In silico characterization of the INO80 subfamily of SWI2/SNF2 chromatin remodeling proteins

Biochem Biophys Res Commun. 2004 Jul 16;320(1):197-204. doi: 10.1016/j.bbrc.2004.05.147.

Abstract

Proteins belonging to SNF2 family of DNA dependent ATPases are important members of the chromatin remodeling complexes that are implicated in epigenetic control of gene expression. The yeast Ino80, the catalytic ATPase subunit of the INO80 complex, is the most recently described member of the SNF2 family. Outside the conserved ATPase domain, it has very little similarity with other well-characterized SNF2 proteins hence it is believed to represent a new subfamily. We have identified new members of this subfamily in different organisms and have detected characteristic features of this subfamily. Using various data mining tools we have identified a new, previously undetected domain in all members of this subfamily. This domain designated DBINO is characteristic of the INO80 subfamily and is predicted to have DNA-binding function. The presence of this domain in all the INO80 subfamily proteins from different organisms suggests its conserved function in evolution.

Publication types

  • Comparative Study
  • Evaluation Study
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amino Acid Sequence
  • Animals
  • Chromatin Assembly and Disassembly / genetics
  • Chromosomal Proteins, Non-Histone / chemistry
  • Chromosomal Proteins, Non-Histone / genetics
  • DNA Helicases
  • DNA-Binding Proteins / chemistry*
  • DNA-Binding Proteins / genetics*
  • Databases, Protein
  • Humans
  • Molecular Sequence Data
  • Nuclear Proteins*
  • Phylogeny
  • Saccharomyces cerevisiae Proteins / chemistry*
  • Saccharomyces cerevisiae Proteins / genetics*
  • Sequence Alignment / methods*
  • Sequence Analysis, Protein / methods*
  • Sequence Homology, Amino Acid
  • Transcription Factors / chemistry*
  • Transcription Factors / genetics*

Substances

  • Chromosomal Proteins, Non-Histone
  • DNA-Binding Proteins
  • INO80 complex, S cerevisiae
  • Nuclear Proteins
  • SMARCA1 protein, human
  • SMARCA2 protein, human
  • Saccharomyces cerevisiae Proteins
  • Transcription Factors
  • SMARCA4 protein, human
  • DNA Helicases