Biopolymer transport protein ExbB4 (VPARA_25810) in Variovorax paradoxus strain TBEA6 is a 238-amino-acid integral inner-membrane multi-pass protein containing three transmembrane alpha-helices (residues 20-41, 127-150, and 174-195) and a conserved MotA/TolQ/ExbB proton-channel domain (Pfam PF01618, InterPro IPR002898, PANTHER PTHR30625:SF14, residues 100-201). Encoded in the syntenic exbD5-exbB4-tonB-bfrD1 (VPARA_25800-VPARA_25830) siderophore-uptake gene cluster, ExbB4 assembles with ExbD5 (VPARA_25800) and TonB (VPARA_25820) into the plasma-membrane TonB-ExbB-ExbD energy-transducing complex, where the ExbB pentamer forms the proton-conducting transmembrane stator that harvests the cytoplasmic-membrane proton-motive force and transmits mechanical energy through TonB to outer-membrane TonB-dependent ferric-siderophore receptors such as BfrD1 (VPARA_25830).
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0005886 plasma membrane | IEA GO_REF:0000120 | ACCEPT | Summary: Accurate core subcellular localization; ExbB4 is an integral inner-membrane multi-pass protein with three transmembrane helices. Reason: ExbB4 (VPARA_25810) contains three transmembrane alpha-helices (residues 20-41, 127-150, and 174-195) that embed the MotA/TolQ/ExbB proton-channel domain in the bacterial plasma (inner) membrane. Supporting Evidence: UniProtKB:A0A0H2MHH3 FT TRANSMEM 20..41 FT /note="Helical" FT /evidence="ECO:0000256|SAM:Phobius" PMID:37219427 Energy is derived from the proton motif force (pmf) of the cytoplasmic membrane (CM) through the action of three proteins, namely, TonB, ExbB, and ExbD, which are located in the CM and extend into the periplasm. |
| GO:0016020 membrane | IEA GO_REF:0000044 | TOO GENERAL | Summary: True but overly general parent term subsumed by the accepted GO:0005886 (plasma membrane) annotation. Reason: GO:0016020 (membrane) is true of ExbB4 but uninformative because the more specific cellular component GO:0005886 (plasma membrane) is already asserted on this review. Supporting Evidence: UniProtKB:A0A0H2MHH3 FT TRANSMEM 20..41 FT /note="Helical" FT /evidence="ECO:0000256|SAM:Phobius" |
| GO:0017038 protein import | IEA GO_REF:0000118 | MARK AS OVER ANNOTATED | Summary: TreeGrafter over-annotation propagated from opportunistic bacteriophage/colicin protein toxin entry in enterobacteria; physiologically ExbB4 energizes small-molecule ferric-siderophore uptake rather than protein import. Reason: PANTHER TreeGrafter (PTN004746216) propagates GO:0017038 (protein import) to ExbB homologs based on opportunistic exploitation of the TonB-ExbB-ExbD system by group B colicin protein toxins in enterobacteria. While the TonB motor can be parasitized by proteinaceous toxins in some bacteria, in Variovorax paradoxus VPARA_25810 (exbB4) is co-localized in the exbD5-exbB4-tonB-bfrD1 (VPARA_25800-VPARA_25830) ferric-siderophore uptake operon and its physiological role is energizing small-molecule nutrient uptake rather than protein import, making GO:0017038 an electronic over-annotation (matching the treatment in PSEPK/exbB). Supporting Evidence: PMID:20420522 TonB-dependent transporters (TBDTs) are bacterial outer membrane proteins that bind and transport ferric chelates, called siderophores, as well as vitamin B(12), nickel complexes, and carbohydrates. The transport process requires energy in the form of proton motive force and a complex of three inner membrane proteins, TonB-ExbB-ExbD, to transduce this energy to the outer membrane. PMID:37219427 ExbB forms a pentamer with a pore inside, in which an ExbD dimer resides. This complex harvests the energy of the pmf and transmits it to TonB. |
