The SANT domain: a putative DNA-binding domain in the SWI-SNF and ADA complexes, the transcriptional co-repressor N-CoR and TFIIIB

Current models of transcriptional co-activators and co-repressors envisage that these complexes function by protein-protein interaction mechanisms, although the details are not well understood. Recently, a new co-repressor, N-CoR, was described as a regulator of thyroid and retinoic acid receptors. In self-comparisons of the N-CoR amino-acid sequence, we found two copies of a similar to 50-residue motif spaced 129 residues apart. These repeats are flanked by two regions that have repressor properties. Sequence-database searches revealed one or two copies of this motif in several other proteins. Some of these are database entries of poorly determined function, but we noticed matches with three proteins from yeast that participate in basal or activated transcription complexes. SWI3 and ADA2 are components of either the SWI-SNF or ADA transcriptional activation complexes, while the B double prime subunit of TFIIIB is a component of the RNA polymerase III initiation complex. Therefore, we call this the SANT (SWI3, ADA2, N-CoR and TFIIIB B double prime ) domain. Further refined database searches identified the I-SWI proteins (HuSN2L, CeSN2L, DmISWI and ScYBR245) as a SANT-domain outgroup.