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13  structures 969  species 1  interaction 1553  sequences 18  architectures

Family: YqaJ (PF09588)

Summary: YqaJ-like viral recombinase domain

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

YqaJ protein domain Edit Wikipedia article

YqaJ protein domain
PDB 1avq EBI.jpg
Toroidal structure of lambda exonuclease, determined at 2.4 angstroms
Identifiers
Symbol YqaJ
Pfam PF09588
Pfam clan CL0236
InterPro IPR019080

In molecular biology, the YqaJ refers to the YqaJ/K domain from the skin prophage of the bacterium, Bacillus subtilis. This protein domain, often found in bacterial species, is actually of viral origin. The protein forms an oligomer and functions as an alkaline exonuclease, or in simpler terms, an enzyme that digests double-stranded DNA. It is a reaction which is dependent on Magnesium. It has a preference for 5'-phosphorylated DNA ends. It thus forms part of the two-component SynExo viral recombinase functional unit.[1]

Function

The function of this protein domain is to digest DNA. Most viruses, inject their host with linear DNA, and this gets incorporated into the host genome through the process of recombination. This recombination is crucial to viral replication.[1]

DNA exonucleases have roles to play in DNA metabolism, such as: replication, repair, and recombination.

Structure

YqaJ is a one of three protein subunits that form a toroid with a tapered channel passing through the middle. The channel changes diameter, the wide end of the channel being about 30 Å, and the narrow end decreases to 15 Å. It is thought that the tapered channel is large enough to accommodate double-stranded DNA at the wide end but only single-stranded DNA at the other end. Furthermore, YqaJ has an alpha/beta fold.[2]

SynExo

SynExo is a viral recombinase functional unit. It is thought that it may have evolved as a portable module that can function wide variety of host organisms without requiring extensive interaction with host-specific functions. This offers the pathogen a great adaptive advantage on viruses exploring new niches.[1]

References

This article incorporates text from the public domain Pfam and InterPro IPR019080

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.

YqaJ-like viral recombinase domain Provide feedback

This protein family is found in many different bacterial species but is of viral origin. The protein forms an oligomer and functions as a processive alkaline exonuclease that digests linear double-stranded DNA in a Mg(2+)-dependent reaction, It has a preference for 5'-phosphorylated DNA ends. It thus forms part of the two-component SynExo viral recombinase functional unit [1].

Literature references

  1. Vellani TS, Myers RS; , J Bacteriol. 2003;185:2465-2474.: Bacteriophage SPP1 Chu is an alkaline exonuclease in the SynExo family of viral two-component recombinases. PUBMED:12670970 EPMC:12670970


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR019080

This protein is found in many different bacterial species but is of viral origin. The protein forms an oligomer and functions as a processive alkaline exonuclease that digests linear double-stranded DNA in a Mg(2+)-dependent reaction, It has a preference for 5'-phosphorylated DNA ends. It thus forms part of the two-component SynExo viral recombinase functional unit [PUBMED:12670970].

Domain organisation

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

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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...

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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
(97)
Full
(1553)
Representative proteomes NCBI
(1400)
Meta
(442)
RP15
(189)
RP35
(280)
RP55
(336)
RP75
(375)
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Format an alignment

  Seed
(97)
Full
(1553)
Representative proteomes NCBI
(1400)
Meta
(442)
RP15
(189)
RP35
(280)
RP55
(336)
RP75
(375)
Alignment:
Format:
Order:
Sequence:
Gaps:
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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
(97)
Full
(1553)
Representative proteomes NCBI
(1400)
Meta
(442)
RP15
(189)
RP35
(280)
RP55
(336)
RP75
(375)
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.

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: Pfam-B_3587 (release 21.0)
Previous IDs: none
Type: Domain
Author: Coggill P
Number in seed: 97
Number in full: 1553
Average length of the domain: 140.60 aa
Average identity of full alignment: 24 %
Average coverage of the sequence by the domain: 46.91 %

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 21.1 21.1
Trusted cut-off 21.1 21.2
Noise cut-off 21.0 21.0
Model length: 152
Family (HMM) version: 5
Download: download the raw HMM for this family

Species distribution

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Interactions

There is 1 interaction for this family. More...

YqaJ

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 YqaJ domain has been found. There are 13 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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