CUT |
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| SMART accession number: | SM01109 |
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| Description: | The CUT domain is a DNA-binding domain often found in combination with a downstream homeodomain. |
| Family alignment: |
There are 591 CUT domains in 329 proteins in SMART's nrdb database.
Click on the following links for more information.
- Evolution (species in which this domain is found)
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to expand nodes. To display all proteins with a CUT domain in a specific node, click on it.This tree shows only several representative species. The complete taxonomic breakdown of all proteins with CUT domain is also avaliable.
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Go to specific node: Anopheles gambiae, Caenorhabditis elegans, Drosophila melanogaster, Homo sapiens, Mus musculus, Rattus norvegicus, Takifugu rubripes - Cellular role (predicted cellular role)
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Cellular role: chromatin
Binding / catalysis: DNA - Literature (relevant references for this domain)
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Primary literature is listed below; Automatically-derived, secondary literature is also avaliable.
- Yamasaki K, Akiba T, Yamasaki T, Harata K
- Structural basis for recognition of the matrix attachment region of DNA bytranscription factor SATB1.
- Nucleic Acids Res. 2007; 35: 5073-84
- Display abstract
Special AT-rich sequence binding protein 1 (SATB1) regulates gene expressionessential in immune T-cell maturation and switching of fetal globin species, bybinding to matrix attachment regions (MARs) of DNA and inducing a local chromatinremodeling. Previously we have revealed a five-helix structure of the N-terminal CUT domain, which is essentially the folded region in the MAR-binding domain, of human SATB1 by NMR. Here we determined crystal structure of the complex of theCUT domain and a MAR DNA, in which the third helix of the CUT domain deeplyenters the major groove of DNA in the B-form. Bases of 5'-CTAATA-3' sequence are contacted by this helix, through direct and water-mediated hydrogen bonds andapolar and van der Waals contacts. Mutations at conserved base-contactingresidues, Gln402 and Gly403, reduced the DNA-binding activity, which confirmedthe importance of the observed interactions involving these residues. Asignificant number of equivalent contacts are observed also for typicallyfour-helix POU-specific domains of POU-homologous proteins, indicating that thesedomains share a common framework of the DNA-binding mode, recognizing partiallysimilar DNA sequences.
- Lannoy VJ, Burglin TR, Rousseau GG, Lemaigre FP
- Isoforms of hepatocyte nuclear factor-6 differ in DNA-binding properties, containa bifunctional homeodomain, and define the new ONECUT class of homeodomainproteins.
- J Biol Chem. 1998; 273: 13552-62
- Display abstract
Hepatocyte nuclear factor-6 (HNF-6) contains a single cut domain and ahomeodomain characterized by a phenylalanine at position 48 and a methionine atposition 50. We describe here two isoforms of HNF-6 which differ by the linkerthat separates these domains. Both isoforms stimulated transcription. Theaffinity of HNF-6alpha and HNF-6beta for DNA differed, depending on the targetsequence. Binding of HNF-6 to DNA involved the cut domain and the homeodomain,but the latter was not required for binding to a subset of sites. Mutations ofthe F48M50 dyad that did not affect DNA binding reduced the transcriptionalstimulation of constructs that do not require the homeodomain for DNA binding,but did not affect the stimulation of constructs that do require the homeodomain.Comparative trees of mammalian, Drosophila, and Caenorhabditis elegans proteinsshowed that HNF-6 defines a new class, which we call ONECUT, of homeodomainproteins. C. elegans proteins of this class bound to HNF-6 DNA targets. Thus,depending on their sequence, these targets determine for HNF-6 at least two modesof DNA binding, which hinge on the homeodomain and on the linker that separatesit from the cut domain, and two modes of transcriptional stimulation, which hingeon the homeodomain.
- Structure (3D structures containing this domain)
3D Structures of CUT domains in PDB
PDB code Main view Title 1s7e 
Solution structure of hnf-6 1wh6 
Solution structure of the second cut domain of human homeobox protein cux-2 1wh8 
Solution structure of the third cut domain of human homeobox protein cux-2 1wiz 
Solution structure of the first cut domain of kiaa1034 protein 1x2l 
Solution structure of the cut domain of human homeobox protein cux-2 (cut-like 2) 1yse 
Solution structure of the mar-binding domain of satb1 2csf 
Solution structure of the second cut domain of human satb2 2d5v 
Crystal structure of hnf-6alpha dna-binding domain in complex with the ttr promoter 2o49 
Crystal structure of the n-terminal cut domain of satb1 bound to matrix attachment region dna 2o4a 
Crystal structure of the n-terminal cut domain of satb1 bound to matrix attachment region dna - Links (links to other resources describing this domain)
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PFAM CUT