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exbD [ Escherichia coli str. K-12 substr. MG1655 ]

Gene ID: 946345, updated on 11-Sep-2024

Summary

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Official Symbol
exbD
Primary source
ECOCYC:EG10272
Locus tag
b3005
See related
ASAP:ABE-0009866
Gene type
protein coding
RefSeq status
PROVISIONAL
Organism
Escherichia coli str. K-12 substr. MG1655 (strain: K-12, substrain: MG1655)
Lineage
Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales; Enterobacteriaceae; Escherichia
Also known as
ECK2998
Summary
ExbB and ExbD proteins function as part of the TonB-dependent energy transduction system for the import of iron-siderophore complexes and vitamin B12 across the outer membrane. [More information is available at EcoCyc: EG10272].
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Genomic context

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Sequence:
NC_000913.3 (3150818..3151243, complement)

NC_000913.3Genomic Context describing neighboring genes Neighboring gene UPF0114 family protein YqhA Neighboring gene NADP(+)-dependent aldehyde reductase Neighboring gene Ton complex subunit ExbB Neighboring gene cystathionine beta-lyase/L-cysteine desulfhydrase/alanine racemase

Genomic regions, transcripts, and products

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Genomic Sequence:
NC_000913.3

Go to nucleotide: Graphics FASTA GenBank

Bibliography

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Related articles in PubMed

  1. Membrane topology of the Escherichia coli ExbD protein. Kampfenkel K, et al. J Bacteriol, 1992 Aug. PMID 1644779, Free PMC Article
  2. Cryo-EM structure of the bacterial Ton motor subcomplex ExbB-ExbD provides information on structure and stoichiometry. Celia H, et al. Commun Biol, 2019. PMID 31602407, Free PMC Article
  3. Hexameric and pentameric complexes of the ExbBD energizer in the Ton system. Maki-Yonekura S, et al. Elife, 2018 Apr 17. PMID 29661272, Free PMC Article
  4. Structural insight into the role of the Ton complex in energy transduction. Celia H, et al. Nature, 2016 Oct 6. PMID 27654919, Free PMC Article
  5. Coordinated rearrangements between cytoplasmic and periplasmic domains of the membrane protein complex ExbB-ExbD of Escherichia coli. Sverzhinsky A, et al. Structure, 2014 May 6. PMID 24657092

See all (51) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Single-particle cryo-electron microscopy shows that the ExbB pentamer encloses a dimer of ExbD in its transmembrane pore, and not a monomer as previously reported. Ton subcomplex consists of a pentamer of ExbB enclosing a dimer of ExbD TM domains. The essential Asp25 residues on ExbD are in close proximity to the conserved Thr 148 and 181 on ExbB.
    Title: Cryo-EM structure of the bacterial Ton motor subcomplex ExbB-ExbD provides information on structure and stoichiometry.
  2. Channel current measurement and 2D crystallography support the existence and transition of the two oligomeric states in membranes. The hexameric complex consists of six ExbB subunits and three ExbD transmembrane helices enclosed within the central channel.
    Title: Hexameric and pentameric complexes of the ExbBD energizer in the Ton system.
  3. ExbB-ExbD-TonB form complex in molar ratios of 4:1:1.
    Title: Membrane Protein Complex ExbB4-ExbD1-TonB1 from Escherichia coli Demonstrates Conformational Plasticity.
  4. These observations supported the hypothesis that ExbD couples TonB to the protonmotive force, with concomitant transitions of ExbD and TonB periplasmic domains from unenergized to energized heterodimers.
    Title: ExbD mutants define initial stages in TonB energization.
  5. ExbD-TonB interactions required ExbD transmembrane domain residue D25.
    Title: The same periplasmic ExbD residues mediate in vivo interactions between ExbD homodimers and ExbD-TonB heterodimers.
  6. ExbB(6) and ExbB(6)ExbD(1) are subcomplexes on which the final complex including TonB is assembled
    Title: Oligomeric structure of ExbB and ExbB-ExbD isolated from Escherichia coli as revealed by LILBID mass spectrometry.
  7. Proton-motive force is required for the interaction of ExbD and TonB periplasmic domains trapped by formaldehyde cross-linking.
    Title: Cytoplasmic membrane protonmotive force energizes periplasmic interactions between ExbD and TonB.
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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Gene Ontology Provided by EcoCyc

Function Evidence Code Pubs
enables energy transducer activity IMP
Inferred from Mutant Phenotype
more info
 PubMed 
enables identical protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables protein homodimerization activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables transmembrane transporter activity IEA
Inferred from Electronic Annotation
more info
  
Process Evidence Code Pubs
involved_in bacteriocin transport IEA
Inferred from Electronic Annotation
more info
  
involved_in cobalamin transport NAS
Non-traceable Author Statement
more info
 PubMed 
involved_in intracellular iron ion homeostasis NAS
Non-traceable Author Statement
more info
 PubMed 
involved_in intracellular monoatomic cation homeostasis NAS
Non-traceable Author Statement
more info
 PubMed 
acts_upstream_of_or_within protein stabilization IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in protein transport IEA
Inferred from Electronic Annotation
more info
  
involved_in transmembrane transport IEA
Inferred from Electronic Annotation
more info
  
Component Evidence Code Pubs
located_in cell outer membrane NAS
Non-traceable Author Statement
more info
 PubMed 
located_in membrane IEA
Inferred from Electronic Annotation
more info
  
located_in membrane NAS
Non-traceable Author Statement
more info
 PubMed 
is_active_in plasma membrane IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in plasma membrane IDA
Inferred from Direct Assay
more info
 PubMed 
located_in plasma membrane IEA
Inferred from Electronic Annotation
more info
  
part_of plasma membrane protein complex IDA
Inferred from Direct Assay
more info
 PubMed 
part_of transmembrane transporter complex NAS
Non-traceable Author Statement
more info
 PubMed 

General protein information

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Preferred Names
Ton complex subunit ExbD

NCBI Reference Sequences (RefSeq)

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Genome Annotation

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference assembly

Genomic

  1. NC_000913.3 Reference assembly

    Range
    3150818..3151243 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NP_417478.1 Ton complex subunit ExbD [Escherichia coli str. K-12 substr. MG1655]

    See identical proteins and their annotated locations for NP_417478.1

    Status: PROVISIONAL

    UniProtKB/TrEMBL
    A0A376M2F8, A0A5D8MUR0
    Conserved Domains (1) summary
    PRK11267
    Location:1 → 141
    PRK11267; biopolymer transport protein ExbD; Provisional
Nucleotide Protein
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