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10  structures 1259  species 0  interactions 1466  sequences 40  architectures

Family: RNase_H2_suC (PF08615)

Summary: Ribonuclease H2 non-catalytic subunit (Ylr154p-like)

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Ribonuclease H2 non-catalytic subunit (Ylr154p-like) Provide feedback

This entry represents the non-catalytic subunit of RNase H2, which in S. cerevisiae is Ylr154p/Rnh203p Q12338 (. Whereas bacterial and archaeal RNases H2 are active as single polypeptides, the Saccharomyces cerevisiae homologue, Rnh2Ap, when expressed in Escherichia coli, fails to produce an active RNase H2. For RNase H2 activity three proteins are required [Rnh2Ap (Rnh201p), Ydr279p (Rnh202p) and Ylr154p (Rnh203p)]. Deletion of any one of the proteins or mutations in the catalytic site in Rnh2A leads to loss of RNase H2 activity [1]. RNase H2 ia an endonuclease that specifically degrades the RNA of RNA:DNA hybrids. It participates in DNA replication, possibly by mediating the removal of lagging-strand Okazaki fragment RNA primers during DNA replication.

Literature references

  1. Jeong HS, Backlund PS, Chen HC, Karavanov AA, Crouch RJ; , Nucleic Acids Res. 2004;32:407-414.: RNase H2 of Saccharomyces cerevisiae is a complex of three proteins. PUBMED:14734815 EPMC:14734815

This tab holds annotation information from the InterPro database.

InterPro entry IPR013924

Whereas bacterial and archaeal RNases H2 are active as single polypeptides, eukaryotic RNase H2 is a heterotrimeric complex of the RNase H2A, RNase H2B, and RNase H2C proteins that are all required for proper function and activity PUBMED:14734815 , PUBMED:19923215 ]. RNase H2 is an endonuclease that specifically degrades the RNA of RNA:DNA hybrids. It participates in DNA replication, possibly by mediating the removal of lagging-strand Okazaki fragment RNA primers during DNA replication.

This entry represents the non-catalytic C subunit of RNase H2.

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 Triple_barrel (CL0662), which has the following description:

Members of this superfamily adopt a triple barrel fold. This fold was first identified in the structure of the homodimer of RAP30 and RAP74. The two proteins form a single core structure composed of three interwoven beta barrels [1]. The central barrel is composed of beta strands from both heterodimer subunits. A similar fold has been observed in the heterodimer of TAF1 and TAF7 [2].

The clan contains the following 9 members:

DUF3591 RNA_pol_I_A49 RNA_pol_Rpc4 RNA_polI_A34 RNase_H2_suC RPC5 TAFII55_N TFIIF_beta_N Ydr279_N


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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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: Pfam-B_36578 (release 18.0)
Previous IDs: RNase_H1_sml;
Type: Family
Sequence Ontology: SO:0100021
Author: Wood V , Finn RD
Number in seed: 19
Number in full: 1466
Average length of the domain: 131.4 aa
Average identity of full alignment: 26 %
Average coverage of the sequence by the domain: 66.02 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 61295632 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 20.8 20.8
Trusted cut-off 20.8 20.8
Noise cut-off 20.6 20.7
Model length: 141
Family (HMM) version: 14
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 RNase_H2_suC domain has been found. There are 10 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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