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282  structures 355  species 1  interaction 7921  sequences 370  architectures

Family: Bromodomain (PF00439)

Summary: Bromodomain

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This is the Wikipedia entry entitled "Bromodomain". More...

Bromodomain Edit Wikipedia article

Bromodomain
1e6i bromodomain.png
Ribbon diagram of the GCN5 bromodomain from Saccharomyces cerevisiae, colored from blue (N-terminus) to red (C-terminus).[1]
Identifiers
Symbol Bromodomain
Pfam PF00439
InterPro IPR001487
SMART SM00297
PROSITE PDOC00550
SCOP 1b91
SUPERFAMILY 1b91
CDD cd04369

A bromodomain is a protein domain that recognizes acetylated lysine residues such as those on the N-terminal tails of histones. This recognition is often a prerequisite for protein-histone association and chromatin remodeling. The domain itself adopts an all-α protein fold, a bundle of four alpha helices.[1][2]

Discovery[edit]

The bromodomain was identified as a novel structural motif by John W. Tamkun and colleagues studying the brm gene, and showed sequence similarity to genes involved in transcriptional activation.[3]

See also[edit]

References[edit]

  1. ^ a b PDB 1e6i; Owen DJ, Ornaghi P, Yang JC, Lowe N, Evans PR, Ballario P, Neuhaus D, Filetici P, Travers AA (November 2000). "The structural basis for the recognition of acetylated histone H4 by the bromodomain of histone acetyltransferase gcn5p". EMBO J. 19 (22): 6141–9. doi:10.1093/emboj/19.22.6141. PMC 305837. PMID 11080160. 
  2. ^ Zeng L, Zhou MM (February 2002). "Bromodomain: an acetyl-lysine binding domain". FEBS Lett. 513 (1): 124–8. doi:10.1016/S0014-5793(01)03309-9. PMID 11911891. 
  3. ^ Tamkun JW, Deuring R, Scott MP, Kissinger M, Pattatucci AM, Kaufman TC, Kennison JA (February 1992). "brahma: a regulator of Drosophila homeotic genes structurally related to the yeast transcriptional activator SNF2/SWI2". Cell 68 (3): 561–72. doi:10.1016/0092-8674(92)90191-E. PMID 1346755. 

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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.

Bromodomain Provide feedback

Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine [3].

Literature references

  1. Haynes SR, Dollard C, Winston F, Beck S, Trowsdale J, Dawid IB; , Nucleic Acids Res 1992;20:2603-2603.: The bromodomain: a conserved sequence found in human, Drosophila and yeast proteins. PUBMED:1350857 EPMC:1350857

  2. Jeanmougin F, Wurtz J-M, Le Douarin B, Chambon P, Losson R; , Trends Biochem Sci 1997;22:151-153.: The bromodomain revisited. PUBMED:9175470 EPMC:9175470

  3. Dhalluin C, Carlson JE, Zeng L, He C, Aggarwal AK, Zhou MM; , Nature 1999;399:491-496.: Structure and ligand of a histone acetyltransferase bromodomain. PUBMED:10365964 EPMC:10365964


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR001487

Bromodomains are found in a variety of mammalian, invertebrate and yeast DNA-binding proteins [PUBMED:1350857]. Bromodomains can interact with acetylated lysine [PUBMED:9175470]. In some proteins, the classical bromodomain has diverged to such an extent that parts of the region are either missing or contain an insertion (e.g., mammalian protein HRX, Caenorhabditis elegans hypothetical protein ZK783.4, yeast protein YTA7). The bromodomain may occur as a single copy, or in duplicate.

The precise function of the domain is unclear, but it may be involved in protein-protein interactions and may play a role in assembly or activity of multi-component complexes involved in transcriptional activation [PUBMED:7580139].

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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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...

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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
(69)
Full
(7921)
Representative proteomes NCBI
(7646)
Meta
(90)
RP15
(1623)
RP35
(2367)
RP55
(3612)
RP75
(4778)
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Format an alignment

  Seed
(69)
Full
(7921)
Representative proteomes NCBI
(7646)
Meta
(90)
RP15
(1623)
RP35
(2367)
RP55
(3612)
RP75
(4778)
Alignment:
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Sequence:
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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
(69)
Full
(7921)
Representative proteomes NCBI
(7646)
Meta
(90)
RP15
(1623)
RP35
(2367)
RP55
(3612)
RP75
(4778)
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.

Pfam alignments:

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: Prosite
Previous IDs: bromodomain;
Type: Domain
Author: Finn RD
Number in seed: 69
Number in full: 7921
Average length of the domain: 84.20 aa
Average identity of full alignment: 26 %
Average coverage of the sequence by the domain: 10.39 %

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 21.0 21.0
Trusted cut-off 21.0 21.0
Noise cut-off 20.9 20.9
Model length: 84
Family (HMM) version: 20
Download: download the raw HMM for this family

Species distribution

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Interactions

There is 1 interaction for this family. More...

Bromodomain

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 Bromodomain domain has been found. There are 282 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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