4.1 Class: HMG domain factors (HMG)
Description: TRANSFAC® class description C0015: Proteins of this class comprise a region of homology with the chromosomal non-histone HMG proteins such as HMG1. This region comprises the DNA-binding domain which in some instances such as HMG1 mediates sequence-unspecific, in other cases such LEF-1 sequence-specific binding to DNA. This domain exhibits a typical L-shaped conformation made up of 3 alpha-helices and an extended N-terminal extension of the first helix. The latter together with helix 1, which contains a kink, form the long arm of the L, whereas helices 1 and 2 form the short arm. Binding to the minor groove induces a sharp bending of the DNA by more than 90 degree, away from the bound protein. The overall topology of the DNA-protein complexes resembles somewhat that of the TBP-TATA box complex.
Aligned domain sequences: Alignment of HMG domains
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Logo plot:
Blue: basic residues (KRH); red: acidic residues (DE); purple: amides (QN); black: hydrophobic residues (AVLIPWFM); green: polar (CSTYG) (http://weblogo.berkeley.edu/)