• 文献检索
  • 文档翻译
  • 深度研究
  • 学术资讯
  • Suppr Zotero 插件Zotero 插件
  • 邀请有礼
  • 套餐&价格
  • 历史记录
应用&插件
Suppr Zotero 插件Zotero 插件浏览器插件Mac 客户端Windows 客户端微信小程序
定价
高级版会员购买积分包购买API积分包
服务
文献检索文档翻译深度研究API 文档MCP 服务
关于我们
关于 Suppr公司介绍联系我们用户协议隐私条款
关注我们

Suppr 超能文献

核心技术专利:CN118964589B侵权必究
粤ICP备2023148730 号-1Suppr @ 2026

文献检索

告别复杂PubMed语法,用中文像聊天一样搜索,搜遍4000万医学文献。AI智能推荐,让科研检索更轻松。

立即免费搜索

文件翻译

保留排版,准确专业,支持PDF/Word/PPT等文件格式,支持 12+语言互译。

免费翻译文档

深度研究

AI帮你快速写综述,25分钟生成高质量综述,智能提取关键信息,辅助科研写作。

立即免费体验

从结构-功能分析到DNA连接酶实际应用的蛋白质工程

From Structure-Function Analyses to Protein Engineering for Practical Applications of DNA Ligase.

作者信息

Tanabe Maiko, Ishino Yoshizumi, Nishida Hirokazu

机构信息

Central Research Laboratory, Hitachi Ltd., 1-280 Higashi-koigakubo, Kokubunji, Tokyo 185-8601, Japan.

Department of Bioscience and Biotechnology, Graduate School of Bioresource and Bioenvironmental Sciences, Faculty of Agriculture, Kyushu University, 6-10-1 Hakozaki, Higashi-ku, Fukuoka-shi, Fukuoka 812-8581, Japan.

出版信息

Archaea. 2015 Oct 5;2015:267570. doi: 10.1155/2015/267570. eCollection 2015.

DOI:10.1155/2015/267570
PMID:26508902
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC4609770/
Abstract

DNA ligases are indispensable in all living cells and ubiquitous in all organs. DNA ligases are broadly utilized in molecular biology research fields, such as genetic engineering and DNA sequencing technologies. Here we review the utilization of DNA ligases in a variety of in vitro gene manipulations, developed over the past several decades. During this period, fewer protein engineering attempts for DNA ligases have been made, as compared to those for DNA polymerases. We summarize the recent progress in the elucidation of the DNA ligation mechanisms obtained from the tertiary structures solved thus far, in each step of the ligation reaction scheme. We also present some examples of engineered DNA ligases, developed from the viewpoint of their three-dimensional structures.

摘要

DNA连接酶在所有活细胞中都是不可或缺的,并且在所有器官中都普遍存在。DNA连接酶广泛应用于分子生物学研究领域,如基因工程和DNA测序技术。在此,我们回顾了过去几十年来开发的DNA连接酶在各种体外基因操作中的应用。在此期间,与DNA聚合酶相比,对DNA连接酶进行蛋白质工程改造的尝试较少。我们总结了迄今为止从已解析的三级结构中获得的DNA连接机制在连接反应方案的每个步骤中的最新进展。我们还从三维结构的角度展示了一些工程化DNA连接酶的实例。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/782f/4609770/1f265a7f0091/ARCHAEA2015-267570.014.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/782f/4609770/ff0706392f54/ARCHAEA2015-267570.001.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/782f/4609770/ba947cf7b703/ARCHAEA2015-267570.002.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/782f/4609770/2dcbe4a571cc/ARCHAEA2015-267570.003.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/782f/4609770/1d1a4351925a/ARCHAEA2015-267570.004.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/782f/4609770/e061d88fe214/ARCHAEA2015-267570.005.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/782f/4609770/d1a05da3ef6a/ARCHAEA2015-267570.006.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/782f/4609770/19a1fba92a32/ARCHAEA2015-267570.007.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/782f/4609770/1f252e2d936d/ARCHAEA2015-267570.008.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/782f/4609770/00f5e4299017/ARCHAEA2015-267570.009.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/782f/4609770/bfa9d7da8559/ARCHAEA2015-267570.010.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/782f/4609770/e743a9b22699/ARCHAEA2015-267570.011.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/782f/4609770/7a2d6dc675c3/ARCHAEA2015-267570.012.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/782f/4609770/14cf082f2d5d/ARCHAEA2015-267570.013.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/782f/4609770/1f265a7f0091/ARCHAEA2015-267570.014.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/782f/4609770/ff0706392f54/ARCHAEA2015-267570.001.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/782f/4609770/ba947cf7b703/ARCHAEA2015-267570.002.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/782f/4609770/2dcbe4a571cc/ARCHAEA2015-267570.003.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/782f/4609770/1d1a4351925a/ARCHAEA2015-267570.004.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/782f/4609770/e061d88fe214/ARCHAEA2015-267570.005.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/782f/4609770/d1a05da3ef6a/ARCHAEA2015-267570.006.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/782f/4609770/19a1fba92a32/ARCHAEA2015-267570.007.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/782f/4609770/1f252e2d936d/ARCHAEA2015-267570.008.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/782f/4609770/00f5e4299017/ARCHAEA2015-267570.009.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/782f/4609770/bfa9d7da8559/ARCHAEA2015-267570.010.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/782f/4609770/e743a9b22699/ARCHAEA2015-267570.011.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/782f/4609770/7a2d6dc675c3/ARCHAEA2015-267570.012.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/782f/4609770/14cf082f2d5d/ARCHAEA2015-267570.013.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/782f/4609770/1f265a7f0091/ARCHAEA2015-267570.014.jpg

