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Title: Structures of human ADAR2 bound to dsRNA reveal base-flipping mechanism and basis for site selectivity

Abstract

Adenosine deaminases acting on RNA (ADARs) are editing enzymes that convert adenosine to inosine in duplex RNA, a modification reaction with wide-ranging consequences in RNA function. Understanding of the ADAR reaction mechanism, the origin of editing-site selectivity, and the effect of mutations is limited by the lack of high-resolution structural data for complexes of ADARs bound to substrate RNAs. In this paper, we describe four crystal structures of the human ADAR2 deaminase domain bound to RNA duplexes bearing a mimic of the deamination reaction intermediate. These structures, together with structure-guided mutagenesis and RNA-modification experiments, explain the basis of the ADAR deaminase domain's dsRNA specificity, its base-flipping mechanism, and its nearest-neighbor preferences. In addition, we identified an ADAR2-specific RNA-binding loop near the enzyme active site, thus rationalizing differences in selectivity observed between different ADARs. In conclusion, our results provide a structural framework for understanding the effects of ADAR mutations associated with human disease.

Authors:
 [1];  [1];  [1];  [1];  [1];  [2];  [1];  [3];  [1]
  1. Univ. of California, Davis, CA (United States). Dept. of Chemistry
  2. Univ. of California, Davis, CA (United States). Dept. of Molecular and Cellular Biology
  3. Univ. of California, Davis, CA (United States). Dept. of Chemistry. Dept. of Molecular and Cellular Biology
Publication Date:
Research Org.:
Univ. of California, Davis, CA (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Basic Energy Sciences (BES) (SC-22); USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23); National Inst. of Health (NIH) (United States)
OSTI Identifier:
1255288
Grant/Contract Number:  
AC02-06CH11357; AC02-76SF00515; R01GM061115; T32 GM007377; P41GM103393; P41 GM103403; S10 RR029205
Resource Type:
Accepted Manuscript
Journal Name:
Nature Structural & Molecular Biology
Additional Journal Information:
Journal Volume: 23; Journal Issue: 5; Journal ID: ISSN 1545-9993
Publisher:
Nature Publishing Group
Country of Publication:
United States
Language:
ENGLISH
Subject:
59 BASIC BIOLOGICAL SCIENCES; RNA; X-ray crystallography

Citation Formats

Matthews, Melissa M., Thomas, Justin M., Zheng, Yuxuan, Tran, Kiet, Phelps, Kelly J., Scott, Anna I., Havel, Jocelyn, Fisher, Andrew J., and Beal, Peter A. Structures of human ADAR2 bound to dsRNA reveal base-flipping mechanism and basis for site selectivity. United States: N. p., 2016. Web. doi:10.1038/nsmb.3203.
Matthews, Melissa M., Thomas, Justin M., Zheng, Yuxuan, Tran, Kiet, Phelps, Kelly J., Scott, Anna I., Havel, Jocelyn, Fisher, Andrew J., & Beal, Peter A. Structures of human ADAR2 bound to dsRNA reveal base-flipping mechanism and basis for site selectivity. United States. doi:10.1038/nsmb.3203.
Matthews, Melissa M., Thomas, Justin M., Zheng, Yuxuan, Tran, Kiet, Phelps, Kelly J., Scott, Anna I., Havel, Jocelyn, Fisher, Andrew J., and Beal, Peter A. Mon . "Structures of human ADAR2 bound to dsRNA reveal base-flipping mechanism and basis for site selectivity". United States. doi:10.1038/nsmb.3203. https://www.osti.gov/servlets/purl/1255288.
@article{osti_1255288,
title = {Structures of human ADAR2 bound to dsRNA reveal base-flipping mechanism and basis for site selectivity},
author = {Matthews, Melissa M. and Thomas, Justin M. and Zheng, Yuxuan and Tran, Kiet and Phelps, Kelly J. and Scott, Anna I. and Havel, Jocelyn and Fisher, Andrew J. and Beal, Peter A.},
abstractNote = {Adenosine deaminases acting on RNA (ADARs) are editing enzymes that convert adenosine to inosine in duplex RNA, a modification reaction with wide-ranging consequences in RNA function. Understanding of the ADAR reaction mechanism, the origin of editing-site selectivity, and the effect of mutations is limited by the lack of high-resolution structural data for complexes of ADARs bound to substrate RNAs. In this paper, we describe four crystal structures of the human ADAR2 deaminase domain bound to RNA duplexes bearing a mimic of the deamination reaction intermediate. These structures, together with structure-guided mutagenesis and RNA-modification experiments, explain the basis of the ADAR deaminase domain's dsRNA specificity, its base-flipping mechanism, and its nearest-neighbor preferences. In addition, we identified an ADAR2-specific RNA-binding loop near the enzyme active site, thus rationalizing differences in selectivity observed between different ADARs. In conclusion, our results provide a structural framework for understanding the effects of ADAR mutations associated with human disease.},
doi = {10.1038/nsmb.3203},
journal = {Nature Structural & Molecular Biology},
number = 5,
volume = 23,
place = {United States},
year = {2016},
month = {4}
}

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    Works referencing / citing this record:

    All I's on the RADAR: role of ADAR in gene regulation
    journal, May 2018


    The emerging and uncultivated potential of CRISPR technology in plant science
    journal, July 2019


    All I's on the RADAR: role of ADAR in gene regulation
    journal, May 2018


    The emerging and uncultivated potential of CRISPR technology in plant science
    journal, July 2019