SWI2/SNF2 chromatin-remodeling domain of eukaryotic Rad54
Danio rerio (zebra fish)
The DNA of eukaryotes is compressed almost 10,000 fold into chromosomes. This compaction is achieved by various proteins that coil and fold the DNA into consecutively higher levels of organization. The complex of DNA with proteins that bind to it to form chromosomes is called chromatin. The proteins in chromatin are of two types: histones and nonhistone chromosomal proteins. Octamers of histones form a protein core around which double-stranded DNA is wound, resulting in a nucleosome. The nucleosome forms the basic level of chromosome organization. DNA is wound into successive nucleosomes with a separation of about 80 nucleotide pairs between adjacent nucleosomes. However, other DNA binding proteins need to access certain regions of the compacted DNA for gene expression, DNA repair and replication. As a result the proteins responsible for the packaging of chromosomes must have the ability to rapidly condense and decondense it in localized regions. This rapid change in the chromatin organization is facilitated by the chromatin remodeling complexes. They use the energy of ATP hydrolysis to change the structure of the nucleosomes and make DNA more accessible. SWI2/SNF2 proteins are a family of ATPases that mobilize the nucleosomes by removing the attached histones and nonhistone chromosomal proteins. These proteins have a characteristic SF2 helicase domain. A helicase domain is normally used by helicases to unwind double stranded DNA and separate the two strands. However, the SWI2/SNF2 proteins use it to generate superhelical torsion in the DNA through ATP hydrolysis.
The structure shown above is that of the nucleosomal remodeling domain of the zebrafish protein, Rad54. Rad54 is necessary for the repair of double strand breaks in Rad5-mediated homologous recombination of DNA. The structure here shows not only the presence of two alpha/beta - lobes similar to SF2 helicases, but also two additional alpha - helical domains that may play a role in the remodeling activity.
Protein Data Bank (PDB)
Thoma, N.H. Czyzewski, B.K. Alexeev, A.A. Mazin, A.V. Kowalczykowski, S.C. Pavletich, N.P.; "Structure of the SWI2/SNF2 chromatin-remodeling domain of eukaryotic Rad54"; Nat.Struct.Mol.Biol.; (2005) 12:350-356 PubMed:15806108.
author: Ashwini Patil