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本文引用的文献

1
Unusual target site disruption by the rare-cutting HNH restriction endonuclease PacI.罕见切割的 HNH 限制内切酶 PacI 的非寻常靶位断裂。
Structure. 2010 Jun 9;18(6):734-43. doi: 10.1016/j.str.2010.03.009.
2
Structure of bacteriophage T4 endonuclease II mutant E118A, a tetrameric GIY-YIG enzyme.T4 噬菌体内切酶 II 突变体 E118A 的结构，一种四聚体 GIY-YIG 酶。
J Mol Biol. 2010 Apr 9;397(4):1003-16. doi: 10.1016/j.jmb.2010.01.076. Epub 2010 Feb 13.
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Phaser crystallographic software.相位结晶学软件。
J Appl Crystallogr. 2007 Aug 1;40(Pt 4):658-674. doi: 10.1107/S0021889807021206. Epub 2007 Jul 13.
4
Oligomeric structure diversity within the GIY-YIG nuclease family.GIY-YIG核酸酶家族内的寡聚体结构多样性。
J Mol Biol. 2009 Mar 20;387(1):10-6. doi: 10.1016/j.jmb.2009.01.048. Epub 2009 Jan 30.
5
Structural and evolutionary classification of Type II restriction enzymes based on theoretical and experimental analyses.基于理论与实验分析的II型限制酶的结构与进化分类
Nucleic Acids Res. 2008 Jun;36(11):3552-69. doi: 10.1093/nar/gkn175. Epub 2008 May 2.
6
Structures of the rare-cutting restriction endonuclease NotI reveal a unique metal binding fold involved in DNA binding.稀有切割限制内切酶NotI的结构揭示了一种参与DNA结合的独特金属结合结构域。
Structure. 2008 Apr;16(4):558-69. doi: 10.1016/j.str.2008.01.017.
7
Tetrameric restriction enzymes: expansion to the GIY-YIG nuclease family.四聚体限制酶：向GIY-YIG核酸酶家族的扩展。
Nucleic Acids Res. 2008 Feb;36(3):938-49. doi: 10.1093/nar/gkm1090. Epub 2007 Dec 17.
8
Inference of macromolecular assemblies from crystalline state.从晶体状态推断大分子组装体
J Mol Biol. 2007 Sep 21;372(3):774-97. doi: 10.1016/j.jmb.2007.05.022. Epub 2007 May 13.
9
Type II restriction endonuclease R.Eco29kI is a member of the GIY-YIG nuclease superfamily.II型限制性核酸内切酶R.Eco29kI是GIY-YIG核酸酶超家族的成员。
BMC Struct Biol. 2007 Jul 12;7:48. doi: 10.1186/1472-6807-7-48.
10
Mutability of an HNH nuclease imidazole general base and exchange of a deprotonation mechanism.HNH核酸酶咪唑通用碱基的可变性及去质子化机制的交换
Biochemistry. 2007 Jun 19;46(24):7215-25. doi: 10.1021/bi700418d. Epub 2007 May 22.

GIY-YIG 内切酶的折叠、DNA 识别和功能：R.Eco29kI 的晶体结构。

Folding, DNA recognition, and function of GIY-YIG endonucleases: crystal structures of R.Eco29kI.

机构信息

Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA.

出版信息

Structure. 2010 Oct 13;18(10):1321-31. doi: 10.1016/j.str.2010.07.006. Epub 2010 Aug 26.

DOI:10.1016/j.str.2010.07.006
PMID:20800503
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC2955809/
Abstract

The GIY-YIG endonuclease family comprises hundreds of diverse proteins and a multitude of functions; none have been visualized bound to DNA. The structure of the GIY-YIG restriction endonuclease R.Eco29kI has been solved both alone and bound to its target site. The protein displays a domain-swapped homodimeric structure with several extended surface loops encircling the DNA. Only three side chains from each protein subunit contact DNA bases, two directly and one via a bridging solvent molecule. Both tyrosine residues within the GIY-YIG motif are positioned in the catalytic center near a putative nucleophilic water; the remainder of the active site resembles the HNH endonuclease family. The structure illustrates how the GIY-YIG scaffold has been adapted for the highly specific recognition of a DNA restriction site, in contrast to nonspecific DNA cleavage by GIY-YIG domains in homing endonucleases or structure-specific cleavage by DNA repair enzymes such as UvrC.

摘要

GIY-YIG 内切酶家族包含数百种不同的蛋白质和多种功能；目前还没有观察到它们与 DNA 结合。GIY-YIG 限制性内切酶 R.Eco29kI 的结构已被单独解决并结合到其靶位点。该蛋白质显示出一种具有交换结构域的同源二聚体结构，几个延伸的表面环环绕 DNA。每个蛋白质亚基只有三个侧链与 DNA 碱基接触，两个直接接触，一个通过桥接溶剂分子接触。GIY-YIG 基序中的两个酪氨酸残基位于催化中心附近的假定亲核水分子附近；活性位点的其余部分类似于 HNH 内切酶家族。该结构说明了 GIY-YIG 支架如何适应高度特异性识别 DNA 限制位点，与同系物内切酶中的 GIY-YIG 结构域的非特异性 DNA 切割或 UvrC 等 DNA 修复酶的结构特异性切割形成对比。