Summary: HD domain
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 "HD domain". More...
HD domain Edit Wikipedia article
HD domain | |||||||||
---|---|---|---|---|---|---|---|---|---|
![]() crystal structure of o67745, a hypothetical protein from aquifex aeolicus at 2.0 a resolution. | |||||||||
Identifiers | |||||||||
Symbol | HD | ||||||||
Pfam | PF01966 | ||||||||
Pfam clan | CL0237 | ||||||||
InterPro | IPR006674 | ||||||||
PROSITE | PDOC00924 | ||||||||
SCOPe | 1f62 / SUPFAM | ||||||||
CDD | cd00077 | ||||||||
|
In molecular biology, the HD domain is a conserved protein domain, named after the conserved histidine (H) and/or aspartate (D) amino acid residues. It is found in a superfamily of enzymes with a predicted or known phosphohydrolase activity. These enzymes appear to be involved in nucleic acid metabolism, signal transduction and possibly other functions in bacteria, archaea and eukaryotes. The fact that all the highly conserved residues in the HD superfamily are histidines or aspartates suggests that coordination of divalent cations is essential for the activity of these proteins.[1]
References
- ^ Aravind L, Koonin EV (December 1998). "The HD domain defines a new superfamily of metal-dependent phosphohydrolases". Trends in Biochemical Sciences. 23 (12): 469–72. doi:10.1016/s0968-0004(98)01293-6. PMID 9868367.
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.
HD domain Provide feedback
HD domains are metal dependent phosphohydrolases.
Literature references
-
Aravind L, Koonin EV; , Trends Biochem Sci 1998;23:469-472.: The HD domain defines a new superfamily of metal-dependent phosphohydrolases. PUBMED:9868367 EPMC:9868367
Internal database links
SCOOP: | HD_2 HD_3 HD_4 HD_5 HD_6 HDOD MIOX PDEase_I TraI_2 tRNA_NucTran2_2 |
Similarity to PfamA using HHSearch: | HDOD HD_2 HD_3 HD_5 |
External database links
SCOP: | 1vj7 |
This tab holds annotation information from the InterPro database.
InterPro entry IPR006674
The HD domain is found in a superfamily of enzymes with a predicted or known phosphohydrolase activity [ PUBMED:17951247 ]. These enzymes appear to be involved in the nucleic acid metabolism, signal transduction and possibly other functions in bacteria, archaea and eukaryotes. The fact that all the highly conserved residues in the HD superfamily are histidines or aspartates suggests that coordination of divalent cations is essential for the activity of these proteins [ PUBMED:9868367 ].
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 HD_PDEase (CL0237), which has the following description:
This clan includes a range of phosphohydrolase enzymes with a common helical fold.
The clan contains the following 13 members:
DUF4202 HD HD_2 HD_3 HD_4 HD_5 HD_6 HDOD MIOX PDEase_I SidE_PDE TraI_2 tRNA_NucTran2_2Alignments
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 (154) |
Full (49957) |
Representative proteomes | UniProt (227500) |
||||
---|---|---|---|---|---|---|---|
RP15 (7660) |
RP35 (26010) |
RP55 (50352) |
RP75 (82453) |
||||
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 (154) |
Full (49957) |
Representative proteomes | UniProt (227500) |
||||
---|---|---|---|---|---|---|---|
RP15 (7660) |
RP35 (26010) |
RP55 (50352) |
RP75 (82453) |
||||
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: | Enright A |
Previous IDs: | none |
Type: | Family |
Sequence Ontology: | SO:0100021 |
Author: |
Enright A |
Number in seed: | 154 |
Number in full: | 49957 |
Average length of the domain: | 124.00 aa |
Average identity of full alignment: | 17 % |
Average coverage of the sequence by the domain: | 29.01 % |
HMM information
HMM build commands: |
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 57096847 -E 1000 --cpu 4 HMM pfamseq
|
||||||||||||
Model details: |
|
||||||||||||
Model length: | 122 | ||||||||||||
Family (HMM) version: | 24 | ||||||||||||
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.
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 HD domain has been found. There are 504 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...