Summary: UvrC Helix-hairpin-helix N-terminal
UvrC Helix-hairpin-helix N-terminal Provide feedback
This domain is found in the C subunits of the bacterial and archaeal UvrABC system which catalyses nucleotide excision repair in a multi-step process. UvrC catalyses the first incision on the fourth or fifth phosphodiester bond 3' and on the eighth phosphodiester bond 5' from the damage that is to be excised . The domain described here is found to the N-terminus of a helix hairpin helix (PF00633) motif and also co-occurs with the PF01541 catalytic domain which is found at the N-terminus of the same proteins.
Verhoeven EE, van Kesteren M, Turner JJ, van der Marel GA, van Boom JH, Moolenaar GF, Goosen N; , Nucleic Acids Res 2002;30:2492-2500.: The C-terminal region of Escherichia coli UvrC contributes to the flexibility of the UvrABC nucleotide excision repair system. PUBMED:12034838 EPMC:12034838
This tab holds annotation information from the InterPro database.
InterPro entry IPR001162
In prokaryotes, nucleotide excision repair, DNA damage recognition and processing are achieved by the action of the uvrA, uvrB, and uvrC protein complex. UvrC proteins contain 4 conserved regions: the UVR domain which interacts with uvrB, a Helix hairpin Helix (HhH) domain important for 5 prime incision of damage DNA, the GIY-YIG domain and a central homology region of unknown function, which is specific for UvrC proteins.This entry represents the homology region 2, which can be found between the Uvr domain and the C-terminal Helix-hairpin-Helix domain.
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This clan contains DNA repair proteins. In E. coli endonuclease V initiates DNA repair of deaminated DNA bases and has similarity to motifs required for the catalytic activity of the UvrC endonuclease .
The clan contains the following 2 members:Endonuclease_5 UvrC_HhH_N
We make a range of alignments for each Pfam-A family:
- the curated alignment from which the HMM for the family is built
- the alignment generated by searching the sequence database using the HMM
- Representative Proteomes (RPs) at 15%, 35%, 55% and 75% co-membership thresholds
- alignment generated by searching the UniProtKB sequence database using the family HMM
- alignment generated by searching the NCBI sequence database using the family HMM
- alignment generated by searching the metagenomics sequence database using the family HMM
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Curation and family details
|Seed source:||Pfam-B_288 (release 18.0)|
|Number in seed:||836|
|Number in full:||1626|
|Average length of the domain:||160.40 aa|
|Average identity of full alignment:||39 %|
|Average coverage of the sequence by the domain:||26.13 %|
|HMM build commands:||
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 11927849 -E 1000 --cpu 4 HMM pfamseq
|Family (HMM) version:||8|
|Download:||download the raw HMM for this family|
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There is 1 interaction for this family. More...
We determine these interactions using iPfam, which considers the interactions between residues in three-dimensional protein structures and maps those interactions back to Pfam families. You can find more information about the iPfam algorithm in the journal article that accompanies the website.
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 UvrC_HhH_N 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 seqence.
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