A Eukaryotic SWI2/SNF2 Domain, an Exquisite Detector of Double-stranded to Single-stranded DNA Transition Elements

Abstract

Many members of the SWI2/SNF2 family of adenosine triphosphatases participate in the assembly/disassembly of multiprotein complexes involved in the DNA metabolic processes of transcription, recombination, repair, and chromatin remodeling. The DNA molecule serves as an essential effector or catalyst for most of the members of this particular class of proteins, and the structure of the DNA may be more important than the nucleotide sequence. Inspection of the DNA structure at sites where multiprotein complexes are assembled/disassembled for these various DNA metabolic processes reveals the presence of a common element: a double-stranded to single-stranded transition region. We now show that this DNA element is crucial for the ATP hydrolytic function of an SWI2/SNF2 family member: DNA-dependent ATPase A. We further demonstrate that a domain containing the seven helicase-related motifs that are common to the SWI2/SNF2 family of proteins mediates the interaction with the DNA, yielding specific DNA structural recognition. This study forms a primary step toward understanding the physico-biochemical nature of the interaction between a particular class of DNA-dependent ATPase and their DNA effectors. Furthermore, this study provides a foundation for development of mechanisms to specifically target this class of DNAdependent ATPases.DNA recognition and the ensuing ATP hydrolysis by DNAdependent ATPases are common denominators of a number of different macromolecular assembly/disassembly processes that are required for DNA metabolic events such as chromatin remodeling, replication, repair, recombination, and transcription. There are a variety of types of known nucleic acid-modifying enzymes that use the energy released by ATP hydrolysis to produce changes in a nucleic acid substrate (i.e. helicases, nucleases, topoisomerases, ligases, and recombinases). However, there are a few nucleic acid-dependent ATPases where the nucleic acid is not obviously modified and consequently does not appear to be a substrate for the enzyme. In these cases, the nucleic acid is generally regarded as an effector of the enzymatic activity. DNA-dependent ATPase A hydrolyzes ATP only in the presence of a DNA effector, without apparent modification of the effector. Originally isolated from calf thymus tissue, ATPase A is a 105-kDa protein that undergoes proteolysis to yield two smaller polypeptides with estimated molecular masses of 68 and 83 kDa (1). All three polypeptides possess ATPase activity that is manifested only in the presence of DNA. Initial studies with the 68-kDa polypeptide indicated that the protein is maximally active in the presence of DNA effectors possessing primer-template junctions (i.e. doublestranded to single-stranded transition). This effector preference is reminiscent of the gp44⅐62 and gp45 protein complex from T4 bacteriophage (2, 3). The gp44⅐62 protein complex hydrolyzes ATP in the presence of primer-template DNA, with the energy release being coupled to the loading of a gp45 sliding clamp complex onto DNA, thereby incre...

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