Structural basis for substrate discrimination by <em>E.?coli</em> repair enzyme, AlkB

Namrata Jayanth; Nirmala Ogirala; Anil Yadav; Mrinalini Puranik

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Structural basis for substrate discrimination by E.?coli repair enzyme, AlkB

机译：大肠杆菌修复酶AlkB识别底物的结构基础

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E. coli AlkB, a repair enzyme of the dioxygenase family, catalyses the removal of mutagenic methylated nucleotides from the genome. Known for substrate promiscuity, AlkB's catalytic mechanism and conformational changes accompanying substrate binding have been extensively dissected. However, the structural parameters of various substrates governing their recognition by AlkB still remain elusive. In this work, through solution-state vibrational spectra of methylated substrates bound to AlkB in combination with computational analysis, we show that the recognition specificity is dictated by the protonation states of the substrates. Specificity is conferred predominantly through hydrogen bonding and cation–π interactions. Furthermore, we report on the interaction of AlkB with normal, unmodified nucleotides, wherein the presence of an exocyclic amino group serves as an essential criterion for the initial process of substrate recognition. Taken together, these results provide a rationale for structural determinants of substrate specificity as well as mode of lesion discrimination employed by AlkB.

机译： E。大肠杆菌AlkB是双加氧酶家族的一种修复酶，可催化从基因组中去除诱变的甲基化核苷酸。以底物混杂为人所知，AlkB的催化机制和伴随底物结合的构象变化已被广泛研究。但是，控制AlkB识别各种底物的结构参数仍然难以捉摸。在这项工作中，通过结合到AlkB的甲基化底物的溶液状态振动光谱结合计算分析，我们表明识别特异性是由底物的质子化状态决定的。特异性主要通过氢键和阳离子-π相互作用赋予。此外，我们报告了AlkB与正常的未修饰核苷酸的相互作用，其中环外氨基的存在作为底物识别的初始过程的必要标准。综上所述，这些结果为底物特异性的结构决定因素以及AlkB所采用的病变识别模式提供了理论依据。 展开▼

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《RSC Advances》 |2018年第3期|共11页

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Namrata Jayanth; Nirmala Ogirala; Anil Yadav; Mrinalini Puranik;
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1. Structural basis for substrate discrimination by E. coli repair enzyme, AlkB [J] . Jayanth Namrata, Ogirala Nirmala, Yadav Anil, RSC Advances . 2018,第3期

机译：大肠杆菌修复酶，ALKB的基材鉴别的结构基础

2. Enzymological and structural studies of the mechanism of promiscuous substrate recognition by the oxidative DNA repair enzyme AlkB [J] . Bomina Yu, John F. Hunt Proceedings of the National Academy of Sciences of the United States of America . 2009,第34期

机译：酶学和结构研究的氧化DNA修复酶AlkB混杂底物识别的机制。

3. Evaluation of the Pathogen Detect~® System and Anthracene-Based Enzyme Substrates for the Detection and Differentiation of E. coli and Total Coliforms in Water Samples [J] . Neville Hewage, Mazen Saleh Journal of water resource and protection . 2015,第9期

机译：评估病原体Detect〜®系统和基于蒽的酶底物，用于检测和区分水样中的大肠杆菌和总大肠菌群

4. Structural basis of the Escherichi coli outer-membrane permeability [C] . Nabil A. Amro, Wayne State Univ., Detroit, Conference on scanning and force microscopies for biomedical applications . 1999

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5. Probing the mechanisms of the AlkB family DNA/RNA repair enzymes with a chemical cross-linking approach. [D] . Yi, Chengqi. 2010

机译：用化学交联方法探索AlkB家族DNA / RNA修复酶的机制。

6. Enzymological and structural studies of the mechanism of promiscuous substrate recognition by the oxidative DNA repair enzyme AlkB [O] . Bomina Yu, John F. Hunt 2009

机译：酶学和结构研究的氧化DNA修复酶AlkB混杂底物识别的机制。

7. Enzymological and structural studies of the mechanism of promiscuous substrate recognition by the oxidative DNA repair enzyme AlkB [O] . Yu, Bomina, Hunt, John F. 2009

机译：酶学和结构研究的氧化DNA修复酶AlkB混杂底物识别的机制。

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3. Membrane filter agar medium containing two enzyme substrates used for the simultaneous detection of total coliforms and E. coli. [P] . 外国专利： US6063590A . 2000-05-16

机译：含有两种酶底物的膜滤琼脂培养基，用于同时检测大肠菌群和大肠杆菌。

4. SYSTEM FOR EXCRETION OF FOREIGN PROTEIN,ENZYMES OR POLYPEPTIDES FROM E. COLI INTO THE CULTURE MEDIA,ESPECIALLY FOR THE PRODUCTION AND PURIFICATION OF THE ENZYME CHITINASE [P] . 外国专利： IL85408D0 . 1988-07-31

机译：从大肠杆菌中提取外源蛋白质，酶或多肽到培养培养基中的系统，特别是用于酶几丁质酶的生产和纯化

5. regulierbares eukaryotisches host vector system on the basis of the ci expts - repressorsystems of e. coli phagen lambda, its production and use method [P] . 外国专利： DD296701A5 . 1991-12-12

机译：基于ci的regulierbares真核生物宿主系统。噬菌体λ及其生产和使用方法

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Structural basis for substrate discrimination by E.?coli repair enzyme, AlkB

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