酵母 Pif1 解旋酶表现出单碱基对的构象变化机制,用于解开双链 DNA。
Yeast Pif1 helicase exhibits a one-base-pair stepping mechanism for unwinding duplex DNA.
机构信息
Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, Arkansas 72205, USA.
出版信息
J Biol Chem. 2013 May 31;288(22):16185-95. doi: 10.1074/jbc.M113.470013. Epub 2013 Apr 17.
Kinetic analysis of the DNA unwinding and translocation activities of helicases is necessary for characterization of the biochemical mechanism(s) for this class of enzymes. Saccharomyces cerevisiae Pif1 helicase was characterized using presteady state kinetics to determine rates of DNA unwinding, displacement of streptavidin from biotinylated DNA, translocation on single-stranded DNA (ssDNA), and ATP hydrolysis activities. Unwinding of substrates containing varying duplex lengths was fit globally to a model for stepwise unwinding and resulted in an unwinding rate of ∼75 bp/s and a kinetic step size of 1 base pair. Pif1 is capable of displacing streptavidin from biotinylated oligonucleotides with a linear increase in the rates as the length of the oligonucleotides increased. The rate of translocation on ssDNA was determined by measuring dissociation from varying lengths of ssDNA and is essentially the same as the rate of unwinding of dsDNA, making Pif1 an active helicase. The ATPase activity of Pif1 on ssDNA was determined using fluorescently labeled phosphate-binding protein to measure the rate of phosphate release. The quantity of phosphate released corresponds to a chemical efficiency of 0.84 ATP/nucleotides translocated. Hence, when all of the kinetic data are considered, Pif1 appears to move along DNA in single nucleotide or base pair steps, powered by hydrolysis of 1 molecule of ATP.
为了阐明该酶类的生化机制,有必要对解旋酶的 DNA 解旋和易位活性进行动力学分析。利用预稳态动力学,对酿酒酵母 Pif1 解旋酶进行了特征描述,以确定 DNA 解旋、链霉亲和素从生物素化 DNA 上的置换、单链 DNA(ssDNA)上的易位以及 ATP 水解活性的速率。通过逐步解旋的模型对含有不同双链长度的底物进行全局拟合,得到了 75bp/s 的解旋速率和 1 个碱基对的动力学步长。Pif1 能够从生物素化寡核苷酸上置换链霉亲和素,随着寡核苷酸长度的增加,其置换速率呈线性增加。通过测量从不同长度的 ssDNA 上的解离来确定 ssDNA 上的易位速率,其与双链 DNA 的解旋速率基本相同,这使得 Pif1 成为一种活性解旋酶。使用荧光标记的磷酸结合蛋白来测定 ssDNA 上 Pif1 的 ATPase 活性,以测量磷酸盐释放的速率。释放的磷酸盐量对应于化学效率为 0.84 ATP/转移核苷酸。因此,当所有的动力学数据都被考虑在内时,Pif1 似乎以单核苷酸或碱基对的步长沿 DNA 移动,由 1 分子 ATP 的水解提供动力。