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1  structure 964  species 0  interactions 1071  sequences 15  architectures

Family: YccV-like (PF08755)

Summary: Hemimethylated DNA-binding protein YccV like

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This is the Wikipedia entry entitled "HspQ protein domain". More...

HspQ protein domain Edit Wikipedia article

HspQ (YccV-like) protein domain
PDB 1vbv EBI.jpg
Crystal structure of hypothetical protein from Esherichia coli
Identifiers
Symbol YccV-like
Pfam PF08755
InterPro IPR011722


In molecular biology, YccV protein domain is also, alternatively named, Heat shock protein HspQ. This entry describes the small protein from Escherichia coli YccV and its homologs in other Proteobacteria. YccV is now described as a hemimethylated DNA binding protein.[1] The model entry describes a protein domain in longer eukaryotic proteins.

Function[edit]

HspQ is involved in the degradation of certain denaturated proteins, including DnaA, during Heat shock stress.[2] HspQ (YccV like protein domain) is a hemimethylated DNA-binding protein. It has been thought to negatively regulate dnaA gene expression when its promoter region is either methylated or hemimethylated. This could occurs through binding of YccV itself to fully or hemimethylated DNA.[1] In addition, studies have identified the yccV gene as one of three insertion sites in mini-Tn10 which suppress dnaA46 thermosensitivity.

Structure[edit]

This protein domain is thought to have a SH3-like barrel structure. Additionally, the structure of a hypothetical protein in this family has been solved and it forms a beta sheet structure with a terminating alpha helix. HspQ forms a stable homodimer in solution and can form homomultimers consisting of about four monomers. The theoretical molecular mass of the HspQ protein were calculated to be 11.8 kDa. It is putatively thought that HspQ requires a cofactor to form a functional hetero-oligomeric complex.[2]

References[edit]

  1. ^ a b d'Alençon E, Taghbalout A, Bristow C, Kern R, Aflalo R, Kohiyama M (May 2003). "Isolation of a new hemimethylated DNA binding protein which regulates dnaA gene expression". J. Bacteriol. 185 (9): 2967–71. PMC 154408. PMID 12700277. 
  2. ^ a b Shimuta TR, Nakano K, Yamaguchi Y, Ozaki S, Fujimitsu K, Matsunaga C et al. (2004). "Novel heat shock protein HspQ stimulates the degradation of mutant DnaA protein in Escherichia coli.". Genes Cells 9 (12): 1151–66. doi:10.1111/j.1365-2443.2004.00800.x. PMID 15569148. 

This article incorporates text from the public domain Pfam and InterPro IPR011722

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.

Hemimethylated DNA-binding protein YccV like Provide feedback

YccV is a hemimethylated DNA binding protein which has been shown to regulate dnaA gene expression [1]. The structure of one of the hypothetical proteins in this family has been solved and it forms a beta sheet structure with a terminating alpha helix.

Literature references

  1. d'Alencon E, Taghbalout A, Bristow C, Kern R, Aflalo R, Kohiyama M; , J Bacteriol. 2003;185:2967-2971.: Isolation of a new hemimethylated DNA binding protein which regulates dnaA gene expression. PUBMED:12700277 EPMC:12700277


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR011722

Heat shock protein HspQ, also known as YccV, is an Escherichia coli hemimethylated DNA binding protein which has been shown to regulate dnaA gene expression [PUBMED:12700277].

This entry represents a YccV-like hemimethylated DNA binding domain that can also be found in longer eukaryotic proteins.

Gene Ontology

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Domain organisation

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Alignments

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(64)
Full
(1071)
Representative proteomes NCBI
(578)
Meta
(1189)
RP15
(90)
RP35
(160)
RP55
(239)
RP75
(318)
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  Seed
(64)
Full
(1071)
Representative proteomes NCBI
(578)
Meta
(1189)
RP15
(90)
RP35
(160)
RP55
(239)
RP75
(318)
Alignment:
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  Seed
(64)
Full
(1071)
Representative proteomes NCBI
(578)
Meta
(1189)
RP15
(90)
RP35
(160)
RP55
(239)
RP75
(318)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download   Download  
Gzipped Download   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.

Pfam alignments:

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Curation and family details

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Seed source: pdb_1bvb
Previous IDs: none
Type: Domain
Author: Mistry J
Number in seed: 64
Number in full: 1071
Average length of the domain: 98.80 aa
Average identity of full alignment: 44 %
Average coverage of the sequence by the domain: 47.48 %

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 22.8 22.8
Trusted cut-off 22.8 22.8
Noise cut-off 22.7 22.7
Model length: 100
Family (HMM) version: 6
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 YccV-like 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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