相似文献

1
From Structure-Function Analyses to Protein Engineering for Practical Applications of DNA Ligase.从结构-功能分析到DNA连接酶实际应用的蛋白质工程
Archaea. 2015 Oct 5;2015:267570. doi: 10.1155/2015/267570. eCollection 2015.
2
Archaeal Nucleic Acid Ligases and Their Potential in Biotechnology.古菌核酸连接酶及其在生物技术中的潜力。
Archaea. 2015 Oct 1;2015:170571. doi: 10.1155/2015/170571. eCollection 2015.
3
Activity-based in vitro selection of T4 DNA ligase.基于活性的T4 DNA连接酶体外筛选
Biochem Biophys Res Commun. 2005 Oct 28;336(3):987-93. doi: 10.1016/j.bbrc.2005.08.200.
4
Structure-based mutational study of an archaeal DNA ligase towards improvement of ligation activity.基于结构的古菌 DNA 连接酶突变研究以提高连接活性。
Chembiochem. 2012 Nov 26;13(17):2575-82. doi: 10.1002/cbic.201200336. Epub 2012 Nov 6.
5
DNA and RNA ligases: structural variations and shared mechanisms.DNA和RNA连接酶:结构变异与共同机制
Curr Opin Struct Biol. 2008 Feb;18(1):96-105. doi: 10.1016/j.sbi.2007.12.008. Epub 2008 Feb 8.
6
Engineered DNA ligases with improved activities in vitro.体外活性得到改善的工程化 DNA 连接酶。
Protein Eng Des Sel. 2013 Jul;26(7):471-8. doi: 10.1093/protein/gzt024. Epub 2013 Jun 10.
7
In vitro evolution and characterization of a ligase ribozyme adapted to acidic conditions: effect of further rounds of evolution.适应酸性条件的连接酶核酶的体外进化与特性研究:进一步进化轮次的影响
Biotechnol Bioeng. 2005 Apr 5;90(1):36-45. doi: 10.1002/bit.20360.
8
Novel DNA ligase with broad nucleotide cofactor specificity from the hyperthermophilic crenarchaeon Sulfophobococcus zilligii: influence of ancestral DNA ligase on cofactor utilization.来自嗜热泉古菌硫化嗜热球菌的具有广泛核苷酸辅因子特异性的新型DNA连接酶:祖先DNA连接酶对辅因子利用的影响
Environ Microbiol. 2008 Dec;10(12):3212-24. doi: 10.1111/j.1462-2920.2008.01710.x. Epub 2008 Jul 16.
9
Mutations of Asp540 and the domain-connecting residues synergistically enhance Pyrococcus furiosus DNA ligase activity.Asp540 突变和结构域连接残基协同增强 Pyrococcus furiosus DNA 连接酶活性。
FEBS Lett. 2014 Jan 21;588(2):230-5. doi: 10.1016/j.febslet.2013.10.037. Epub 2013 Nov 5.
10
Effects of deletion and site-directed mutations on ligation steps of NAD+-dependent DNA ligase: a biochemical analysis of BRCA1 C-terminal domain.缺失和定点突变对NAD+依赖性DNA连接酶连接步骤的影响:BRCA1 C末端结构域的生化分析
Biochemistry. 2004 Oct 5;43(39):12648-59. doi: 10.1021/bi049451c.

