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185  structures 3709  species 0  interactions 86128  sequences 158  architectures

Family: TonB_dep_Rec (PF00593)

Summary: TonB dependent receptor

Pfam includes annotations and additional family information from a range of different sources. These sources can be accessed via the tabs below.

This is the Wikipedia entry entitled "Outer membrane receptor". More...

Outer membrane receptor Edit Wikipedia article

TonB dependent receptor
1qfg opm.png
Structure of ferric hydroxamate uptake receptor.[1]
Identifiers
SymbolTonB_dep_Rec
PfamPF00593
Pfam clanCL0193
InterProIPR000531
PROSITEPDOC00354
SCOP22fcp / SCOPe / SUPFAM
TCDB1.B.14
OPM superfamily33
OPM protein1qfg
CDDcd01347

Outer membrane receptors, also known as TonB-dependent receptors, are a family of beta barrel proteins named for their localization in the outer membrane of gram-negative bacteria. TonB complexes sense signals from the outside of bacterial cells and transmit them into the cytoplasm, leading to transcriptional activation of target genes. TonB-dependent receptors in gram-negative bacteria are associated with the uptake and transport of large substrates such as iron siderophore complexes and vitamin B12.[2]

TonB interactions with other proteins

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.[3] These substrates are either poorly transported through non-specific 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 protein protein components.[4]

The proteins that are currently known or presumed to interact with TonB include BtuB,[5] CirA, FatA, FcuT, FecA,[6] FhuA,[7] FhuE, FepA,[8] FptA, HemR, IrgA, IutA, PfeA, PupA, LbpA and TbpA. The TonB protein also interacts with some colicins. Most of these proteins contain a short conserved region at their N-terminus.[9]

TonB-dependent receptor plug domain

TonB-dependent Receptor Plug Domain
Identifiers
SymbolPlug
PfamPF07715
InterProIPR012910
SCOP21fi1 / SCOPe / SUPFAM

TonB-dependent receptors include a plug domain, an independently folding subunit that acts as the channel gate, blocking the pore until the channel is bound by ligand. At this point it undergoes conformational changes, opening the channel.[10]

TonB as phage receptor

TonB also acts as a receptor for Salmonella bacteriophage H8. In fact, H8 infection is TonB dependent.[11]

References

  1. ^ Ferguson AD, Welte W, Hofmann E, et al. (June 2000). "A conserved structural motif for lipopolysaccharide recognition by procaryotic and eucaryotic proteins". Structure. 8 (6): 585–92. doi:10.1016/S0969-2126(00)00143-X. PMID 10873859.
  2. ^ Koebnik, Ralf (2000). "Structures and function of bacterial outer membrane proteins: barrels in a nutshell". MicroReview. 37 (2): 239–253.
  3. ^ Kadner RJ, Chimento DP, Wiener MC (2003). "The Escherichia coli outer membrane cobalamin transporter BtuB: structural analysis of calcium and substrate binding, and identification of orthologous transporters by sequence/structure conservation". J. Mol. Biol. 332 (5): 999–1014. doi:10.1016/j.jmb.2003.07.005. PMID 14499604.
  4. ^ Koebnik R (2005). "TonB-dependent trans-envelope signalling: the exception or the rule?". Trends Microbiol. 13 (8): 343–7. doi:10.1016/j.tim.2005.06.005. PMID 15993072.
  5. ^ Kadner RJ, Chimento DP, Wiener MC, Mohanty AK (2003). "Substrate-induced transmembrane signaling in the cobalamin transporter BtuB". Nat. Struct. Biol. 10 (5): 394–401. doi:10.1038/nsb914. PMID 12652322. S2CID 24883519.
  6. ^ Deisenhofer J, Smith BS, Esser L, Chakraborty R, van der Helm D, Ferguson AD (2002). "Structural basis of gating by the outer membrane transporter FecA". Science. 295 (5560): 1715–1719. Bibcode:2002Sci...295.1715F. doi:10.1126/science.1067313. PMID 11872840. S2CID 86844549.
  7. ^ Moras D, Rosenbusch JP, Mitschler A, Rees B, Locher KP, Koebnik R, Moulinier L (1998). "Transmembrane signaling across the ligand-gated FhuA receptor: crystal structures of free and ferrichrome-bound states reveal allosteric changes". Cell. 95 (6): 771–778. doi:10.1016/S0092-8674(00)81700-6. PMID 9865695. S2CID 16899072.
  8. ^ Deisenhofer J, Xia D, Buchanan SK, Smith BS, Venkatramani L, Esser L, Palnitkar M, Chakraborty R, van der Helm D (1999). "Crystal structure of the outer membrane active transporter FepA from Escherichia coli". Nat. Struct. Biol. 6 (1): 56–63. doi:10.1038/4931. PMID 9886293. S2CID 20231287.
  9. ^ Klebba PE (2003). "Three paradoxes of ferric enterobactin uptake". Front. Biosci. 8 (6): s1422–s1436. doi:10.2741/1233. PMID 12957833.
  10. ^ Buchanan SK, Evans RW, Ghirlando R, Oke M, Sarra R, Farnaud S, Gorringe AR (2004). "The plug domain of a neisserial TonB-dependent transporter retains structural integ rity in the absence of its transmembrane beta-barrel". FEBS Lett. 564 (3): 294–300. doi:10.1016/S0014-5793(04)00196-6. PMID 15111112. S2CID 20056753.
  11. ^ Rabsch, W.; Ma, L.; Wiley, G.; Najar, F. Z.; Kaserer, W.; Schuerch, D. W.; Klebba, J. E.; Roe, B. A.; Laverde Gomez, J. A. L.; Schallmey, M.; Newton, S. M. C.; Klebba, P. E. (2007). "FepA- and TonB-Dependent Bacteriophage H8: Receptor Binding and Genomic Sequence". Journal of Bacteriology. 189 (15): 5658–5674. doi:10.1128/JB.00437-07. PMC 1951831. PMID 17526714.


