A crystallographic study of the role of sequence context in thymine glycol bypass by a replicative DNA polymerase serendipitously sheds light on the exonuclease complex.
A crystallographic study of the role of sequence context in thymine glycol bypass by a replicative DNA polymerase serendipitously sheds light on the exonuclease complex.
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DOI：
10.1016/j.jmb.2011.07.007
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发表时间：
2011-09-09
影响因子：
5.6
通讯作者：
Doublié S
中科院分区：
文献类型：
--
作者：
Aller P;Duclos S;Wallace SS;Doublié S
胸腺嘧啶二醇(Tg)是胸腺嘧啶最常见的氧化产物，被认为是复制DNA聚合酶的强阻断剂。先前已解决的噬菌体RB69 DNA聚合酶(RB69 Gp43)与Tg在5‘-G-Tg-G序列中的复合体的结构揭示了Tg是如何阻止引物延伸的：被氧化的胸腺嘧啶的突出甲基取代了邻近的5’-G，后者不能再作为引物延伸的模板。[Aler，P.，Rould，M.A.，Hogg，M，Wallace，S.S.，&DoubliéS.(2007)PNA104,814-818]几项研究表明，在5‘-C-TG-嘌呤序列上下文中，TG更有可能被A家族DNA聚合酶Klenow片段绕过。我们研究了序列背景对B家族聚合酶中TG旁路的作用，并解决了噬菌体RB69 DNA聚合酶与TG的复合体中含有DNA的晶体结构：N=A、T或C的5‘-N-TG-G。影响TG旁路的多种因素的组合，包括相关的外切酶活性、TG周围3’和5‘碱基的性质以及TG的顺式/反式相互转化。我们还首次可视化了有序的核酸外切酶复合体的结构，使我们能够识别和确认关键残基(Phe123、Met256和Tyr257)在链分离和核酸外切酶位点的引物链稳定中的作用。
Thymine glycol (Tg) is the most common oxidation product of thymine and is known to be a strong block for replicative DNA polymerases. A previously solved structure of the bacteriophage RB69 DNA polymerase (RB69 gp43) in complex with Tg in the sequence context 5’-G-Tg-G shed light on how Tg blocks primer elongation: The protruding methyl group of the oxidized thymine displaces the adjacent 5’-G which can no longer serve as a template for primer elongation. [Aller, P., Rould, M.A., Hogg, M, Wallace, S.S., & Doublié S. (2007) PNAS 104, 814–818] Several studies showed that in the 5’-C-Tg-Purine sequence context Tg is more likely to be bypassed by Klenow fragment, a family A DNA polymerase. We set out to investigate the role of sequence context on Tg bypass in a B family polymerase and solved the crystal structures of the bacteriophage RB69 DNA polymerase in complex with Tg containing DNA in the three remaining sequence contexts: 5’-N-Tg-G with N=A, T, or C. A combination of several factors influence Tg bypass, including the associated exonuclease activity, the nature of the 3’and 5’ bases surrounding Tg and the cis/trans interconversion of Tg. We also visualized for the first time the structure of a well-ordered exonuclease complex, allowing us to identify and confirm the role of key residues (Phe123, Met256, and Tyr257) in strand separation and the stabilization of the primer strand in the exonuclease site.
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影响因子：
4.8
作者：
Elisseeva, E;Mandal, SS;Reha-Krantz, LJ
通讯作者：
Reha-Krantz, LJ
影响因子：
14.9
作者：
CLARK, JM;BEARDSLEY, GP
通讯作者：
BEARDSLEY, GP
DOI：
10.1107/s0907444998003254
发表时间：
1998-09-01
期刊：
ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY
影响因子：
--
作者：
Brunger, AT;Adams, PD;Warren, GL
通讯作者：
Warren, GL
影响因子：
11.4
作者：
BEESE, LS;STEITZ, TA
通讯作者：
STEITZ, TA
影响因子：
2.9
作者：
Aller, Pierre;Ye, Yu;Wallace, Susan S.;Burrows, Cynthia J.;Doublie, Sylvie
通讯作者：
Doublie, Sylvie