| GO:0015078 proton transmembrane transporter activity | IC PMID:37219427 Energization of Outer Membrane Transport by the ExbB ExbD Mo... | NEW | Summary: Core molecular function of the MotA/TolQ/ExbB proton-channel stator subunit (Pfam PF01618, residues 100-201). Reason: ExbB4 contains a conserved MotA/TolQ/ExbB proton-channel domain (Pfam PF01618, InterPro IPR002898, residues 100-201) spanning transmembrane helices 2 and 3 (residues 127-150 and 174-195, including conserved polar residues Ser135, Thr136, and Thr178) that conducts protons across the cytoplasmic membrane to harvest the proton-motive force. Supporting Evidence: UniProtKB:A0A0H2MHH3 FT DOMAIN 100..201 FT /note="MotA/TolQ/ExbB proton channel" FT /evidence="ECO:0000259|Pfam:PF01618" PMID:37219427 ExbB forms a pentamer with a pore inside, in which an ExbD dimer resides. This complex harvests the energy of the pmf and transmits it to TonB. |
| GO:1902600 proton transmembrane transport | IC PMID:37219427 Energization of Outer Membrane Transport by the ExbB ExbD Mo... | NEW | Summary: Direct biological process mediated by the ExbB4 proton-channel domain across the bacterial inner membrane. Reason: Together with the transmembrane aspartate of ExbD5, the pentameric ExbB4 MotA/TolQ/ExbB channel (Pfam PF01618) mediates proton translocation across the cytoplasmic membrane to convert the electrochemical proton gradient into mechanical work on TonB. Supporting Evidence: UniProtKB:A0A0H2MHH3 FT DOMAIN 100..201 FT /note="MotA/TolQ/ExbB proton channel" FT /evidence="ECO:0000259|Pfam:PF01618" PMID:37219427 Energy is derived from the proton motif force (pmf) of the cytoplasmic membrane (CM) through the action of three proteins, namely, TonB, ExbB, and ExbD, which are located in the CM and extend into the periplasm. |
| GO:0015891 siderophore transport | IC PMID:20420522 TonB-dependent transporters: regulation, structure, and func... | NEW | Summary: Pathway-level biological process supported by syntenic co-localization in the exbD5-exbB4-tonB-bfrD1 (VPARA_25800-VPARA_25830) ferric-siderophore import cluster. Reason: In Variovorax paradoxus TBEA6, exbB4 (VPARA_25810) is encoded in the four-gene exbD5-exbB4-tonB-bfrD1 (VPARA_25800-VPARA_25830) cluster immediately upstream of tonB (VPARA_25820) and the outer-membrane ferric-siderophore receptor bfrD1 (VPARA_25830), supplying the proton-motive-force energy required for active siderophore transport. Supporting Evidence: PMID:20420522 These transporters show high affinity and specificity for metal chelates called siderophores and require energy derived from the protonmotive force across the inner membrane to transport them (33, 87). To tap this energy source, TBDTs must interact with an inner membrane protein complex consisting of TonB, ExbB, and ExbD (72). |
| GO:0098797 plasma membrane protein complex | IC PMID:37219427 Energization of Outer Membrane Transport by the ExbB ExbD Mo... | NEW | Summary: Subunit of the inner-membrane TonB-ExbB-ExbD proton-motive-force harvesting complex. Reason: ExbB4 forms a pentameric pore in the inner membrane that encloses the ExbD5 dimer and associates with TonB to form the plasma-membrane TonB-ExbB-ExbD motor complex. Supporting Evidence: PMID:37219427 ExbB forms a pentamer with a pore inside, in which an ExbD dimer resides. This complex harvests the energy of the pmf and transmits it to TonB. PMID:20420522 The transport process requires energy in the form of proton motive force and a complex of three inner membrane proteins, TonB-ExbB-ExbD, to transduce this energy to the outer membrane. |
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Download this section (compressed HTML)Q: Can the several exbB/exbD paralogs in Variovorax paradoxus TBEA6 functionally substitute for exbB4 (VPARA_25810) and exbD5 (VPARA_25800) in energizing the co-localized TonB (VPARA_25820) and BfrD1 (VPARA_25830) ferric-siderophore transport system?
Suggested experts: Buchanan SK, Celia H, Noinaj N
Experiment: Construct single ΞexbB4 (VPARA_25810) and double ΞexbB4 ΞexbD5 deletion mutants in Variovorax paradoxus TBEA6 and measure ferric-siderophore uptake and iron-limited growth compared with ΞtonB (VPARA_25820).
Hypothesis: Deletion of exbB4 impairs BfrD1-mediated ferric-siderophore uptake, with any residual activity attributable to cross-complementation by TolQ/TolR or paralogous ExbB/ExbD complexes.
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