Please note: this site relies heavily on the use of javascript. Without a javascript-enabled browser, this site will not function correctly. Please enable javascript and reload the page, or switch to a different browser.
326  structures 5553  species 3  interactions 16021  sequences 176  architectures

Family: Hist_deacetyl (PF00850)

Summary: Histone deacetylase 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 "Histone deacetylase". More...

Histone deacetylase Edit Wikipedia article

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.

Histone deacetylase domain Provide feedback

Histones can be reversibly acetylated on several lysine residues. Regulation of transcription is caused in part by this mechanism. Histone deacetylases catalyse the removal of the acetyl group. Histone deacetylases are related to other proteins [1].

Literature references

  1. Leipe DD, Landsman D; , Nucleic Acids Res 1997;25:3693-3697.: Histone deacetylases, acetoin utilization proteins and acetylpolyamine amidohydrolases are members of an ancient protein superfamily. PUBMED:9278492 EPMC:9278492


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR023801

Regulation of transcription is, in part, modulated by reversible histone acetylation on several lysine. Histone deacetylases (HDA) catalyse the removal of the acetyl group. Histone deacetylases, acetoin utilization proteins and acetylpolyamine amidohydrolases are all members of this ancient protein superfamily [PUBMED:9278492].

HDAs function in multi-subunit complexes, reversing the acetylation of histones by histone acetyltransferases [PUBMED:10322454, PUBMED:10072350], and are also believed to deacetylate general transcription factors such as TFIIF and sequence-specific transcription factors such as p53 [PUBMED:10322454]. Thus, HDAs contribute to the regulation of transcription, in particular transcriptional repression [PUBMED:10072350]. At N-terminal tails of histones, removal of the acetyl group from the epsilon-amino group of a lysine side chain will restore its positivecharge, which may stabilise the histone-DNA interaction and prevent activating transcription factors binding to promoter elements [PUBMED:9278492]. HDAs play important roles in the cell cycle and differentiation, and their deregulation can contribute to the development of cancer [PUBMED:10072350, PUBMED:10322142].

This entry represents the structural domain found in histone deacetylases. It consists of a 3-layer(alpha-beta-alpha) sandwich.

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 Arginase (CL0302), which has the following description:

This superfamily includes arginase enzymes as well as histone deacetylases and related enzymes [1].

The clan contains the following 3 members:

Arginase Hist_deacetyl UPF0489

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, 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
(79)
Full
(16021)
Representative proteomes UniProt
(33529)
NCBI
(46405)
Meta
(3274)
RP15
(4172)
RP35
(9465)
RP55
(14022)
RP75
(18430)
Jalview View  View  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
(79)
Full
(16021)
Representative proteomes UniProt
(33529)
NCBI
(46405)
Meta
(3274)
RP15
(4172)
RP35
(9465)
RP55
(14022)
RP75
(18430)
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
(79)
Full
(16021)
Representative proteomes UniProt
(33529)
NCBI
(46405)
Meta
(3274)
RP15
(4172)
RP35
(9465)
RP55
(14022)
RP75
(18430)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download   Download   Download  
Gzipped Download   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.

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: Pfam-B_343 (release 3.0)
Previous IDs: none
Type: Domain
Sequence Ontology: SO:0000417
Author: Bateman A
Number in seed: 79
Number in full: 16021
Average length of the domain: 282.20 aa
Average identity of full alignment: 28 %
Average coverage of the sequence by the domain: 60.60 %

HMM information View help on HMM parameters

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:
Parameter Sequence Domain
Gathering cut-off 27.9 27.9
Trusted cut-off 28.1 27.9
Noise cut-off 27.7 27.7
Model length: 307
Family (HMM) version: 19
Download: download the raw HMM for this family

Species distribution

Sunburst controls

Hide

Weight segments by...


Change the size of the sunburst

Small
Large

Colour assignments

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

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...

Loading sunburst data...

Tree controls

Hide

The 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

There are 3 interactions for this family. More...

Arb2 Hist_deacetyl ELM2

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 Hist_deacetyl domain has been found. There are 326 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...