Summary: HAND
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This is the Wikipedia entry entitled "HAND domain". More...
HAND domain Edit Wikipedia article
HAND | |||||||||
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![]() nucleosome recognition module of iswi atpase
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Identifiers | |||||||||
Symbol | HAND | ||||||||
Pfam | PF09110 | ||||||||
InterPro | IPR015194 | ||||||||
SCOP | 1ofc | ||||||||
SUPERFAMILY | 1ofc | ||||||||
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In molecular biology, the HAND domain is a protein domain which adopts a secondary structure consisting of four alpha helices, three of which (H2, H3, H4) form an L-like configuration. Helix H2 runs antiparallel to helices H3 and H4, packing closely against helix H4, whilst helix H1 reposes in the concave surface formed by these three helices and runs perpendicular to them. This domain confers DNA and nucleosome binding properties to the proteins in which it occurs.[1] It is named the HAND domain because its 4-helical structure resembles an open hand.
HAND domain-containing proteins include proteins involved in nucleosome remodelling, an energy-dependent process that alters histone-DNA interactions within nucleosomes, thereby rendering nucleosomal DNA accessible to regulatory factors. The ATPases involved in nucleosome remodelling belong to the SWI2/SNF2 subfamily of DEAD/H-helicases, which contain a conserved ATPase domain characterised by seven motifs. Proteins within this family differ with regard to domain organisation, their associated proteins and the remodelling complex in which they reside. The ATPase ISWI is a member of this family. ISWI can be divided into two regions: an N-terminal region that contains the SWI2/SNF2 ATPase domain, and a C-terminal region that is responsible for substrate recognition. The C-terminal region contains 12 alpha-helices and can be divided into three domains and a spacer region: a HAND domain, a SANT domain (c-Myb DNA-binding like), a spacer helix, and a SLIDE domain (SANT-like but with several insertions).
References
- ^ Grune T, Brzeski J, Eberharter A, Clapier CR, Corona DF, Becker PB, Muller CW (August 2003). "Crystal structure and functional analysis of a nucleosome recognition module of the remodeling factor ISWI". Mol. Cell. 12 (2): 449–60. doi:10.1016/S1097-2765(03)00273-9. PMID 14536084.
This article incorporates text from the public domain Pfam and InterPro IPR015194
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HAND Provide feedback
The HAND domain adopts a secondary structure consisting of four alpha helices, three of which (H2, H3, H4) form an L-like configuration. Helix H2 runs antiparallel to helices H3 and H4, packing closely against helix H4, whilst helix H1 reposes in the concave surface formed by these three helices and runs perpendicular to them. The domain confers DNA and nucleosome binding properties to the protein [1].
Literature references
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Grune T, Brzeski J, Eberharter A, Clapier CR, Corona DF, Becker PB, Muller CW; , Mol Cell. 2003;12:449-460.: Crystal structure and functional analysis of a nucleosome recognition module of the remodeling factor ISWI. PUBMED:14536084 EPMC:14536084
External database links
SCOP: | 1ofc |
This tab holds annotation information from the InterPro database.
InterPro entry IPR015194
Nucleosome remodelling is an energy-dependent process that alters histone-DNA interactions within nucleosomes, thereby rendering nucleosomal DNA accessible to regulatory factors. The ATPases involved belong to the SWI2/SNF2 subfamily of DEAD/H-helicases, which contain a conserved ATPase domain characterised by seven motifs. Proteins within this family differ with regard to domain organisation, their associated proteins and the remodelling complex in which they reside.
The ATPase ISWI is a member of this family. ISWI can be divided into two regions: an N-terminal region that contains the SWI2/SNF2 ATPase domain, and a C-terminal region that is responsible for substrate recognition. The C-terminal region contains 12 alpha-helices and can be divided into three domains and a spacer region: a HAND domain (named because its 4-helical structure resembles an open hand), a SANT domain (c-Myb DNA-binding like), a spacer helix, and a SLIDE domain (SANT-like but with several insertions).
This entry represents the HAND domain, which adopts a secondary structure consisting of four alpha helices, three of which (H2, H3, H4) form an L-like configuration. Helix H2 runs antiparallel to helices H3 and H4, packing closely against helix H4, whilst helix H1 reposes in the concave surface formed by these three helices and runs perpendicular to them. This domain confers DNA and nucleosome binding properties to the protein [PUBMED:14536084].
Gene Ontology
The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.
Molecular function | nucleosome binding (GO:0031491) |
Biological process | ATP-dependent chromatin remodeling (GO:0043044) |
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
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Seed (103) |
Full (1738) |
Representative proteomes | UniProt (2786) |
NCBI (3523) |
Meta (3) |
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RP15 (251) |
RP35 (741) |
RP55 (1281) |
RP75 (1793) |
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HTML | |||||||||
PP/heatmap | 1 |
1Cannot generate PP/Heatmap alignments for seeds; no PP data available
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Seed (103) |
Full (1738) |
Representative proteomes | UniProt (2786) |
NCBI (3523) |
Meta (3) |
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RP15 (251) |
RP35 (741) |
RP55 (1281) |
RP75 (1793) |
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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
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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.
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Curation and family details
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Curation
Seed source: | pdb_1ofc |
Previous IDs: | none |
Type: | Domain |
Sequence Ontology: | SO:0000417 |
Author: |
Sammut SJ |
Number in seed: | 103 |
Number in full: | 1738 |
Average length of the domain: | 98.50 aa |
Average identity of full alignment: | 43 % |
Average coverage of the sequence by the domain: | 9.61 % |
HMM information
HMM build commands: |
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 47079205 -E 1000 --cpu 4 HMM pfamseq
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Model details: |
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Model length: | 112 | ||||||||||||
Family (HMM) version: | 12 | ||||||||||||
Download: | download the raw HMM for this family |
Species distribution
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Interactions
There is 1 interaction for this family. More...
HANDStructures
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 HAND domain has been found. There are 5 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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