exbD5

UniProt ID: A0A0H2M1F3
Organism: Variovorax paradoxus
Review Status: COMPLETE
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Gene Description

Biopolymer transport protein ExbD5 (VPARA_25800) in Variovorax paradoxus strain TBEA6 is a 137-amino-acid inner-membrane type II single-pass protein (Pfam PF02472, InterPro IPR003400, PANTHER PTHR30558) containing an N-terminal transmembrane alpha-helix (residues 20-39) with the invariant proton-binding aspartate residue Asp23 (within 20-PLVDVMLVLLIIFIITVPVM-39) and a C-terminal periplasmic domain (residues 40-137). Encoded at the 5' end of the syntenic exbD5-exbB4-tonB-bfrD1 (VPARA_25800-VPARA_25830) ferric-siderophore uptake cluster, ExbD5 forms a central transmembrane dimer inside the inner-membrane ExbB4 pentamer pore, coupling proton translocation via Asp23 to periplasmic conformational changes that energize TonB (VPARA_25820) and drive active outer-membrane ferric-siderophore import through BfrD1 (VPARA_25830).

Existing Annotations Review

GO Term Evidence Action Reason
GO:0005886 plasma membrane
IEA
GO_REF:0000120 		ACCEPT
Summary: Accurate core subcellular localization; ExbD5 is anchored in the bacterial plasma (inner) membrane via its N-terminal transmembrane helix (residues 20-39).
Reason: ExbD5 (VPARA_25800) is a single-pass type II inner-membrane protein anchored in the cytoplasmic membrane by its N-terminal transmembrane alpha-helix (residues 20-39) within the central pore of the ExbB4 pentamer.
Supporting Evidence:
UniProtKB:A0A0H2M1F3
FT TRANSMEM 20..39 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:0022857 transmembrane transporter activity
IEA
GO_REF:0000002 		MODIFY
Summary: Correct but overly general molecular function; refine to GO:0015078 (proton transmembrane transporter activity) to reflect proton conduction via the conserved transmembrane aspartate Asp23 inside the ExbB-ExbD motor.
Reason: ExbD5 does not directly transport ferric-siderophores across the membrane; rather, its transmembrane helix (residues 20-39, carrying the invariant proton-binding residue Asp23) resides inside the ExbB4 pentamer pore to conduct protons across the inner membrane (GO:0015078).
Supporting Evidence:
UniProtKB:A0A0H2M1F3
DR PANTHER; PTHR30558; EXBD MEMBRANE COMPONENT OF PMF-DRIVEN MACROMOLECULE IMPORT SYSTEM; 1.
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:0055085 transmembrane transport
IEA
GO_REF:0000002 		MODIFY
Summary: Correct but overly general biological process; refine to GO:1902600 (proton transmembrane transport) and GO:0015891 (siderophore transport).
Reason: GO:0055085 (transmembrane transport) is a generic parent term. ExbD5 directly mediates inner-membrane proton transmembrane transport (GO:1902600) within the ExbB4-ExbD5 motor and is encoded in the exbD5-exbB4-tonB-bfrD1 (VPARA_25800-VPARA_25830) operon to energize outer-membrane siderophore transport (GO:0015891).
Supporting Evidence:
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.
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:0030288 outer membrane-bounded periplasmic space
IC
PMID:37219427
Energization of Outer Membrane Transport by the ExbB ExbD Mo... 		NEW
Summary: The C-terminal globular domain of ExbD5 (residues 40-137, Pfam PF02472) extends into the Gram-negative periplasmic space to interact with TonB.
Reason: While anchored in the plasma membrane (`GO:0005886`) via its N-terminal transmembrane helix (residues 20-39), the C-terminal soluble ExbD domain (residues 40-137) of single-pass type II VPARA_25800 resides in the outer membrane-bounded periplasmic space, where it couples proton translocation to conformational changes in TonB.
Supporting Evidence:
UniProtKB:A0A0H2M1F3
CC membrane {ECO:0000256|RuleBase:RU003879}; Single-pass type II membrane CC protein {ECO:0000256|RuleBase:RU003879}.
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:0098797 plasma membrane protein complex
IC
PMID:37219427
Energization of Outer Membrane Transport by the ExbB ExbD Mo... 		NEW
Summary: Dimeric inner-membrane rotor/coupling subunit residing within the ExbB pentamer pore of the TonB-ExbB-ExbD complex.
Reason: ExbD5 forms a homodimer inside the central lumen of the ExbB4 pentamer in the plasma-membrane TonB-ExbB-ExbD energy-transducing 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.

Core Functions

Dimeric inner-membrane proton-coupling subunit residing inside the ExbB4 pentamer pore of the TonB-ExbB-ExbD complex that uses its conserved transmembrane Asp23 residue to couple proton translocation to periplasmic energization of TonB-dependent ferric-siderophore import.

Molecular Function:
proton transmembrane transporter activity
Directly Involved In:
proton transmembrane transport siderophore transport
Cellular Locations:
plasma membrane outer membrane-bounded periplasmic space
In Complex:
plasma membrane protein complex
Supporting Evidence:
  • UniProtKB:A0A0H2M1F3
    FT TRANSMEM 20..39 FT /note="Helical" FT /evidence="ECO:0000256|SAM:Phobius"
  • 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.

References

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Suggested Questions for Experts

Q: How does protonation and deprotonation of the conserved transmembrane Asp23 residue in Variovorax paradoxus ExbD5 (VPARA_25800) coordinate periplasmic heterodimerization with TonB (VPARA_25820) during BfrD1-mediated siderophore import?

Suggested experts: Buchanan SK, Celia H, Postle K

Suggested Experiments

Experiment: Perform site-directed mutagenesis of the conserved transmembrane aspartate Asp23 (D23N and D23A) in Variovorax paradoxus TBEA6 ExbD5 (VPARA_25800) and assay iron-starvation growth and ferric-siderophore uptake.

Hypothesis: Substitution of Asp23 abolishes proton translocation through the ExbB4-ExbD5 motor and eliminates TonB-dependent ferric-siderophore import via BfrD1.

📚 Additional Documentation

Notes

(exbD5-notes.md)

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