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10  structures 4381  species 1  interaction 4453  sequences 20  architectures

Family: UvrC_HhH_N (PF08459)

Summary: UvrC Helix-hairpin-helix N-terminal

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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.

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 [1]. 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.

Literature references

  1. 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


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR001162

During the process of Escherichia coli nucleotide excision repair, DNA damage recognition and processing are achieved by the action of the uvrA, uvrB, and uvrC gene products [PUBMED:12034838]. The UvrC proteins contain 4 conserved regions: a domain which interacts with UvrB (Uvr domain), a Helix hairpin Helix (HhH) domain important for 5 prime incision of damage DNA and the homology regions 1 and 2 of unknown function. UvrC homology region 2 is specific for UvrC proteins, whereas UvrC homology region 1 is also shared by few other nucleases.

This entry represents the homology region 2, which can be found between the Uvr domain and the C-terminal Helix-hairpin-Helix domain.

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 Endonuclease (CL0189), which has the following description:

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 [1].

The clan contains the following 2 members:

Endonuclease_5 UvrC_HhH_N

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
(110)
Full
(4453)
Representative proteomes NCBI
(3406)
Meta
(2670)
RP15
(335)
RP35
(662)
RP55
(843)
RP75
(982)
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1Cannot generate PP/Heatmap alignments for seeds; no PP data available

Key: ✓ available, x not generated, not available.

Format an alignment

  Seed
(110)
Full
(4453)
Representative proteomes NCBI
(3406)
Meta
(2670)
RP15
(335)
RP35
(662)
RP55
(843)
RP75
(982)
Alignment:
Format:
Order:
Sequence:
Gaps:
Download/view:

Download options

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
(110)
Full
(4453)
Representative proteomes NCBI
(3406)
Meta
(2670)
RP15
(335)
RP35
(662)
RP55
(843)
RP75
(982)
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_288 (release 18.0)
Previous IDs: none
Type: Family
Author: Wuster A
Number in seed: 110
Number in full: 4453
Average length of the domain: 161.00 aa
Average identity of full alignment: 40 %
Average coverage of the sequence by the domain: 26.34 %

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 21.3 21.3
Trusted cut-off 22.8 24.4
Noise cut-off 20.5 19.4
Model length: 155
Family (HMM) version: 6
Download: download the raw HMM for this family

Species distribution

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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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Interactions

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

UvrC_HhH_N

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 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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