Summary: SAND domain
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This is the Wikipedia entry entitled "SAND DNA-binding protein domain". More...
SAND DNA-binding protein domain Edit Wikipedia article
SAND | |||||||||
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![]() solution structure of the sand domain of the putative nuclear protein homolog (5830484a20rik) | |||||||||
Identifiers | |||||||||
Symbol | SAND | ||||||||
Pfam | PF01342 | ||||||||
InterPro | IPR000770 | ||||||||
SCOP2 | 1h5p / SCOPe / SUPFAM | ||||||||
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The SAND domain (named after Sp100, AIRE-1, NucP41/75, DEAF-1) is a conserved ~80 residue region found in a number of nuclear proteins, many of which function in chromatin-dependent transcriptional control. These include proteins linked to various human diseases, such as the Sp100 (Speckled protein 100 kDa), NUDR (Nuclear DEAF-1 related), GMEB (Glucocorticoid Modulatory Element Binding) proteins and AIRE-1 (Autoimmune regulator 1) proteins.
Proteins containing the SAND domain have a modular structure; the SAND domain can be associated with a number of other modules, including the bromodomain, the PHD finger and the MYND finger. Because no SAND domain has been found in yeast, it is thought that the SAND domain could be restricted to animal phyla. Many SAND domain-containing proteins, including NUDR, DEAF-1 (Deformed epidermal autoregulatory factor-1) and GMEB, have been shown to bind DNA sequences specifically. The SAND domain has been proposed to mediate the DNA binding activity of these proteins.[1][2]
The resolution of the 3D structure of the SAND domain from Sp100b has revealed that it consists of a novel alpha/beta fold. The SAND domain adopts a compact fold consisting of a strongly twisted, five-stranded antiparallel beta-sheet with four alpha-helices packing against one side of the beta-sheet. The opposite side of the beta-sheet is solvent exposed. The beta-sheet and alpha-helical parts of the structure form two distinct regions. Multiple hydrophobic residues pack between these regions to form a structural core. A conserved KDWK sequence motif is found within the alpha-helical, positively charged surface patch. The DNA binding surface has been mapped to the alpha-helical region encompassing the KDWK motif.[2]
References
- ^ Gibson TJ, Ramu C, Gemünd C, Aasland R (1998). "The APECED polyglandular autoimmune syndrome protein, AIRE-1, contains the SAND domain and is probably a transcription factor". Trends Biochem. Sci. 23 (7): 242–4. PMID 9697411.
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ignored (help)CS1 maint: multiple names: authors list (link) - ^ a b Bottomley MJ, Collard MW, Huggenvik JI, Liu Z, Gibson TJ, Sattler M (2001). "The SAND domain structure defines a novel DNA-binding fold in transcriptional regulation". Nat. Struct. Biol. 8 (7): 626–33. doi:10.1038/89675. PMID 11427895.
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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.
SAND domain Provide feedback
The DNA binding activity of two proteins has been mapped to the SAND domain. The conserved KDWK motif is necessary for DNA binding, and it appears to be important for dimerisation [2]. This region is also found in the putative transcription factor RegA from the multicellular green alga Volvox cateri. This region of RegA is known as the VARL domain [3].
Literature references
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Gibson TJ, Ramu C, Gemund C, Aasland R; , Trends Biochem Sci 1998;23:242-244.: The APECED polyglandular autoimmune syndrome protein, AIRE-1, contains the SAND domain and is probably a transcription factor. PUBMED:9697411 EPMC:9697411
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Bottomley MJ, Collard MW, Huggenvik JI, Liu Z, Gibson TJ, Sattler M; , Nat Struct Biol 2001;8:626-633.: The SAND domain structure defines a novel DNA-binding fold in transcriptional regulation. PUBMED:11427895 EPMC:11427895
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Duncan L, Nishii I, Harryman A, Buckley S, Howard A, Friedman NR, Miller SM; , J Mol Evol. 2007;65:1-11.: The VARL gene family and the evolutionary origins of the master cell-type regulatory gene, regA, in Volvox carteri. PUBMED:17646893 EPMC:17646893
External database links
SCOP: | 1h5p |
This tab holds annotation information from the InterPro database.
InterPro entry IPR000770
The SAND domain (named after Sp100, AIRE-1, NucP41/75, DEAF-1) is a conserved ~80 residue region found in a number of nuclear proteins, many of which function in chromatin-dependent transcriptional control. These include proteins linked to various human diseases, such as the Sp100 (Speckled protein 100kDa) [ PUBMED:9636146 ], NUDR (Nuclear DEAF-1 related), GMEB (Glucocorticoid Modulatory Element Binding) proteins [ PUBMED:10894151 ] and AIRE-1 (Autoimmune regulator 1) proteins.
Proteins containing the SAND domain have a modular structure; the SAND domain can be associated with a number of other modules, including the bromodomain, the PHD finger and the MYND finger. Because no SAND domain has been found in yeast, it is thought that the SAND domain could be restricted to animal phyla. Many SAND domain-containing proteins, including NUDR, DEAF-1 (Deformed epidermal autoregulatory factor-1) and GMEB, have been shown to bind DNA sequences specifically. The SAND domain has been proposed to mediate the DNA binding activity of these proteins [ PUBMED:9697411 , PUBMED:11427895 ].
The resolution of the 3D structure of the SAND domain from Sp100b has revealed that it consists of a novel alpha/beta fold. The SAND domain adopts a compact fold consisting of a strongly twisted, five-stranded antiparallel beta-sheet with four alpha-helices packing against one side of the beta-sheet. The opposite side of the beta-sheet is solvent exposed. The beta-sheet and alpha-helical parts of the structure form two distinct regions. Multiple hydrophobic residues pack between these regions to form a structural core. A conserved KDWK sequence motif is found within the alpha-helical, positively charged surface patch. The DNA binding surface has been mapped to the alpha-helical region encompassing the KDWK motif [ PUBMED:11427895 ].
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
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Alignments
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Seed (58) |
Full (3059) |
Representative proteomes | UniProt (4860) |
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RP15 (311) |
RP35 (912) |
RP55 (2128) |
RP75 (3111) |
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PP/heatmap | 1 |
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Seed (58) |
Full (3059) |
Representative proteomes | UniProt (4860) |
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---|---|---|---|---|---|---|---|
RP15 (311) |
RP35 (912) |
RP55 (2128) |
RP75 (3111) |
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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.
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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: | Family |
Sequence Ontology: | SO:0100021 |
Author: |
Christensen J, Bateman A |
Number in seed: | 58 |
Number in full: | 3059 |
Average length of the domain: | 74.5 aa |
Average identity of full alignment: | 36 % |
Average coverage of the sequence by the domain: | 13.33 % |
HMM information
HMM build commands: |
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 61295632 -E 1000 --cpu 4 HMM pfamseq
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Model details: |
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Model length: | 77 | ||||||||||||
Family (HMM) version: | 24 | ||||||||||||
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 SAND domain has been found. There are 4 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.