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8  structures 6932  species 0  interactions 8112  sequences 22  architectures

Family: RuvX (PF03652)

Summary: Holliday junction resolvase

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Holliday junction resolvase Provide feedback

The central intermediate formed during mitotic and meiotic recombination is a four stranded DNA structure, also known as the Holliday junction (HJ), and its efficient resolution is essential for proper segregation of chromosomes. Resolution of HJs is mediated by a diverse group of DNA structure specific endonucleases known as Holliday junction resolvases (HJR) [1]. This entry is specific for RuvX also known as YqgF a family of nucleases which resolves the Holliday junction intermediates in genetic recombination[2-3]. Studies carried out in M. tuberculosis, have shown that YqgF/RuvX is a genuine HJR analogous to RuvC from E. coli. Furthermore, a single cysteine present in M. tuberculosis RuvX was found to be required for disulfide-bond mediated intermolecular dimerization and HJ resolution activity, suggesting that M. tuberculosis RuvX has adapted its YqgF protein to function like a typical RuvC family HJR [1].

Literature references

  1. Nautiyal A, Rani PS, Sharples GJ, Muniyappa K;, Mol Microbiol. 2016;100:656-674.: Mycobacterium tuberculosis RuvX is a Holliday junction resolvase formed by dimerisation of the monomeric YqgF nuclease domain. PUBMED:26817626 EPMC:26817626

  2. Aravind L, Makarova KS, Koonin EV; , Nucleic Acids Res. 2000;28:3417-3432.: Holliday junction resolvases and related nucleases: identification of new families, phyletic distribution and evolutionary trajectories. PUBMED:10982859 EPMC:10982859

  3. Iwasaki H, Takahagi M, Shiba T, Nakata A, Shinagawa H;, EMBO J. 1991;10:4381-4389.: Escherichia coli RuvC protein is an endonuclease that resolves the Holliday structure. PUBMED:1661673 EPMC:1661673

Internal database links

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR005227

This entry represents a group of predicted nucleases involved in processing of the 5'-end of pre-16S rRNA. This entry typified by the Escherichia coli protein YqgF, which exhibits an RNAse H fold in crystal structure and is involved in the processing of pre-16S rRNA during ribosome maturation [ PUBMED:25545592 ].

Gene Ontology

The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.

Domain organisation

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

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Pfam Clan

This family is a member of clan YqgF (CL0580), which has the following description:

This clain contains the bacterial YqgF family [1-2] and homologous domains in bacterial Tex proteins [3], involved in transcriptional processes, and eukaryotic transcription elongation factor SPT6 [4-5].

The clan contains the following 3 members:

RuvX Tex_YqgF YqgF


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 (reference proteomes) using the family HMM. We also generate alignments using four representative proteomes (RP) sets and the UniProtKB 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.

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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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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...


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.

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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: SWISS-PROT
Previous IDs: UPF0081;
Type: Family
Sequence Ontology: SO:0100021
Author: Bateman A , Eberhardt R , El-Gebali S
Number in seed: 113
Number in full: 8112
Average length of the domain: 133.00 aa
Average identity of full alignment: 32 %
Average coverage of the sequence by the domain: 86.00 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 57096847 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 29.2 29.2
Trusted cut-off 29.3 29.2
Noise cut-off 29.1 29.1
Model length: 135
Family (HMM) version: 17
Download: download the raw HMM for this family

Species distribution

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Colour assignments

Archea Archea Eukaryota Eukaryota
Bacteria Bacteria Other sequences Other sequences
Viruses Viruses Unclassified Unclassified
Viroids Viroids Unclassified sequence Unclassified sequence


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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...

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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 RuvX 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 sequence.

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