引用本文的文献

1
Structural insight into DNA joining: from conserved mechanisms to diverse scaffolds.DNA 连接的结构见解:从保守机制到多样的支架。
Nucleic Acids Res. 2020 Sep 4;48(15):8225-8242. doi: 10.1093/nar/gkaa307.
2
(ADP-ribosyl)hydrolases: structure, function, and biology.(ADP-核糖基)水解酶:结构、功能和生物学。
Genes Dev. 2020 Mar 1;34(5-6):263-284. doi: 10.1101/gad.334631.119. Epub 2020 Feb 6.
3
Rational design of an XNA ligase through docking of unbound nucleic acids to toroidal proteins.通过将未结合的核酸对接至环形蛋白质实现 XNA 连接酶的合理设计。

本文引用的文献

1
Mutations of Asp540 and the domain-connecting residues synergistically enhance Pyrococcus furiosus DNA ligase activity.Asp540 突变和结构域连接残基协同增强 Pyrococcus furiosus DNA 连接酶活性。
FEBS Lett. 2014 Jan 21;588(2):230-5. doi: 10.1016/j.febslet.2013.10.037. Epub 2013 Nov 5.
2
Engineered DNA ligases with improved activities in vitro.体外活性得到改善的工程化 DNA 连接酶。
Protein Eng Des Sel. 2013 Jul;26(7):471-8. doi: 10.1093/protein/gzt024. Epub 2013 Jun 10.
3
ATP-dependent DNA ligase from Thermococcus sp. 1519 displays a new arrangement of the OB-fold domain.
Nucleic Acids Res. 2019 Jul 26;47(13):7130-7142. doi: 10.1093/nar/gkz551.
4
Structural intermediates of a DNA-ligase complex illuminate the role of the catalytic metal ion and mechanism of phosphodiester bond formation.DNA 连接酶复合物的结构中间体阐明了催化金属离子的作用和磷酸二酯键形成的机制。
Nucleic Acids Res. 2019 Aug 22;47(14):7147-7162. doi: 10.1093/nar/gkz596.
5
Temperature adaptation of DNA ligases from psychrophilic organisms.嗜冷生物DNA连接酶的温度适应性
Extremophiles. 2019 May;23(3):305-317. doi: 10.1007/s00792-019-01082-y. Epub 2019 Mar 2.
6
Biochemical and Structural Characterisation of DNA Ligases from Bacteria and Archaea.细菌和古菌DNA连接酶的生化与结构表征
Biosci Rep. 2016 Oct 6;36(5):00391. doi: 10.1042/BSR20160003.
嗜热栖热菌1519株的ATP依赖性DNA连接酶展示了OB折叠结构域的一种新排列。
Acta Crystallogr Sect F Struct Biol Cryst Commun. 2012 Dec 1;68(Pt 12):1440-7. doi: 10.1107/S1744309112043394. Epub 2012 Nov 14.
4
Structure-based mutational study of an archaeal DNA ligase towards improvement of ligation activity.基于结构的古菌 DNA 连接酶突变研究以提高连接活性。
Chembiochem. 2012 Nov 26;13(17):2575-82. doi: 10.1002/cbic.201200336. Epub 2012 Nov 6.
5
Kinetic analysis of DNA strand joining by Chlorella virus DNA ligase and the role of nucleotidyltransferase motif VI in ligase adenylylation.绿藻病毒 DNA 连接酶催化 DNA 链连接的动力学分析及核苷酸转移酶基序 VI 在连接酶腺苷酰化中的作用。
J Biol Chem. 2012 Aug 17;287(34):28609-18. doi: 10.1074/jbc.M112.380428. Epub 2012 Jun 28.
6
DNA ligases.DNA连接酶
Curr Protoc Mol Biol. 2011 Apr;Chapter 3:Unit3.14. doi: 10.1002/0471142727.mb0314s94.
7
Rolling Circle DNA Synthesis: Small Circular Oligonucleotides as Efficient Templates for DNA Polymerases.滚环DNA合成:小环状寡核苷酸作为DNA聚合酶的高效模板
J Am Chem Soc. 1996 Feb 21;118(7):1587-1594. doi: 10.1021/ja952786k.
8
ATP-dependent DNA ligase from Archaeoglobus fulgidus displays a tightly closed conformation.来自嗜热栖热菌的ATP依赖性DNA连接酶呈现出紧密闭合的构象。
Acta Crystallogr Sect F Struct Biol Cryst Commun. 2009 Jun 1;65(Pt 6):544-50. doi: 10.1107/S1744309109017485. Epub 2009 May 22.
9
DNA ligases: progress and prospects.DNA连接酶:进展与展望
J Biol Chem. 2009 Jun 26;284(26):17365-9. doi: 10.1074/jbc.R900017200. Epub 2009 Mar 27.
10
Next-generation DNA sequencing.下一代DNA测序
Nat Biotechnol. 2008 Oct;26(10):1135-45. doi: 10.1038/nbt1486.