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4  structures 542  species 0  interactions 2152  sequences 167  architectures

Family: AT_hook (PF02178)

Summary: AT hook motif

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AT-hook Edit Wikipedia article

AT_hook
PDB 2eze EBI.jpg
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
SCOP 2eze
SUPERFAMILY 2eze
The second AT-hook of HMGA1 (black ribbon) bound to the minor-groove of AT-rich DNA. The amino-acid side chains and nucleotides have been hidden.

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[edit]

  1. ^ 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. 
  2. ^ 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. 
  3. ^ 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. 
  4. ^ 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. 
  5. ^ 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. 
  6. ^ 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. 
  7. ^ 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. 


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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

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].

High mobility group (HMG) proteins are a family of relatively low molecular weight non-histone components in chromatin [PUBMED:11406267]. HMG-I and HMG-Y (HMGA) are proteins of about 100 amino acid residues which are produced by the alternative splicing of a single gene. HMG-I/Y proteins bind preferentially to the minor groove of AT-rich regions in double-stranded DNA in a non-sequence specific manner [PUBMED:1692833, PUBMED:8414980]. It is suggested that these proteins could function in nucleosome phasing and in the 3' end processing of mRNA transcripts. They are also involved in the transcription regulation of genes containing, or in close proximity to, AT-rich regions.

Gene Ontology

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Domain organisation

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  Seed
(40)
Full
(2152)
Representative proteomes NCBI
(2051)
Meta
(224)
RP15
(380)
RP35
(638)
RP55
(979)
RP75
(1233)
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  Seed
(40)
Full
(2152)
Representative proteomes NCBI
(2051)
Meta
(224)
RP15
(380)
RP35
(638)
RP55
(979)
RP75
(1233)
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Seed source: Alignment kindly provided by SMART
Previous IDs: none
Type: Motif
Author: SMART
Number in seed: 40
Number in full: 2152
Average length of the domain: 12.60 aa
Average identity of full alignment: 52 %
Average coverage of the sequence by the domain: 7.35 %

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 14.5 0.1
Trusted cut-off 14.5 4.0
Noise cut-off 14.4 -1000000.0
Model length: 13
Family (HMM) version: 14
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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 AT_hook 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 seqence.

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