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186  structures 8937  species 0  interactions 21646  sequences 110  architectures

Family: UDG (PF03167)

Summary: Uracil DNA glycosylase superfamily

Pfam includes annotations and additional family information from a range of different sources. These sources can be accessed via the tabs below.

This is the Wikipedia entry entitled "DNA glycosylase". More...

DNA glycosylase Edit Wikipedia article

An enzyme which cleaves nucleotide bases from DNA.

This page is based on a Wikipedia article. The text is available under the Creative Commons Attribution/Share-Alike License.

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.

Uracil DNA glycosylase superfamily Provide feedback

No Pfam abstract.

Literature references

  1. Barrett TE, Savva R, Panayotou G, Barlow T, Brown T, Jiricny J, Pearl LH; , Cell 1998;92:117-129.: Crystal structure of a G:T/U mismatch-specific DNA glycosylase: mismatch recognition by complementary-strand interactions. PUBMED:9489705 EPMC:9489705

  2. Aravind L, Koonin EV; , Genome Biol 2000;1:RESEARCH0007.: The alpha/beta fold uracil DNA glycosylases: a common origin with diverse fates. PUBMED:11178247 EPMC:11178247


Internal database links

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR005122

This entry represents various uracil-DNA glycosylases and related DNA glycosylases ( EC ), such as uracil-DNA glycosylase [ PUBMED:7697717 ], thermophilic uracil-DNA glycosylase [ PUBMED:10339434 ], G:T/U mismatch-specific DNA glycosylase (Mug) [ PUBMED:9489705 ], and single-strand selective monofunctional uracil-DNA glycosylase (SMUG1) [ PUBMED:2820976 ]. These proteins have a 3-layer alpha/beta/alpha structure.

Uracil-DNA glycosylases are DNA repair enzymes that excise uracil residues from DNA by cleaving the N-glycosylic bond, initiating the base excision repair pathway. Uracil in DNA can arise either through the deamination of cytosine to form mutagenic U:G mispairs, or through the incorporation of dUMP by DNA polymerase to form U:A pairs [ PUBMED:17116429 ]. These aberrant uracil residues are genotoxic [ PUBMED:16860315 ]. The sequence of uracil-DNA glycosylase is extremely well conserved [ PUBMED:2555154 ] in bacteria and eukaryotes as well as in herpes viruses. More distantly related uracil-DNA glycosylases are also found in poxviruses [ PUBMED:8389453 ].

Domain organisation

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

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

View options

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
(147)
Full
(21646)
Representative proteomes UniProt
(95751)
RP15
(3024)
RP35
(10320)
RP55
(21803)
RP75
(37051)
Jalview View  View  View  View  View  View  View 
HTML View             
PP/heatmap 1            

1Cannot generate PP/Heatmap alignments for seeds; no PP data available

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

Format an alignment

  Seed
(147)
Full
(21646)
Representative proteomes UniProt
(95751)
RP15
(3024)
RP35
(10320)
RP55
(21803)
RP75
(37051)
Alignment:
Format:
Order:
Sequence:
Gaps:
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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
(147)
Full
(21646)
Representative proteomes UniProt
(95751)
RP15
(3024)
RP35
(10320)
RP55
(21803)
RP75
(37051)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download  
Gzipped 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.

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: Aravind L
Previous IDs: none
Type: Domain
Sequence Ontology: SO:0000417
Author: Aravind L
Number in seed: 147
Number in full: 21646
Average length of the domain: 161 aa
Average identity of full alignment: 21 %
Average coverage of the sequence by the domain: 62.62 %

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 31.8 31.8
Trusted cut-off 31.8 31.8
Noise cut-off 31.7 31.7
Model length: 155
Family (HMM) version: 22
Download: download the raw HMM for this family

Species distribution

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

Selections

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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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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 UDG domain has been found. There are 186 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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AlphaFold Structure Predictions

The list of proteins below match this family and have AlphaFold predicted structures. Click on the protein accession to view the predicted structure.

Protein Predicted structure External Information
A0A044V1D4 View 3D Structure Click here
A0A077Z7P7 View 3D Structure Click here
A0A077ZD33 View 3D Structure Click here
A0A096MIY3 View 3D Structure Click here
A0A0D2FEL2 View 3D Structure Click here
A0A0D2H002 View 3D Structure Click here
A0A0H3GTH2 View 3D Structure Click here
A0A0H3GTU7 View 3D Structure Click here
A0A0K0E7S9 View 3D Structure Click here
A0A0K0JQ14 View 3D Structure Click here
A0A0N4UAB9 View 3D Structure Click here
A0A175W917 View 3D Structure Click here
A0A175WG80 View 3D Structure Click here
A0A1C1CMV2 View 3D Structure Click here
A0A1C1CZF5 View 3D Structure Click here
A0A1D6DTQ2 View 3D Structure Click here
A0A1D8PKH5 View 3D Structure Click here
A0A1D8PKI0 View 3D Structure Click here
A0A2R8QH35 View 3D Structure Click here
A0A3P7DIR5 View 3D Structure Click here
A0A3Q0KPH0 View 3D Structure Click here
A0A5K4F0G3 View 3D Structure Click here
A0A7I4KPA4 View 3D Structure Click here
A0KMZ1 View 3D Structure Click here
A0QV01 View 3D Structure Click here
A1SNW4 View 3D Structure Click here
A1SUE5 View 3D Structure Click here
A1T717 View 3D Structure Click here
A1UEC0 View 3D Structure Click here
A2BIQ2 View 3D Structure Click here
A3CN85 View 3D Structure Click here
A3MZ80 View 3D Structure Click here
A4HXS3 View 3D Structure Click here
A4VV30 View 3D Structure Click here
A5EVB8 View 3D Structure Click here
A5VIJ2 View 3D Structure Click here
A6L7T5 View 3D Structure Click here
A6TCJ2 View 3D Structure Click here
A6TE50 View 3D Structure Click here
A6TVW5 View 3D Structure Click here