I类内含子自我剪接过程中金属离子与共底物的相互作用
Metal ion interaction with cosubstrate in self-splicing of group I introns.
作者信息
Sjögren A S, Pettersson E, Sjöberg B M, Strömberg R
机构信息
Department of Molecular Biology, Arrhenius Laboratory, Stockholm University, S-10691 Stockholm, Sweden.
出版信息
Nucleic Acids Res. 1997 Feb 1;25(3):648-53. doi: 10.1093/nar/25.3.648.
Abstract
The catalytic mechanism for self-splicing of the group I intron in the pre-mRNA from the nrdB gene in bacteriophage T4 has been investigated using 2'-amino- 2'-deoxyguanosine or guanosine as cosubstrates in the presence of Mg2+, Mn2+and Zn2+. The results show that a divalent metal ion interacts with the cosubstrate and thereby influences the efficiency of catalysis in the first step of splicing. This suggests the existence of a metal ion that catalyses the nucleophilic attack of the cosubstrate. Of particular significance is that the transesterification reactions of the first step of splicing with 2'-amino-2'-deoxyguanosine as cosubstrate are more efficient in mixtures containing either Mn2+or Zn2+together with Mg2+than with only magnesium ions present. The experiments in metal ion mixtures show that two (or more) metal ions are crucial for the self-splicing of group I introns and suggest the possibility that more than one of these have a direct catalytic role. A working model for a two-metal-ion mechanism in the transesterification steps is suggested.
摘要
利用2'-氨基-2'-脱氧鸟苷或鸟苷作为共底物，在Mg2+、Mn2+和Zn2+存在的条件下，研究了噬菌体T4的nrdB基因前体mRNA中I组内含子的自我剪接催化机制。结果表明，二价金属离子与共底物相互作用，从而影响剪接第一步的催化效率。这表明存在一种催化共底物亲核攻击的金属离子。特别重要的是，以2'-氨基-2'-脱氧鸟苷作为共底物时，剪接第一步的酯交换反应在含有Mn2+或Zn2+以及Mg2+的混合物中比仅存在镁离子时更有效。金属离子混合物实验表明，两种（或更多）金属离子对I组内含子的自我剪接至关重要，并暗示其中不止一种可能具有直接催化作用。提出了酯交换步骤中双金属离子机制的工作模型。
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本文引用的文献
1
The environment of two metal ions surrounding the splice site of a group I intron.位于I组内含子剪接位点周围的两个金属离子的环境。
EMBO J. 1996 May 15;15(10):2556-64.
2
Binding of guanosine and 3' splice site analogues to a group I ribozyme: interactions with functional groups of guanosine and with additional nucleotides.鸟苷和3'剪接位点类似物与I型核酶的结合：与鸟苷官能团及其他核苷酸的相互作用
Biochemistry. 1993 May 18;32(19):5247-56. doi: 10.1021/bi00070a037.
3
How many catalytic RNAs? Ions and the Cheshire cat conjecture.有多少种催化性RNA？离子与柴郡猫猜想。
FASEB J. 1993 Jan;7(1):31-9. doi: 10.1096/fasebj.7.1.8422972.
4
Theoretical analyses on the role of Mg2+ ions in ribozyme reactions.镁离子在核酶反应中作用的理论分析。
FASEB J. 1993 Jan;7(1):137-42. doi: 10.1096/fasebj.7.1.8422960.
5
Metal ion catalysis in the Tetrahymena ribozyme reaction.嗜热四膜虫核酶反应中的金属离子催化作用。
Nature. 1993 Jan 7;361(6407):85-8. doi: 10.1038/361085a0.
6
Modeling study on the cleavage step of the self-splicing reaction in group I introns.I组内含子自我剪接反应切割步骤的建模研究
J Biomol Struct Dyn. 1993 Jun;10(6):945-72. doi: 10.1080/07391102.1993.10508689.
7
A general two-metal-ion mechanism for catalytic RNA.催化性RNA的一般双金属离子机制。
Proc Natl Acad Sci U S A. 1993 Jul 15;90(14):6498-502. doi: 10.1073/pnas.90.14.6498.
8
Comparison of pH dependencies of the Tetrahymena ribozyme reactions with RNA 2'-substituted and phosphorothioate substrates reveals a rate-limiting conformational step.嗜热四膜虫核酶与RNA 2'-取代底物及硫代磷酸酯底物反应的pH依赖性比较揭示了一个限速构象步骤。
Biochemistry. 1994 May 3;33(17):5291-7. doi: 10.1021/bi00183a036.
9
The importance of being ribose at the cleavage site in the Tetrahymena ribozyme reaction.在四膜虫核酶反应中切割位点处为核糖的重要性。
Biochemistry. 1993 Aug 17;32(32):8312-21. doi: 10.1021/bi00083a035.
10
Metal coordination sites that contribute to structure and catalysis in the group I intron from Tetrahymena.对嗜热四膜虫I组内含子的结构和催化作用有贡献的金属配位位点。
Biochemistry. 1993 May 4;32(17):4475-80. doi: 10.1021/bi00068a001.
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