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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); 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:
Journal Article: 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. 2016. "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},
url = {https://www.osti.gov/biblio/1255288}, journal = {Nature Structural & Molecular Biology},
issn = {1545-9993},
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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Cited by: 124 works
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Works referenced in this record:

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Mice with altered serotonin 2C receptor RNA editing display characteristics of Prader–Willi syndrome
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Mutations in ADAR1 cause Aicardi-Goutières syndrome associated with a type I interferon signature
text, January 2012


Structure, dynamics, and elasticity of free 16s rRNA helix 44 studied by molecular dynamics simulations
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The flip side of DNA methylation
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The Solution Structure of the ADAR2 dsRBM-RNA Complex Reveals a Sequence-Specific Readout of the Minor Groove
journal, October 2010


The RNA-Editing Enzyme ADAR1 Controls Innate Immune Responses to RNA
journal, November 2014


Mice with altered serotonin 2C receptor RNA editing display characteristics of Prader–Willi syndrome
journal, August 2010


HhaI DNA Methyltransferase Uses the Protruding Gln237 for Active Flipping of Its Target Cytosine
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RNA-Seq Analysis Identifies a Novel Set of Editing Substrates for Human ADAR2 Present in Saccharomyces cerevisiae
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Click Modification of RNA at Adenosine: Structure and Reactivity of 7-Ethynyl- and 7-Triazolyl-8-aza-7-deazaadenosine in RNA
journal, June 2014


A Transition State Analogue for an RNA-Editing Reaction
journal, September 2004


N 2 -Modified 2-aminopurine ribonucleosides as minor-groove-modulating adenosine replacements in duplex RNA
journal, March 2010


Regulation of alternative splicing by RNA editing
journal, May 1999


Structural basis for recognition and repair of the endogenous mutagen 8-oxoguanine in DNA
journal, February 2000


Mutations in ADAR1 cause Aicardi-Goutières syndrome associated with a type I interferon signature
journal, September 2012


Recoding RNA editing of AZIN1 predisposes to hepatocellular carcinoma
journal, January 2013


RNA editing changes the lesion specificity for the DNA repair enzyme NEIL1
journal, November 2010


Mechanistic insights into editing-site specificity of ADARs
journal, November 2012


Mutations of the RNA-Specific Adenosine Deaminase Gene (DSRAD) Are Involved in Dyschromatosis Symmetrica Hereditaria
journal, September 2003


Recognition of duplex RNA by the deaminase domain of the RNA editing enzyme ADAR2
journal, January 2015


Genome-Wide Identification of Human RNA Editing Sites by Parallel DNA Capturing and Sequencing
journal, May 2009


Functions and Regulation of RNA Editing by ADAR Deaminases
journal, June 2010


Base Flipping
journal, June 1998


Adenosine-to-inosine RNA editing and human disease
journal, January 2013


RNA editing of the GLI1 transcription factor modulates the output of Hedgehog signaling
journal, February 2013


Works referencing / citing this record:

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


ADAR RNA editing in human disease; more to it than meets the I
journal, September 2017


Programmable base editing of A•T to G•C in genomic DNA without DNA cleavage
journal, October 2017


Structural basis for targeted DNA cytosine deamination and mutagenesis by APOBEC3A and APOBEC3B
journal, December 2016


The emerging and uncultivated potential of CRISPR technology in plant science
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Base editing: precision chemistry on the genome and transcriptome of living cells
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In vivo RNA editing of point mutations via RNA-guided adenosine deaminases
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Identification of RNA-binding protein targets with HyperTRIBE
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Site-directed RNA repair of endogenous Mecp2 RNA in neurons
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Adenosine Deaminase That Acts on RNA 3 (ADAR3) Binding to Glutamate Receptor Subunit B Pre-mRNA Inhibits RNA Editing in Glioblastoma
journal, February 2017


A protein–protein interaction underlies the molecular basis for substrate recognition by an adenosine-to-inosine RNA-editing enzyme
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RNA binding candidates for human ADAR3 from substrates of a gain of function mutant expressed in neuronal cells
journal, September 2019


Learning cis -regulatory principles of ADAR-based RNA editing from CRISPR-mediated mutagenesis
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RNA editing with CRISPR-Cas13
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A cytosine deaminase for programmable single-base RNA editing
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A-to-I editing of Malacoherpesviridae RNAs supports the antiviral role of ADAR1 in mollusks
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Long-read sequencing uncovers a complex transcriptome topology in varicella zoster virus
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Population and allelic variation of A-to-I RNA editing in human transcriptomes
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Massive A-to-I RNA editing is common across the Metazoa and correlates with dsRNA abundance
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Editing inducer elements increases A-to-I editing efficiency in the mammalian transcriptome
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Rewriting the transcriptome: adenosine-to-inosine RNA editing by ADARs
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ADAR RNA editing below the backbone
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Functions of the RNA Editing Enzyme ADAR1 and Their Relevance to Human Diseases
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RNA Editing as a Therapeutic Approach for Retinal Gene Therapy Requiring Long Coding Sequences
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Learning cis-regulatory principles of ADAR-based RNA editing from CRISPR-mediated mutagenesis
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Adar RNA editing-dependent and -independent effects are required for brain and innate immune functions in Drosophila
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