isoleucine was also altered in some cases PMID:31627455 ITC experiments revealed binding with nanomolar affinities for the five ligands identified in the study by Hoshino et al. [58] (Figure 6A), whereas no binding was detected for l-Met and d-Ala. |
| GO:1903806 L-isoleucine import across plasma membrane | IMP PMID:18833300 High-throughput phenotypic characterization of Pseudomonas a... | ACCEPT | Summary: PseudoCAP seed row for PTN002524712 (isoleucine transport). Full text: the PA1074 mutant grows less well on L-isoleucine. Seed verdict SOUND. Reason: Consistent with direct nanomolar isoleucine binding and LIV-I complementation. Supporting Evidence: PMID:18833300 In this work, mutants for each of these genes were found to be defective in Alanine metabolism, while utilization of L-Valine and L-Isoleucine was also altered in some cases PMID:2509433 The plasmid carrying the LIVAT-BP gene restored the activity of the high-affinity branched-chain amino acid transport system (the leucine, isoleucine, valine [LIV-I] transport system) in the braC310 mutant of P. aeruginosa |
| GO:0070728 L-leucine binding | IDA PMID:31627455 Determination of Ligand Profiles for Pseudomonas aeruginosa ... | NEW | Summary: Proposed MF. ITC with purified BraC shows nanomolar binding of the LIVAT ligands, including L-leucine; no binding molecular function is annotated at present. Reason: Direct binding data, and the defining activity of the substrate-binding protein of LIV-I. Supporting Evidence: PMID:31627455 ITC experiments revealed binding with nanomolar affinities for the five ligands identified in the study by Hoshino et al. [58] (Figure 6A), whereas no binding was detected for l-Met and d-Ala. |
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