Please note: this site relies heavily on the use of javascript. Without a javascript-enabled browser, this site will not function correctly. Please enable javascript and reload the page, or switch to a different browser.
8  structures 159  species 2  interactions 184  sequences 6  architectures

Family: YopE (PF03545)

Summary: Yersinia virulence determinant (YopE)

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 "YopE protein domain". More...

YopE protein domain Edit Wikipedia article

YopE
PDB 1hy5 EBI.jpg
crystal structure of the catalytic domain of yope-yersinia pestis gap effector protein.
Identifiers
Symbol YopE
Pfam PF03545
InterPro IPR014773
SCOP 1g4w
SUPERFAMILY 1g4w

In molecular biology, the protein domain YopE refers to the secretion of virulence factors in Gram-negative bacteria involves transportation of the protein across two membranes to reach the cell exterior. It not only infects the host cell but also protects the bacteria. It undergoes several mechanisms to evade the hosts immune system. This particular protein domain can be referred to as a Rho GTPase-activating protein (GAP).

Function

YopE is an effector protein of the bacteriaYersinia. It functions as a Rho GTPase-activating protein (GAP). YopE acts as both a virulence factor and a protective antigen. In order to evade detection by the host, YopE uses a number of different eukaryotic signalling pathways to counteract innate and adaptive immune responses of the host. YopE targets the small GTPases: RhoA, Rac1, and Rac2. YopE GAP activity inhibits two common methods of host immunity - phagocytosis and reactive oxygen species generation. Additionally, it is thought that YopE targets the following immune cells, in particular:

Evidence also suggests that CD8 T lymphocyte cells mediate protection against Yersinia by production of cytokines (e.g., tumor necrosis factor alpha [TNF-alpha] and gamma interferon [IFN]) and by killing bacteria-associated host cells to promote internalization by neighbouring phagocytes.[1][2]

Structure

Structurally speaking, YopE has 4 alpha helices arranged in a left handed Four-helical up-and-down bundle. This bundle acts as the GAP domain, because arginine from an alpha helix is inserted into a GTP-ase which catalyses GTP hydrolysis through stabilisation of the transition state.[3]

References

  1. ^ Rosqvist R, Forsberg A, Rimpiläinen M, Bergman T, Wolf-Watz H (April 1990). "The cytotoxic protein YopE of Yersinia obstructs the primary host defence". Mol. Microbiol. 4 (4): 657–67. doi:10.1111/j.1365-2958.1990.tb00635.x. PMID 2191183. 
  2. ^ Cheng LW, Schneewind O (July 1999). "Yersinia enterocolitica type III secretion. On the role of SycE in targeting YopE into HeLa cells". J. Biol. Chem. 274 (31): 22102–8. doi:10.1074/jbc.274.31.22102. PMID 10419539. 
  3. ^ Stebbins CE, Galán JE (2000). "Modulation of host signaling by a bacterial mimic: structure of the Salmonella effector SptP bound to Rac1.". Mol Cell 6 (6): 1449–60. PMID 11163217. 

This article incorporates text from the public domain Pfam and InterPro IPR014773

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.

Yersinia virulence determinant (YopE) Provide feedback

No Pfam abstract.

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR014773

Secretion of virulence factors in Gram-negative bacteria involves transportation of the protein across two membranes to reach the cell exterior. There have been four secretion systems described in animal enteropathogens, such as Salmonella and Yersinia, with further sequence similarities in plant pathogens like Ralstonia and Erwinia [PUBMED:9618447].

The type III secretion system is of great interest, as it is used to transport virulence factors from the pathogen directly into the host cell and is only triggered when the bacterium comes into close contact with the host. The protein subunits of the system are very similar to those of bacterial flagellar biosynthesis. However, while the latter forms a ring structure to allow secretion of flagellin and is an integral part of the flagellum itself [PUBMED:9618447], type III subunits in the outer membrane translocate secreted proteins through a channel-like structure.

Exotoxins secreted by the type III system do not possess a secretion signal, and are considered unique for this reason [PUBMED:9618447]. Yersinia secrete a Rho GTPase-activating protein, YopE [PUBMED:2307658, PUBMED:2191183], that disrupts the host cell actin cytoskeleton. YopE is regulated by another bacterial gene, SycE [PUBMED:10419539], that enables the exotoxin to remain soluble in the bacterial cytoplasm. A similar protein, exoenzyme S from Pseudomonas aeruginosa, has both ADP-ribosylation and GTPase activity [PUBMED:2191183, PUBMED:10419539].

Domain organisation

Below is a listing of the unique domain organisations or architectures in which this domain is found. More...

Loading domain graphics...

Alignments

We store a range of different sequence alignments for families. As well as the seed alignment from which the family is built, we provide the full alignment, generated by searching the sequence database using the family HMM. We also generate alignments using four representative proteomes (RP) sets, the NCBI sequence database, and our metagenomics sequence database. More...

View options

We make a range of alignments for each Pfam-A family. You can see a description of each above. You can view these alignments in various ways but please note that some types of alignment are never generated while others may not be available for all families, most commonly because the alignments are too large to handle.

  Seed
(8)
Full
(184)
Representative proteomes NCBI
(96)
Meta
(0)
RP15
(2)
RP35
(3)
RP55
(4)
RP75
(7)
Jalview View  View  View  View  View  View  View   
HTML View  View  View  View  View  View     
PP/heatmap 1 View  View  View  View  View     
Pfam viewer View  View             

1Cannot generate PP/Heatmap alignments for seeds; no PP data available

Key: ✓ available, x not generated, not available.

Format an alignment

  Seed
(8)
Full
(184)
Representative proteomes NCBI
(96)
Meta
(0)
RP15
(2)
RP35
(3)
RP55
(4)
RP75
(7)
Alignment:
Format:
Order:
Sequence:
Gaps:
Download/view:

Download options

We make all of our alignments available in Stockholm format. You can download them here as raw, plain text files or as gzip-compressed files.

  Seed
(8)
Full
(184)
Representative proteomes NCBI
(96)
Meta
(0)
RP15
(2)
RP35
(3)
RP55
(4)
RP75
(7)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download    
Gzipped Download   Download   Download   Download   Download   Download   Download    

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.

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.

Note: You can also download the data file for the tree.

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: PRINTS
Previous IDs: Yers_vir_YopE;
Type: Family
Author: Griffiths-Jones SR
Number in seed: 8
Number in full: 184
Average length of the domain: 69.90 aa
Average identity of full alignment: 55 %
Average coverage of the sequence by the domain: 15.70 %

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 25.0 25.0
Trusted cut-off 26.0 59.5
Noise cut-off 23.4 22.7
Model length: 70
Family (HMM) version: 8
Download: download the raw HMM for this family

Species distribution

Sunburst controls

Show

This visualisation provides a simple graphical representation of the distribution of this family across species. You can find the original interactive tree in the adjacent tab. More...

Loading sunburst data...

Tree controls

Hide

The tree shows the occurrence of this domain across different species. More...

Loading...

Please note: for large trees this can take some time. While the tree is loading, you can safely switch away from this tab but if you browse away from the family page entirely, the tree will not be loaded.

Interactions

There are 2 interactions for this family. More...

Ras YopE

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 YopE domain has been found. There are 8 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.

Loading structure mapping...