Summary: BED zinc finger
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BED zinc finger Edit Wikipedia article
| zf-BED | |||||||||
|---|---|---|---|---|---|---|---|---|---|
 Solution structure of the zinc finger bed domain of the zinc finger BED domain containing protein 1 | |||||||||
| Identifiers | |||||||||
| Symbol | zf-BED | ||||||||
| Pfam | PF02892 | ||||||||
| Pfam clan | CL0361 | ||||||||
| InterPro | IPR003656 | ||||||||
| |||||||||
In molecular biology the BED-type zinc finger domain is a protein domain which was named after the Drosophila proteins BEAF and DREF, is found in one or more copies in cellular regulatory factors and transposases from plants, animals and fungi. The BED finger is an about 50 to 60 amino acid residues domain that contains a characteristic motif with two highly conserved aromatic positions, as well as a shared pattern of cysteines and histidines that is predicted to form a zinc finger. As diverse BED fingers are able to bind DNA, it has been suggested that DNA-binding is the general function of this domain.[1] Some proteins known to contain a BED domain include animal, plant and fungi AC1 and Hobo-like transposases; Caenorhabditis elegans Dpy-20 protein, a predicted cuticular gene transcriptional regulator; Drosophila BEAF (boundary element-associated factor), thought to be involved in chromatin insulation; Drosophila DREF, a transcriptional regulator for S-phase genes; and tobacco 3AF1 and tomato E4/E8-BP1, light- and ethylene-regulated DNA binding proteins that contain two BED fingers. Most genes in this family are believed to have evolved from the hAT family of DNA transposons.[2]
See also
References
- ^ Aravind L (September 2000). "The BED finger, a novel DNA-binding domain in chromatin-boundary-element-binding proteins and transposases". Trends in Biochemical Sciences. 25 (9): 421–3. doi:10.1016/s0968-0004(00)01620-0. PMID 10973053.
- ^ Hayward, Alexander; Ghazal, Awaisa; Andersson, Göran; Andersson, Leif; Jern, Patric; Robinson-Rechavi, Marc (22 March 2013). "ZBED Evolution: Repeated Utilization of DNA Transposons as Regulators of Diverse Host Functions". PLoS ONE. 8 (3): e59940. doi:10.1371/journal.pone.0059940. PMC 3606216.
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BED zinc finger Provide feedback
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Internal database links
| SCOOP: | zf-C2H2 zf-C2H2_12 zf-C2H2_4 zf-H2C2_2 |
| Similarity to PfamA using HHSearch: | zf-C2H2 ROS_MUCR zf-C2H2_12 |
This tab holds annotation information from the InterPro database.
InterPro entry IPR003656
The BED finger, which was named after the Drosophila proteins BEAF and DREF, is found in one or more copies in cellular regulatory factors and transposases from plants, animals and fungi. The BED finger is an about 50 to 60 amino acid residues domain that contains a characteristic motif with two highly conserved aromatic positions, as well as a shared pattern of cysteines and histidines that is predicted to form a zinc finger. As diverse BED fingers are able to bind DNA, it has been suggested that DNA-binding is the general function of this domain [ PUBMED:10973053 ].
Some proteins known to contain a BED domain are listed below:
- Animal, fungal and plant AC1 and Hobo-like transposases.
- Caenorhabditis elegans protein dpy-20, a predicted cuticular-gene transcriptional regulator.
- Drosophila BEAF (boundary element-associated factor), which is thought to be involved in chromatin insulation.
- Drosophila DREF, a transcriptional regulator for S-phase genes.
- Tobacco 3AF1 and tomato E4/E8-BP1, which are light- and ethylene-regulated DNA binding proteins that contain two BED fingers [ PUBMED:2152132 , PUBMED:9225464 ].
Gene Ontology
The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.
| Molecular function | DNA binding (GO:0003677) |
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 C2H2-zf (CL0361), which has the following description:
Superfamily of classical and closely related C2H2 or beta-beta-alpha zinc finger DNA-binding domains.
The clan contains the following 52 members:
ARS2 GAGA Hat1_N Integrase_H2C2 KN17_SH3 Nairovirus_M ROS_MUCR SF3a60_Prp9_C Sgf11 UBZ_FAAP20 Zap1_zf2 zf-AD zf-BED zf-C2H2 zf-C2H2_10 zf-C2H2_11 zf-C2H2_2 zf-C2H2_3 zf-C2H2_3rep zf-C2H2_4 zf-C2H2_6 zf-C2H2_7 zf-C2H2_8 zf-C2H2_9 zf-C2H2_aberr zf-C2H2_jaz zf-C2HC_2 zf-C2HE zf-CRD zf-DBF zf-Di19 zf-H2C2 zf-H2C2_2 zf-H2C2_5 zf-H3C2 zf-LYAR zf-met zf-met2 zf-MYST zf-RAG1 zf-U1 zf-U11-48K zf-WRNIP1_ubi zf_C2H2_10 zf_C2H2_13 zf_C2H2_6 zf_C2H2_ZHX zf_C2HC_14 zf_Hakai zf_UBZ zf_ZIC Zn-C2H2_12Alignments
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...
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| Seed (17) |
Full (6753) |
Representative proteomes | UniProt (11682) |
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| RP15 (1381) |
RP35 (3576) |
RP55 (6202) |
RP75 (7815) |
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| PP/heatmap | 1 | ||||||
1Cannot generate PP/Heatmap alignments for seeds; no PP data available
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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 (17) |
Full (6753) |
Representative proteomes | UniProt (11682) |
||||
|---|---|---|---|---|---|---|---|
| RP15 (1381) |
RP35 (3576) |
RP55 (6202) |
RP75 (7815) |
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| 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: | [1] |
| Previous IDs: | none |
| Type: | Domain |
| Sequence Ontology: | SO:0000417 |
| Author: |
Bateman A 
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| Number in seed: | 17 |
| Number in full: | 6753 |
| Average length of the domain: | 46.50 aa |
| Average identity of full alignment: | 26 % |
| Average coverage of the sequence by the domain: | 10.19 % |
HMM information
| HMM build commands: |
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 57096847 -E 1000 --cpu 4 HMM pfamseq
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| Model details: |
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| Model length: | 44 | ||||||||||||
| Family (HMM) version: | 17 | ||||||||||||
| Download: | download the raw HMM for this family |
Species distribution
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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 zf-BED domain has been found. There are 2 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.
