与过渡态类似物结合的锤头状核酶晶体结构中的两个活性位点二价离子。
Two Active Site Divalent Ions in the Crystal Structure of the Hammerhead Ribozyme Bound to a Transition State Analogue.
作者信息
Mir Aamir, Golden Barbara L
机构信息
Department of Biochemistry, Purdue University , West Lafayette, Indiana 47907, United States.
出版信息
Biochemistry. 2016 Feb 2;55(4):633-6. doi: 10.1021/acs.biochem.5b01139. Epub 2016 Jan 19.
Abstract
The crystal structure of the hammerhead ribozyme bound to the pentavalent transition state analogue vanadate reveals significant rearrangements relative to the previously determined structures. The active site contracts, bringing G10.1 closer to the cleavage site and repositioning a divalent metal ion such that it could, ultimately, interact directly with the scissile phosphate. This ion could also position a water molecule to serve as a general acid in the cleavage reaction. A second divalent ion is observed coordinated to O6 of G12. This metal ion is well-placed to help tune the pKA of G12. On the basis of this crystal structure as well as a wealth of biochemical studies, we propose a mechanism in which G12 serves as the general base and a magnesium-bound water serves as a general acid.
摘要
与五价过渡态类似物钒酸盐结合的锤头状核酶的晶体结构显示，相对于先前确定的结构有显著的重排。活性位点收缩，使G10.1更靠近切割位点，并重新定位二价金属离子，使其最终能够直接与可切割的磷酸基团相互作用。该离子还可以定位一个水分子，使其在切割反应中作为广义酸。观察到第二个二价离子与G12的O6配位。该金属离子位置合适，有助于调节G12的pKA。基于此晶体结构以及大量的生化研究，我们提出了一种机制，其中G12作为广义碱，与镁结合的水作为广义酸。
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