Summary: T4 RNase H, C terminal
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T4 RNase H, C terminal Provide feedback
Members of this family are found in T4 RNaseH ribonuclease, and adopt a SAM domain-like fold, consisting of a bundle of four/five helices. These residues may have a role in providing a docking site for other proteins or enzymes in the replication fork .
Mueser TC, Nossal NG, Hyde CC; , Cell. 1996;85:1101-1112.: Structure of bacteriophage T4 RNase H, a 5' to 3' RNA-DNA and DNA-DNA exonuclease with sequence similarity to the RAD2 family of eukaryotic proteins. PUBMED:8674116 EPMC:8674116
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This tab holds annotation information from the InterPro database.
InterPro entry IPR020045
This entry represents the C-terminal domain of 5' to 3' exonucleases. The 5'-3' exonucleases are conserved in organisms as diverse as bacteriophage and mammals. It adopts a SAM fold consisting of 4-5 helices packed into a bundle of two orthogonally packed alpha-hairpins. This domain is involved in interactions with DNA and proteins. 5' to 3' exonucleases that contain this domain include:
- Bacteriophage T4 RNase H, which has sequence similarity to the RAD2 family of eukaryotic proteins [PUBMED:8674116].
- 5' to 3' exonuclease domain of DNA polymerase Taq, which is homologous to Escherichia coli DNA polymerase I (pol I) [PUBMED:7637814, PUBMED:10666572].
- Bacteriophage T5 5'-exonuclease, which are structure-specific endonucleases [PUBMED:9874768].
- Flap endonuclease-1 (Fen-1 nuclease), a structure specific nuclease that is an essential enzyme for eukaryotic DNA replication and repair [PUBMED:9699635].
|Molecular function||DNA binding (GO:0003677)|
|catalytic activity (GO:0003824)|
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This superfamily includes C-terminal domains from a number of DNA-processing enzymes including T4 RNase H, 5' to 3' exonuclease domain of DNA polymerase Taq, T5 5'-exonuclease, Flap endonuclease-1 (Fen-1 nuclease), and other eukaryotic endonucleases.
The clan contains the following 4 members:5_3_exonuc RNaseH_C XPG_I XPG_I_2
We make a range of alignments for each Pfam-A family:
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Curation and family details
|Number in seed:||2|
|Number in full:||73|
|Average length of the domain:||116.50 aa|
|Average identity of full alignment:||39 %|
|Average coverage of the sequence by the domain:||39.45 %|
|HMM build commands:||
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 80369284 -E 1000 --cpu 4 HMM pfamseq
|Family (HMM) version:||6|
|Download:||download the raw HMM for this family|
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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 RNaseH_C domain has been found. There are 6 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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