Crystal structure of the yeast heterodimeric ADAT2/3 deaminase
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RESEARCH ARTICLE
Open Access
Crystal structure of the yeast heterodimeric ADAT2/3 deaminase Xiwen Liu1,2 , Ruoyu Chen1, Yujie Sun1, Ran Chen1, Jie Zhou1, Qingnan Tian3, Xuan Tao4, Zhang Zhang1, Guan-zheng Luo1 and Wei Xie1*
Abstract Background: The adenosine-to-inosine (A-to-I) editing in anticodons of tRNAs is critical for wobble base-pairing during translation. This modification is produced via deamination on A34 and catalyzed by the adenosine deaminase acting on tRNA (ADAT) enzyme. Eukaryotic ADATs are heterodimers composed of the catalytic subunit ADAT2 and the structural subunit ADAT3, but their molecular assemblies and catalytic mechanisms are largely unclear. Results: Here, we report a 2.8-Å crystal structure of Saccharomyces cerevisiae ADAT2/3 (ScADAT2/3), revealing its heterodimeric assembly and substrate recognition mechanism. While each subunit clearly contains a domain resembling their prokaryotic homolog TadA, suggesting an evolutionary gene duplication event, they also display accessory domains for additional structural or functional purposes. The N-lobe of ScADAT3 exhibits a positively charged region with a potential role in the recognition and binding of tRNA, supported by our biochemical analysis. Interestingly, ScADAT3 employs its C-terminus to block tRNA’s entry into its pseudo-active site and thus inactivates itself for deamination despite the preservation of a zinc-binding site, a mechanism possibly shared only among yeasts. Conclusions: Combining the structural with biochemical, bioinformatic, and in vivo functional studies, we propose a stepwise model for the pathway of deamination by ADAT2/3. Our work provides insight into the molecular mechanism of the A-to-I editing by the eukaryotic ADAT heterodimer, especially the role of ADAT3 in catalysis. Keywords: Adenosine-to-inosine editing, tRNA modifications, ADAT, Deaminase, Molecular mechanism
Background Post-transcriptional modification on RNA is an elegant strategy adopted by nature to diversify gene expression products and expand the functionality of the transcripts. Among various modifications, the adenosine-to-inosine (A-to-I) editing via deamination is a major type that is widely occurring in mRNA and tRNA. In tRNA, this deamination event takes place at positions 34 (the first position of the anticodon) and 37 (immediately 3′ to * Correspondence: [email protected] 1 MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory for Biocontrol, School of Life Sciences, Sun Yat-sen University, 135 W. Xingang Rd., Guangzhou 510275, Guangdong, People’s Republic of China Full list of author information is available at the end of the article
anticodon). Specifically, I34 allows the decoding of three different nucleotides at the third position of mRNA codons, as inosine is able to pair with U, C, and A. Such expanded base-pairing capability results in an enhancement in the decoding capacity of tRNA and promotes translational efficacy [1]. Therefore, the I34 modification in tRNA is essential for cell viability [2–7]. The enz
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