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证据表明,在病毒 DNA 包装马达中,一个催化谷氨酸和一个“精氨酸切换”协同作用,介导 ATP 水解和机械化学偶联。

Evidence that a catalytic glutamate and an 'Arginine Toggle' act in concert to mediate ATP hydrolysis and mechanochemical coupling in a viral DNA packaging motor.

机构信息

Department of Medicinal Chemistry, University of Washington, Seattle, WA 98195, USA.

Department of Physics, University of California, San Diego, La Jolla, CA 92093, USA.

出版信息

Nucleic Acids Res. 2019 Feb 20;47(3):1404-1415. doi: 10.1093/nar/gky1217.

Abstract

ASCE ATPases include ring-translocases such as cellular helicases and viral DNA packaging motors (terminases). These motors have conserved Walker A and B motifs that bind Mg2+-ATP and a catalytic carboxylate that activates water for hydrolysis. Here we demonstrate that Glu179 serves as the catalytic carboxylate in bacteriophage λ terminase and probe its mechanistic role. All changes of Glu179 are lethal: non-conservative changes abrogate ATP hydrolysis and DNA translocation, while the conservative E179D change attenuates ATP hydrolysis and alters single molecule translocation dynamics, consistent with a slowed chemical hydrolysis step. Molecular dynamics simulations of several homologous terminases suggest a novel mechanism, supported by experiments, wherein the conserved Walker A arginine 'toggles' between interacting with a glutamate residue in the 'lid' subdomain and the catalytic glutamate upon ATP binding; this switch helps mediate a transition from an 'open' state to a 'closed' state that tightly binds nucleotide and DNA, and also positions the catalytic glutamate next to the γ-phosphate to align the hydrolysis transition state. Concomitant reorientation of the lid subdomain may mediate mechanochemical coupling of ATP hydrolysis and DNA translocation. Given the strong conservation of these structural elements in terminase enzymes, this mechanism may be universal for viral packaging motors.

摘要

ASCE ATPases 包括环移位酶,如细胞解旋酶和病毒 DNA 包装马达(末端酶)。这些马达具有保守的 Walker A 和 B 基序,可结合 Mg2+-ATP,并具有激活水进行水解的催化羧酸基。在这里,我们证明 Glu179 是噬菌体 λ末端酶的催化羧酸基,并探讨其机械作用。G179 的所有变化都是致命的:非保守变化会使 ATP 水解和 DNA 易位失活,而保守的 E179D 变化则会减弱 ATP 水解并改变单分子易位动力学,与化学水解步骤减慢一致。几种同源末端酶的分子动力学模拟提出了一种新的机制,实验结果支持了这一机制,即保守的 Walker A 精氨酸在与“盖子”亚基中的谷氨酸残基相互作用和与 ATP 结合时与催化谷氨酸相互作用之间“切换”;这种开关有助于介导从“开放”状态到紧密结合核苷酸和 DNA 的“封闭”状态的转变,并且还将催化谷氨酸定位在γ-磷酸的旁边,以对准水解过渡态。盖子亚基的伴随重新定向可能介导 ATP 水解和 DNA 易位的机械化学偶联。鉴于末端酶中这些结构元件的强保守性,这种机制可能对病毒包装马达普遍适用。

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