This page is based on a Wikipedia article. The text is available under the Creative Commons Attribution/Share-Alike License.

This is the Wikipedia entry entitled "TonB-dependent receptors". More...

TonB-dependent receptors Edit Wikipedia article

This page is based on a Wikipedia article. The text is available under the Creative Commons Attribution/Share-Alike License.

This tab holds the annotation information that is stored in the Pfam database. As we move to using Wikipedia as our main source of annotation, the contents of this tab will be gradually replaced by the Wikipedia tab.

TonB dependent receptor Provide feedback

This model now only covers the conserved part of the barrel structure.

Literature references

  1. 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

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 domain structure at the C terminus. This beta-barrel domain is also found in vitamin B12 transporter BtuB [ PUBMED:17548346 ] and ferric citrate outer membrane transporter FecA [ PUBMED:11872840 ] among others.

Domain organisation

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Alignments

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  Seed
(657)
Full
(86128)
Representative proteomes UniProt
(453374)
RP15
(7201)
RP35
(33771)
RP55
(88851)
RP75
(176577)
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  Seed
(657)
Full
(86128)
Representative proteomes UniProt
(453374)
RP15
(7201)
RP35
(33771)
RP55
(88851)
RP75
(176577)
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  Seed
(657)
Full
(86128)
Representative proteomes UniProt
(453374)
RP15
(7201)
RP35
(33771)
RP55
(88851)
RP75
(176577)
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Gzipped Download     Download   Download        

You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.

HMM logo

HMM logos is one way of visualising profile HMMs. Logos provide a quick overview of the properties of an HMM in a graphical form. You can see a more detailed description of HMM logos and find out how you can interpret them here. More...

Trees

This page displays the phylogenetic tree for this family's seed alignment. We use FastTree to calculate neighbour join trees with a local bootstrap based on 100 resamples (shown next to the tree nodes). FastTree calculates approximately-maximum-likelihood phylogenetic trees from our seed alignment.

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Curation and family details

This section shows the detailed information about the Pfam family. You can see the definitions of many of the terms in this section in the glossary and a fuller explanation of the scoring system that we use in the scores section of the help pages.

Curation View help on the curation process

Seed source: Yeats C
Previous IDs: TonB_boxC;
Type: Family
Sequence Ontology: SO:0100021
Author: Bateman A , Yeats C
Number in seed: 657
Number in full: 86128
Average length of the domain: 544.90 aa
Average identity of full alignment: 11 %
Average coverage of the sequence by the domain: 63.82 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 61295632 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 27.0 27.0
Trusted cut-off 27.0 27.0
Noise cut-off 26.9 26.9
Model length: 470
Family (HMM) version: 27
Download: download the raw HMM for this family

Species distribution

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Archea Archea Eukaryota Eukaryota
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Viroids Viroids Unclassified sequence Unclassified sequence

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Structures

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 185 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 sequence.

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AlphaFold Structure Predictions

The list of proteins below match this family and have AlphaFold predicted structures. Click on the protein accession to view the predicted structure.

Protein Predicted structure External Information
O86241 View 3D Structure Click here
P05825 View 3D Structure Click here
P06129 View 3D Structure Click here
P06971 View 3D Structure Click here
P0C6R0 View 3D Structure Click here
P0CL48 View 3D Structure Click here
P13036 View 3D Structure Click here
P16869 View 3D Structure Click here
P17315 View 3D Structure Click here
P37409 View 3D Structure Click here
P42512 View 3D Structure Click here
P44600 View 3D Structure Click here
P44795 View 3D Structure Click here
P44809 View 3D Structure Click here
P44836 View 3D Structure Click here
P44970 View 3D Structure Click here
P45114 View 3D Structure Click here
P46359 View 3D Structure Click here
P48632 View 3D Structure Click here
P75780 View 3D Structure Click here
P76115 View 3D Structure Click here
P81549 View 3D Structure Click here
Q05098 View 3D Structure Click here
Q06379 View 3D Structure Click here
Q2YJB2 View 3D Structure Click here
Q32AE6 View 3D Structure Click here
Q47162 View 3D Structure Click here
Q47952 View 3D Structure Click here
Q56989 View 3D Structure Click here
Q57408 View 3D Structure Click here
Q6CZB5 View 3D Structure Click here
Q6LLU3 View 3D Structure Click here
Q7DDB6 View 3D Structure Click here
Q7MQ42 View 3D Structure Click here
Q7MYE3 View 3D Structure Click here
Q7VNU1 View 3D Structure Click here
Q83IS4 View 3D Structure Click here
Q87KN9 View 3D Structure Click here
Q8A1G1 View 3D Structure Click here
Q8X714 View 3D Structure Click here