Summary: TonB dependent receptor
This is the Wikipedia entry entitled "TonB-dependent receptors". More...
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TonB dependent receptor Provide feedback
This model now only covers the conserved part of the barrel structure.
Buchanan SK, Smith BS, Venkatramani L, Xia D, Esser L, Palnitkar M, Chakraborty R, van der Helm D, Deisenhofer J; , Nat Struct Biol 1999;6:56-63.: Crystal structure of the outer membrane active transporter FepA from Escherichia coli. PUBMED:9886293 EPMC:9886293
Internal database links
|SCOOP:||DUF560 MtrB_PioB OMP_b-brl_3|
|Similarity to PfamA using HHSearch:||OMP_b-brl_3|
External database links
This tab holds annotation information from the InterPro database.
InterPro entry IPR000531
In Escherichia coli the TonB protein interacts with outer membrane receptor proteins that carry out high-affinity binding and energy-dependent uptake of specific substrates into the periplasmic space [PUBMED:14499604]. These substrates are either poorly permeable through the porin channels or are encountered at very low concentrations. In the absence of TonB, these receptors bind their substrates but do not carry out active transport. TonB-dependent regulatory systems consist of six components: a specialised outer membrane-localised TonB-dependent receptor (TonB-dependent transducer) that interacts with its energising TonB-ExbBD protein complex, a cytoplasmic membrane-localised anti-sigma factor and an extracytoplasmic function (ECF)-subfamily sigma factor [PUBMED:15993072]. The TonB complex senses signals from outside the bacterial cell and transmits them via two membranes into the cytoplasm, leading to transcriptional activation of target genes. The proteins that are currently known or presumed to interact with TonB include BtuB [PUBMED:12652322], CirA, FatA, FcuT, FecA [PUBMED:11872840], FhuA [PUBMED:9865695], FhuE, FepA [PUBMED:9886293], FptA, HemR, IrgA, IutA, PfeA, PupA and Tbp1. The TonB protein also interacts with some colicins. Most of these proteins contain a short conserved region at their N terminus [PUBMED:12957833].
This entry covers the conserved part of the beta-barrel structure at the C-terminal.
|Cellular component||membrane (GO:0016020)|
|Molecular function||receptor activity (GO:0004872)|
|Biological process||transport (GO:0006810)|
- the number of sequences which exhibit this architecture
a textual description of the architecture, e.g. Gla, EGF x 2, Trypsin.
This example describes an architecture with one
Gladomain, followed by two consecutive
EGFdomains, and finally a single
- the UniProt description of the protein sequence
- the number of residues in the sequence
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This clan gathers together a large set of beta barrel membrane proteins.Although these proteins have different numbers of beta strands in the barrel they have significant sequence similarity between families.
The clan contains the following 63 members:Ail_Lom Autotransporter Bac_surface_Ag BBP2 BBP2_2 Campylo_MOMP Channel_Tsx CopB DUF2490 DUF2860 DUF3078 DUF3138 DUF3187 DUF3308 DUF3575 DUF481 DUF560 Gcw_chp HP_OMP HP_OMP_2 KdgM LamB Legionella_OMP Lipoprot_C MDM10 MipA MSP MtrB_PioB Omp_AT OMP_b-brl OMP_b-brl_2 OMP_b-brl_3 OmpA_like OmpA_membrane Omptin OmpW Opacity OpcA OprB OprD OprF OstA_C PagL PagP Phenol_MetA_deg Porin_1 Porin_10 Porin_2 Porin_3 Porin_4 Porin_7 Porin_8 Porin_O_P Porin_OmpG ShlB Surface_Ag_2 TcfC Toluene_X TonB_dep_Rec TraF_2 TSA Usher YfaZ
We make a range of alignments for each Pfam-A family:
- the curated alignment from which the HMM for the family is built
- the alignment generated by searching the sequence database using the HMM
- Representative Proteomes (RPs) at 15%, 35%, 55% and 75% co-membership thresholds
- alignment generated by searching the UniProtKB sequence database using the family HMM
- alignment generated by searching the NCBI sequence database using the family HMM
- alignment generated by searching the metagenomics sequence database using the family HMM
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1Cannot generate PP/Heatmap alignments for seeds; no PP data available
Key: available, not generated, — not available.
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Curation and family details
|Seed source:||Yeats C|
|Author:||Bateman A, Yeats C|
|Number in seed:||658|
|Number in full:||10062|
|Average length of the domain:||277.30 aa|
|Average identity of full alignment:||15 %|
|Average coverage of the sequence by the domain:||35.47 %|
|HMM build commands:||
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 11927849 -E 1000 --cpu 4 HMM pfamseq
|Family (HMM) version:||21|
|Download:||download the raw HMM for this family|
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There are 8 interactions for this family. More...
We determine these interactions using iPfam, which considers the interactions between residues in three-dimensional protein structures and maps those interactions back to Pfam families. You can find more information about the iPfam algorithm in the journal article that accompanies the website.
For those sequences which have a structure in the Protein DataBank, we use the mapping between UniProt, PDB and Pfam coordinate systems from the PDBe group, to allow us to map Pfam domains onto UniProt sequences and three-dimensional protein structures. The table below shows the structures on which the TonB_dep_Rec domain has been found. There are 70 instances of this domain found in the PDB. Note that there may be multiple copies of the domain in a single PDB structure, since many structures contain multiple copies of the same protein seqence.
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