Summary: AT hook motif
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AT-hook Edit Wikipedia article
AT-hook | |||||||||
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![]() solution structure of a complex of the second dna binding domain of human hmg-i(y) bound to dna dodecamer containing the prdii site of the interferon-beta promoter, nmr, 35 structures | |||||||||
Identifiers | |||||||||
Symbol | AT_hook | ||||||||
Pfam | PF02178 | ||||||||
InterPro | IPR017956 | ||||||||
SMART | AT_hook | ||||||||
SCOPe | 2eze / SUPFAM | ||||||||
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The AT-hook is a DNA-binding motif present in many proteins, including the high mobility group (HMG) proteins,[1] DNA-binding proteins from plants [2] and hBRG1 protein, a central ATPase of the human switching/sucrose non-fermenting (SWI/SNF) remodeling complex.[3]
This motif consists of a conserved, palindromic, core sequence of proline-arginine-glycine-arginine-proline, although some AT-hooks contain only a single proline in the core sequence. AT-hooks also include a variable number of positively charged lysine and arginine residues on either side of the core sequence.[4] The AT-hook binds to the minor groove of adenine-thymine (AT) rich DNA, hence the AT in the name. The rest of the name derives from a predicted asparagine/aspartate "hook" in the earliest AT-hooks reported in 1990.[5] In 1997 structural studies using NMR determined that a DNA-bound AT-hook adopted a crescent or hook shape around the minor groove of a target DNA strand (pictured at right).[6] HMGA proteins contain three AT-hooks, although some proteins contain as many as 30.[5] The optimal binding sequences for AT-hook proteins are repeats of the form (ATAA)n or (TATT)n, although the optimal binding sequences for the core sequence of the AT-hook are AAAT and AATT.[7]
References
- ^ Reeves R, Beckerbauer L (May 2001). "HMGI/Y proteins: flexible regulators of transcription and chromatin structure". Biochim. Biophys. Acta. 1519 (1–2): 13–29. doi:10.1016/S0167-4781(01)00215-9. PMID 11406267.
- ^ Meijer AH, van Dijk EL, Hoge JH (June 1996). "Novel members of a family of AT hook-containing DNA-binding proteins from rice are identified through their in vitro interaction with consensus target sites of plant and animal homeodomain proteins". Plant Mol. Biol. 31 (3): 607–18. doi:10.1007/BF00042233. PMID 8790293.
- ^ Singh M, D'Silva L, Holak TA (2006). "DNA-binding properties of the recombinant high-mobility-group-like AT-hook-containing region from human BRG1 protein". Biol. Chem. 387 (10–11): 1469–78. doi:10.1515/BC.2006.184. PMID 17081121.
- ^ Reeves R (October 2001). "Molecular biology of HMGA proteins: hubs of nuclear function". Gene. 277 (1–2): 63–81. doi:10.1016/S0378-1119(01)00689-8. PMID 11602345.
- ^ a b Reeves R, Nissen MS (May 1990). "The A.T-DNA-binding domain of mammalian high mobility group I chromosomal proteins. A novel peptide motif for recognizing DNA structure". J. Biol. Chem. 265 (15): 8573–82. PMID 1692833.
- ^ Huth JR, Bewley CA, Nissen MS, et al. (August 1997). "The solution structure of an HMG-I(Y)-DNA complex defines a new architectural minor groove binding motif". Nat. Struct. Biol. 4 (8): 657–65. doi:10.1038/nsb0897-657. PMID 9253416.
- ^ Reeves R (October 2000). "Structure and function of the HMGI(Y) family of architectural transcription factors". Environ. Health Perspect. 108 (Suppl 5): 803–9. doi:10.2307/3454310. JSTOR 3454310. PMID 11035986. Archived from the original on 2009-01-09.
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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.
AT hook motif Provide feedback
At hooks are DNA binding motifs with a preference for A/T rich regions.
External database links
SCOP: | 2eze |
SMART: | AT_hook |
This tab holds annotation information from the InterPro database.
InterPro entry IPR017956
AT hooks are DNA-binding motifs with a preference for A/T rich regions. These motifs are found in a variety of proteins, including the high mobility group (HMG) proteins [PUBMED:11406267], in DNA-binding proteins from plants [PUBMED:8790293] and in hBRG1 protein, a central ATPase of the human switching/sucrose non-fermenting (SWI/SNF) remodeling complex [PUBMED:17081121].
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 (39) |
Full (5111) |
Representative proteomes | UniProt (8373) |
NCBI (10926) |
Meta (85) |
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RP15 (714) |
RP35 (2112) |
RP55 (3487) |
RP75 (5162) |
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PP/heatmap | 1 |
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Seed (39) |
Full (5111) |
Representative proteomes | UniProt (8373) |
NCBI (10926) |
Meta (85) |
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RP15 (714) |
RP35 (2112) |
RP55 (3487) |
RP75 (5162) |
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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
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Curation
Seed source: | Alignment kindly provided by SMART |
Previous IDs: | none |
Type: | Motif |
Sequence Ontology: | SO:0001067 |
Author: | SMART |
Number in seed: | 39 |
Number in full: | 5111 |
Average length of the domain: | 12.60 aa |
Average identity of full alignment: | 52 % |
Average coverage of the sequence by the domain: | 10.37 % |
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: | 13 | ||||||||||||
Family (HMM) version: | 20 | ||||||||||||
Download: | download the raw HMM for this family |
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