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:
-
- Univ. of California, Davis, CA (United States). Dept. of Chemistry
- Univ. of California, Davis, CA (United States). Dept. of Molecular and Cellular Biology
- 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); USDOE Office of Science (SC), Biological and Environmental Research (BER); 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. https://doi.org/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. https://doi.org/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 = {Mon Apr 11 00:00:00 EDT 2016},
month = {Mon Apr 11 00:00:00 EDT 2016}
}
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- Genes, Vol. 7, Issue 12
Differential Enzymatic Activity of Rat ADAR2 Splicing Variants Is Due to Altered Capability to Interact with RNA in the Deaminase Domain
journal, February 2018
- Filippini, Alice; Bonini, Daniela; Giacopuzzi, Edoardo
- Genes, Vol. 9, Issue 2
Role of Inosine–Uracil Base Pairs in the Canonical RNA Duplexes
journal, June 2018
- Špačková, Naďa; Réblová, Kamila
- Genes, Vol. 9, Issue 7