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504  structures 8509  species 0  interactions 49957  sequences 653  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
SymbolHD
PfamPF01966
Pfam clanCL0237
InterProIPR006674
PROSITEPDOC00924
SCOPe1f62 / SUPFAM
CDDcd00077

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

  1. ^ 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 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 ].

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 13 members:

DUF4202 HD HD_2 HD_3 HD_4 HD_5 HD_6 HDOD MIOX PDEase_I SidE_PDE 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 (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)
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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
(154)
Full
(49957)
Representative proteomes UniProt
(227500)
RP15
(7660)
RP35
(26010)
RP55
(50352)
RP75
(82453)
Alignment:
Format:
Order:
Sequence:
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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
(154)
Full
(49957)
Representative proteomes UniProt
(227500)
RP15
(7660)
RP35
(26010)
RP55
(50352)
RP75
(82453)
Raw Stockholm Download   Download   Download   Download   Download   Download    
Gzipped 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: Enright A
Previous IDs: none
Type: Family
Sequence Ontology: SO:0100021
Author: Enright A , Ouzounis C , Bateman 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 View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 57096847 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 21.5 21.5
Trusted cut-off 21.5 21.5
Noise cut-off 21.4 21.4
Model length: 122
Family (HMM) version: 24
Download: download the raw HMM for this family

Species distribution

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Colour assignments

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 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.

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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
A0A0G2KT98 View 3D Structure Click here
A0A0P0UXJ0 View 3D Structure Click here
A0A0R4II71 View 3D Structure Click here
A0A1D6FCM9 View 3D Structure Click here
A0A1D6MND9 View 3D Structure Click here
A4HSQ7 View 3D Structure Click here
A4I875 View 3D Structure Click here
B0G107 View 3D Structure Click here
B6SZF0 View 3D Structure Click here
C6T179 View 3D Structure Click here
D3Z898 View 3D Structure Click here
F4HZF4 View 3D Structure Click here
F4KHB6 View 3D Structure Click here
I1M011 View 3D Structure Click here
K7K683 View 3D Structure Click here
K7MVU4 View 3D Structure Click here
L7N672 View 3D Structure Click here
P06961 View 3D Structure Click here
P0AG24 View 3D Structure Click here
P0CH63 View 3D Structure Click here
P0CH64 View 3D Structure Click here
P15723 View 3D Structure Click here
P27249 View 3D Structure Click here
P38331 View 3D Structure Click here
P46144 View 3D Structure Click here
P53144 View 3D Structure Click here
P76491 View 3D Structure Click here
P87242 View 3D Structure Click here
P9WN29 View 3D Structure Click here
P9WNY7 View 3D Structure Click here
Q09374 View 3D Structure Click here
Q2FWG7 View 3D Structure Click here
Q2FZ08 View 3D Structure Click here
Q2G0G3 View 3D Structure Click here
Q2G297 View 3D Structure Click here
Q2G2T1 View 3D Structure Click here
Q337J5 View 3D Structure Click here
Q4CTE5 View 3D Structure Click here
Q4DB46 View 3D Structure Click here
Q4DND3 View 3D Structure Click here
Q502K2 View 3D Structure Click here
Q58188 View 3D Structure Click here
Q58247 View 3D Structure Click here
Q58426 View 3D Structure Click here
Q58554 View 3D Structure Click here
Q59066 View 3D Structure Click here
Q5ALX7 View 3D Structure Click here
Q60710 View 3D Structure Click here
Q86JB3 View 3D Structure Click here
Q8GUM8 View 3D Structure Click here
Q8I533 View 3D Structure Click here
Q9FL05 View 3D Structure Click here
Q9SYH1 View 3D Structure Click here
Q9VAM9 View 3D Structure Click here
Q9VMB3 View 3D Structure Click here
Q9VVY4 View 3D Structure Click here
Q9Y3Z3 View 3D Structure Click here