PROSITE documentation PDOC00305HMG boxes A and B DNA-binding domains signature and profile
High mobility group (HMG) chromosomal proteins are a family of relatively low molecular weight non-histone components that bind DNA without sequence specificity. HMG1 (also called HMG-T in fish) and HMG2 are related proteins that have two distinguishing features: two HMG boxes (A and B), homologous folded domains of around 80 amino acid residues, and a long acidic tail containing 20 to 30 aspartic or glutamic acid residues [1,2]. The HMG box A is only found in HMG 1 and 2 proteins whereas the HMG box B is also present in various transcription factors. HMG boxes have unusual DNA binding activity. They bind preferentially to distorted DNAs, such as four-way junctions, kinked cisplatin-modified DNA, DNA bulges, and have the property to bend DNA [2]. They can bind DNA without sequence specificity like in HMG1 and 2 or recognize a specific site.
Several structures of HMG-boxes have been solved (see <PDB:1AAB>) [3,4]. They have a common fold consisting of three α helices arranged in an "L-shape". The HMG box binds DNA through its concave face to the minor groove of B-form DNA and causes bending by partial intercalation of a hydrophobic residue close to the N-terminus of helix I [4,5].
Some proteins known to contain a HMG box are listed below:
- Eukaryotic HMG1, HMG2 and related proteins.
- Animal sex determining region Y (SRY) and related proteins, a transcriptional activator which regulates a genetic switch in male development.
- Animal SOX family of transcription factors, a conserved family of proteins related to the testis-determining factor SRY.
- Mammalian lymphoid enhancer binding factor 1 (LEF1), a transcriptional activator which regulates a genetic switch in male development.
- Eukaryotic structure-specific recognition protein 1 (SSRP). It binds specifically to double-stranded and, at low levels, to single-stranded DNA which has been modified by the anticancer drug cisplatin.
- Mitochondrial transcription factor 1 (MTF1). It confers selective promoter recognition on the core subunit of the yeast mitochondrial RNA polymerase.
- Vertebrate nucleolar transcription factors (UBF1/2). They recognize the ribosomal RNA gene promoter and activate transcription mediated by RNA polymerase I.
- Yeast ARS-binding factor (ABF2). It binds specifically to the autonomously replicating sequence 1 (ARS1).
- Yeast transcription factors IXR1, ROX1, NHP6A/B, SPP41.
- Drosophila capicua protein. A transcription cofactor involved in negative regulation of transcription.
- Fission yeast mismatch binding protein 1 (cmb1). It binds to cytosines in base mismatches and opposite chemically altered guanines.
- Tetrahymena thermophila micronuclear linker histone polyprotein (MIC LH).
- Mammalian nuclear autoantigen Speckled 100 kDa protein (Sp-100).
The pattern we developed covers the second helix of the HMG box A and therefore is specific for HMG1/2 proteins. We also developed a profile that covers the whole domain and recognizes both types of HMG boxes.
Last update:December 2004 / Pattern and text revised.
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PROSITE methods (with tools and information) covered by this documentation:
1 | Authors | Bustin M. Lehn D.A. Landsman D. |
Title | Structural features of the HMG chromosomal proteins and their genes. | |
Source | Biochim. Biophys. Acta 1049:231-243(1990). | |
PubMed ID | 2200521 |
2 | Authors | Thomas J.O. |
Title | HMG1 and 2: architectural DNA-binding proteins. | |
Source | Biochem. Soc. Trans. 29:395-401(2001). | |
PubMed ID | 11497996 |
3 | Authors | Hardman C.H. Broadhurst R.W. Raine A.R. Grasser K.D. Thomas J.O. Laue E.D. |
Title | Structure of the A-domain of HMG1 and its interaction with DNA as studied by heteronuclear three- and four-dimensional NMR spectroscopy. | |
Source | Biochemistry 34:16596-16607(1995). | |
PubMed ID | 8527432 |
4 | Authors | Werner M.H. Huth J.R. Gronenborn A.M. Clore G.M. |
Title | Molecular basis of human 46X,Y sex reversal revealed from the three-dimensional solution structure of the human SRY-DNA complex. | |
Source | Cell 81:705-714(1995). | |
PubMed ID | 7774012 |
5 | Authors | Love J.J. Li X. Case D.A. Giese K. Grosschedl R. Wright P.E. |
Title | Structural basis for DNA bending by the architectural transcription factor LEF-1. | |
Source | Nature 376:791-795(1995). | |
PubMed ID | 7651541 | |
DOI | 10.1038/376791a0 |
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