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6  structures 146  species 0  interactions 188  sequences 3  architectures

Family: SopE_GEF (PF07487)

Summary: SopE GEF domain

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SopE GEF domain Provide feedback

This family represents the C-terminal guanine nucleotide exchange factor (GEF) domain of SopE. Salmonella typhimurium employs a type III secretion system to inject bacterial toxins into the host cell cytosol. These toxins transiently activate Rho family GTP-binding protein-dependent signaling cascades to induce cytoskeletal rearrangements. SopE, can activate Cdc42, an essential component of the host cellular signaling cascade, in a Dbl-like fashion despite its lack of sequence similarity to Dbl-like proteins, the Rho-specific eukaryotic guanine nucleotide exchange factors [1].

Literature references

  1. Buchwald G, Friebel A, Galan JE, Hardt WD, Wittinghofer A, Scheffzek K; , EMBO J 2002;21:3286-3295.: Structural basis for the reversible activation of a Rho protein by the bacterial toxin SopE. PUBMED:12093730 EPMC:12093730


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR016019

The type III secretion system of Gram-negative bacteria is used to transport virulence factors from the pathogen directly into the host cell [PUBMED:9618447] and is only triggered when the bacterium comes into close contact with the host. Effector proteins secreted by the type III system do not possess a secretion signal, and are considered unique because of this. Salmonella spp. secrete an effector protein called SopE that is responsible for stimulating the reorganisation of the host cell actin cytoskeleton, and ruffling of the cellular membrane [PUBMED:9482928]. It acts as a guanyl-nucleotide-exchange factor on Rho-GTPase proteins such as Cdc42 and Rac. As it is imperative for the bacterium to revert the cell back to its "normal" state as quickly as possible, another tyrosine phosphatase effector called SptP reverses the actions brought about by SopE [PUBMED:11316807].

Recently, it has been found that SopE and its protein homologue SopE2 can activate different sets of Rho-GTPases in the host cell [PUBMED:11316807]. Far from being a redundant set of two similar type III effectors, they both act in unison to specifically activate different Rho-GTPase signalling cascades in the host cell during infection.

This entry represents the guanine nucleotide exchange factor domain of SopE. This domain has an alpha-helical structure consisting of two three-helix bundles arranged in a lamdba shape [PUBMED:12093730, PUBMED:15379540].

Gene Ontology

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Domain organisation

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Alignments

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Representative proteomes NCBI
(80)
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RP35
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  Seed
(2)
Full
(188)
Representative proteomes NCBI
(80)
Meta
(0)
RP15
(3)
RP35
(3)
RP55
(4)
RP75
(6)
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  Seed
(2)
Full
(188)
Representative proteomes NCBI
(80)
Meta
(0)
RP15
(3)
RP35
(3)
RP55
(4)
RP75
(6)
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You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.

External links

MyHits provides a collection of tools to handle multiple sequence alignments. For example, one can refine a seed alignment (sequence addition or removal, re-alignment or manual edition) and then search databases for remote homologs using HMMER3.

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Curation and family details

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Curation View help on the curation process

Seed source: Pfam-B_18665 (release 7.8)
Previous IDs: none
Type: Domain
Author: Finn RD, Moxon SJ
Number in seed: 2
Number in full: 188
Average length of the domain: 160.40 aa
Average identity of full alignment: 71 %
Average coverage of the sequence by the domain: 70.50 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 19.6 19.6
Trusted cut-off 20.8 22.6
Noise cut-off 18.7 16.7
Model length: 165
Family (HMM) version: 8
Download: download the raw HMM for this family

Species distribution

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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 SopE_GEF domain has been found. There are 6 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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