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1  structure 69  species 0  interactions 74  sequences 1  architecture

Family: YopR_core (PF09025)

Summary: YopR Core

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This is the Wikipedia entry entitled "YopR bacterial protein domain". More...

YopR bacterial protein domain Edit Wikipedia article

YopR_core
PDB 1z21 EBI.jpg
crystal structure of the core domain of yersinia pestis virulence factor yopr
Identifiers
Symbol YopR_core
Pfam PF09025
InterPro IPR013349

In molecular biology, YopR is a protein domain commonly found in gram negative bacteria, in particular Yersinia and is a core domain. Proteins in this entry are type III secretion system effectors. They are named differently in different species and in Yersinia has been designated YopR (Yersinia outer protein R) which is encoded by the YscH (Yersinia secretion H) gene. This Yop protein is unusual in that it is released to the extracellular environment rather than injected directly into the target cell as are most Yop proteins. A hallmark of Yersinia type III machines is the presence of needles extending from the bacterial surface. Needles perform two functions, firstly, as a channel to export effectors into the immune cells and secondly as a sensor.

Function[edit]

In summary, YopR may play a role in the regulation of type III secretion. It is important to note, however, that the precise function of the YopR domain remains to be elucidated but YopR is thought to be involved in with YscF which develops needles. There are two different hypotheses for this. The first explanation is that YopR is possibly controlling the secretion of YscF, which impacts the assembly of type III machines. Alternatively, it is thought that YopR directly polymerizes YscF; this explanation is thought to be less likely since YopR does not associated with purified needles.[1]

Structure[edit]

YopR, is composed of five alpha-helices, four of which are arranged in an antiparallel bundle.[1]

Secretion systems[edit]

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. This is useful for further work with the YopR protein domain as comparative sequence and structure homology can be made.[2] The type III secretion system is of great interest, as the YopR protein domain plays an important role. The type III secretion system transports virulence factors from the pathogen directly into the host cell when the bacterium is in close contact with the host.

References[edit]

  1. ^ a b Schubot FD, Cherry S, Austin BP, Tropea JE, Waugh DS (2005). "Crystal structure of the protease-resistant core domain of Yersinia pestis virulence factor YopR.". Protein Sci 14 (6): 1679–83. doi:10.1110/ps.051446405. PMC 2253397. PMID 15930010. 
  2. ^ Hueck CJ (June 1998). "Type III protein secretion systems in bacterial pathogens of animals and plants". Microbiol. Mol. Biol. Rev. 62 (2): 379–433. PMC 98920. PMID 9618447. 

This article incorporates text from the public domain Pfam and InterPro IPR013349

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.

YopR Core Provide feedback

The YopR core domain, predominantly found in the Yersinia pestis virulence factor YopR, is composed of five alpha-helices, four of which are arranged in an antiparallel bundle. Little is known about this domain, though it may contribute to the virulence of the protein YopR [1].

Literature references

  1. Schubot FD, Cherry S, Austin BP, Tropea JE, Waugh DS; , Protein Sci. 2005;14:1679-1683.: Crystal structure of the protease-resistant core domain of Yersinia pestis virulence factor YopR. PUBMED:15930010 EPMC:15930010


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR013349

Proteins in this entry are type III secretion system effectors, named differently in different species and designated YopR (Yersinia outer protein R), encoded by the YscH (Yersinia secretion H) gene. This Yop protein is unusual in that it is released to the extracellular environment rather than injected directly into the target cell as are most Yop proteins.

Gene Ontology

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Domain organisation

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RP55
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RP75
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(9)
Full
(74)
Representative proteomes NCBI
(35)
Meta
(16)
RP15
(1)
RP35
(3)
RP55
(4)
RP75
(9)
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You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.

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Seed source: pdb_1z21
Previous IDs: none
Type: Domain
Author: Mistry J, Sammut SJ
Number in seed: 9
Number in full: 74
Average length of the domain: 140.50 aa
Average identity of full alignment: 43 %
Average coverage of the sequence by the domain: 81.11 %

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 98.3 98.1
Noise cut-off 22.2 21.2
Model length: 142
Family (HMM) version: 5
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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 YopR_core domain has been found. There are 1 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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