Summary: HhH-GPD superfamily base excision DNA repair protein
Pfam includes annotations and additional family information from a range of different sources. These sources can be accessed via the tabs below.
The Pfam group coordinates the annotation of Pfam families in Wikipedia, but we have not yet assigned a Wikipedia article to this family. If you think that a particular Wikipedia article provides good annotation, please let us know.
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.
HhH-GPD superfamily base excision DNA repair protein Provide feedback
This family contains a diverse range of structurally related DNA repair proteins. The superfamily is called the HhH-GPD family after its hallmark Helix-hairpin-helix and Gly/Pro rich loop followed by a conserved aspartate [2]. This includes endonuclease III, EC:4.2.99.18 and MutY an A/G-specific adenine glycosylase, both have a C terminal 4Fe-4S cluster. The family also includes 8-oxoguanine DNA glycosylases such as P53397. The methyl-CPG binding protein MBD4 Q9Z2D7 also contains a related domain [1] that is a thymine DNA glycosylase. The family also includes DNA-3-methyladenine glycosylase II EC:3.2.2.21 and other members of the AlkA family.
Literature references
-
Hendrich B, Hardeland U, Ng HH, Jiricny J, Bird A; , Nature 1999;401:301-304.: The thymine glycosylase MBD4 can bind to the product of deamination at methylated CpG sites. PUBMED:10499592 EPMC:10499592
-
Bruner SD, Norman DP, Verdine GL; , Nature 2000;403:859-866.: Structural basis for recognition and repair of the endogenous mutagen 8-oxoguanine in DNA. PUBMED:10706276 EPMC:10706276
Internal database links
SCOOP: | Adenine_glyco HHH HHH_5 |
Similarity to PfamA using HHSearch: | HHH |
External database links
HOMSTRAD: | Endonuclease_3 |
PROSITE: | PDOC00615 PDOC00447 |
SCOP: | 2abk |
This tab holds annotation information from the InterPro database.
InterPro entry IPR003265
The HhH-GPD superfamily gets its name from its hallmark helix-hairpin-helix and Gly/Pro rich loop followed by a conserved aspartate [PUBMED:10706276, PUBMED:8805338]. This domain is found in a diverse range of structurally related DNA repair proteins that include: endonuclease III, EC and DNA glycosylase MutY, an A/G-specific adenine glycosylase. Both of these enzymes have a C-terminal iron-sulphur cluster loop (FCL). The methyl-CPG binding protein (MBD4) also contain a related domain that is a thymine DNA glycosylase [PUBMED:10499592]. The family also includes DNA-3-methyladenine glycosylase II EC, 8-oxoguanine DNA glycosylases and other members of the AlkA family.
Gene Ontology
The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.
Biological process | base-excision repair (GO:0006284) |
Domain organisation
Below is a listing of the unique domain organisations or architectures in which this domain is found. More...
Loading domain graphics...
Pfam Clan
This family is a member of clan HHH (CL0198), which has the following description:
This superfamily includes Helix-hairpin-helix DNA-binding domains.
The clan contains the following 23 members:
Cdd1 DNA_pol_B_N DNA_pol_lambd_f DUF3173 DUF3701 DUF4332 DUF655 HHH HhH-GPD HHH_2 HHH_3 HHH_4 HHH_5 HHH_6 HHH_7 HHH_8 HHH_9 IMS_HHH PsbU RNA_pol_A_CTD T2SSK TfoX_C Transposase_20Alignments
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, the UniProtKB sequence database, the NCBI sequence database, and our metagenomics 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 (52) |
Full (25249) |
Representative proteomes | UniProt (68227) |
NCBI (92473) |
Meta (5922) |
||||
---|---|---|---|---|---|---|---|---|---|
RP15 (6270) |
RP35 (16203) |
RP55 (24528) |
RP75 (34242) |
||||||
Jalview | |||||||||
HTML | |||||||||
PP/heatmap | 1 |
1Cannot generate PP/Heatmap alignments for seeds; no PP data available
Key:
available,
not generated,
— not available.
Format an alignment
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 (52) |
Full (25249) |
Representative proteomes | UniProt (68227) |
NCBI (92473) |
Meta (5922) |
||||
---|---|---|---|---|---|---|---|---|---|
RP15 (6270) |
RP35 (16203) |
RP55 (24528) |
RP75 (34242) |
||||||
Raw Stockholm | |||||||||
Gzipped |
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
Seed source: | Pfam-B_854 (release 2.1) |
Previous IDs: | Endonuclease_3; |
Type: | Domain |
Sequence Ontology: | SO:0000417 |
Author: |
Bateman A |
Number in seed: | 52 |
Number in full: | 25249 |
Average length of the domain: | 141.70 aa |
Average identity of full alignment: | 21 % |
Average coverage of the sequence by the domain: | 47.01 % |
HMM information
HMM build commands: |
build method: hmmbuild -o /dev/null --hand HMM SEED
search method: hmmsearch -Z 45638612 -E 1000 --cpu 4 HMM pfamseq
|
||||||||||||
Model details: |
|
||||||||||||
Model length: | 108 | ||||||||||||
Family (HMM) version: | 25 | ||||||||||||
Download: | download the raw HMM for this family |
Species distribution
Sunburst controls
HideWeight segments by...
Change the size of the sunburst
Colour assignments
![]() |
![]() |
![]() |
![]() |
![]() |
![]() |
![]() |
![]() |
Selections
Align selected sequences to HMM
Generate a FASTA-format file
Clear selection
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...
Tree controls
HideThe tree shows the occurrence of this domain across different species. More...
Loading...
Please note: for large trees this can take some time. While the tree is loading, you can safely switch away from this tab but if you browse away from the family page entirely, the tree will not be loaded.
Interactions
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 HhH-GPD domain has been found. There are 132 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.
Loading structure mapping...