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70  structures 4881  species 2  interactions 24448  sequences 317  architectures

Family: HD (PF01966)

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
PDB 2hek EBI.jpg
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
SCOP 1f62
SUPERFAMILY 1f62
CDD cd00077

In molecular biology, the HD domain is a conserved protein domain. 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

  1. ^ Aravind L, Koonin EV (December 1998). "The HD domain defines a new superfamily of metal-dependent phosphohydrolases". Trends Biochem. Sci. 23 (12): 469–72. doi:10.1016/s0968-0004(98)01293-6. PMID 9868367. 

This article incorporates text from the public domain Pfam and InterPro IPR006674

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

  1. 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

External database links

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].

Gene Ontology

The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.

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 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 10 members:

DUF706 HD HD_2 HD_3 HD_4 HD_5 HDOD PDEase_I TraI_2 tRNA_NucTran2_2

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...

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
(24448)
Representative proteomes NCBI
(26042)
Meta
(7473)
RP15
(2723)
RP35
(4803)
RP55
(5965)
RP75
(6755)
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PP/heatmap 1   View  View         
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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
(154)
Full
(24448)
Representative proteomes NCBI
(26042)
Meta
(7473)
RP15
(2723)
RP35
(4803)
RP55
(5965)
RP75
(6755)
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
(154)
Full
(24448)
Representative proteomes NCBI
(26042)
Meta
(7473)
RP15
(2723)
RP35
(4803)
RP55
(5965)
RP75
(6755)
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: Enright A
Previous IDs: none
Type: Family
Author: Enright A, Ouzounis C, Bateman A
Number in seed: 154
Number in full: 24448
Average length of the domain: 120.90 aa
Average identity of full alignment: 18 %
Average coverage of the sequence by the domain: 28.53 %

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 20.9 20.9
Trusted cut-off 20.9 20.9
Noise cut-off 20.8 20.8
Model length: 122
Family (HMM) version: 17
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 are 2 interactions for this family. More...

HD RelA_SpoT

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 70 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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