Curatorial Notes for phoB1 (A0A0H2M7F4, VPARA_10430) in Variovorax paradoxus TBEA6
1. Gene & Protein Identity
- UniProt Accession:
A0A0H2M7F4 (A0A0H2M7F4_VARPD)
- Gene Symbol:
phoB1
- Locus Tag / EMBL CDS:
VPARA_10430 / KLN58031.1 on contig JZWI01000005 (RefSeq:WP_021007058.1)
- Protein Length: 230 aa (25,832 Da); two-component response regulator consisting of an N-terminal CheY-like receiver domain (
PROSITE:PS50110 RESPONSE_REGULATORY at residues 5–121, Pfam:PF00072 Response_reg, CDD:cd17618 REC_OmpR_PhoB) with the conserved phosphoacceptor Asp54 (FT MOD_RES 54 /note="4-aspartylphosphate" in 50-LILLDWMLPGQSG-62), and a C-terminal OmpR/PhoB-type winged-helix DNA-binding effector domain (PROSITE:PS51755 OMPR_PHOB at residues 130–226, Pfam:PF00486 Trans_reg_C, CDD:cd00383).
- Specific Family:
InterPro:IPR011879 (Sig_transdc_resp-reg_PhoB), NCBIfam:TIGR02154 (PhoB), PANTHER:PTHR48111:SF40 (PHOSPHATE REGULON TRANSCRIPTIONAL REGULATORY PROTEIN PHOB).
2. Operon Context on Contig JZWI01000005
- Encoded immediately between
phoR1 (VPARA_10420, KLN58030.1) and phoU (VPARA_10440, KLN58032.1) within the phoR1-phoB1-phoU-pstB-pstA-pstC-pstS-ppx (VPARA_10420–VPARA_10490) phosphate regulon gene cluster.
3. Literature & Comparative Evidence
- PMID:24563032 (Gardner et al. 2014 J Bacteriol): Describes how PhoB is a winged-helix response regulator that upon aspartyl phosphorylation by PhoR under phosphate limitation forms a dimer, binds Pho-box DNA sequences upstream of Pho regulon genes (including
pstSCAB-phoU), and recruits RNA polymerase to activate transcription.
4. Annotation Review Decisions
GO:0000156 (phosphorelay response regulator activity, IEA GO_REF:0000120): ACCEPT — core MF of the N-terminal receiver domain (Asp54 phosphorylation site).GO:0000160 (phosphorelay signal transduction system, IEA GO_REF:0000002): ACCEPT — core BP.GO:0000976 (transcription cis-regulatory region binding, IEA GO_REF:0000120): ACCEPT — core MF of the C-terminal winged-helix domain binding Pho-box operators.GO:0003677 (DNA binding, IEA GO_REF:0000120): TOO_GENERAL — entailed by GO:0000976.GO:0005737 (cytoplasm, IEA GO_REF:0000044): TOO_GENERAL — entailed by GO:0005829 (cytosol).GO:0005829 (cytosol, IEA GO_REF:0000118): ACCEPT — core CC.GO:0006355 (regulation of DNA-templated transcription, IEA GO_REF:0000120): MODIFY -> GO:0045893 (positive regulation of DNA-templated transcription) — phosphorylated PhoB1 acts as a positive transcriptional activator of the Pho regulon (PMID:24563032, CC FUNCTION in file:VARPD/phoB1/phoB1-uniprot.txt).GO:0006817 (phosphate ion transport, IEA GO_REF:0000002): MODIFY -> GO:0016036 (cellular response to phosphate starvation) — PhoB1 is a cytoplasmic transcription factor that activates phosphate starvation response genes (including pstSCAB) rather than a membrane transporter.GO:0032993 (protein-DNA complex, IEA GO_REF:0000118): KEEP_AS_NON_CORE — transient nucleoprotein complex when bound to Pho-box promoters.GO:0001216 (DNA-binding transcription activator activity, IC from file:VARPD/phoB1/phoB1-uniprot.txt): NEW.GO:0045893 (positive regulation of DNA-templated transcription, IC from file:VARPD/phoB1/phoB1-uniprot.txt): NEW.GO:0016036 (cellular response to phosphate starvation, IC from file:VARPD/phoB1/phoB1-uniprot.txt): NEW.