Volume 26, No 9, Sep 2016

ISSN: 1001-0602 
EISSN: 1748-7838 2018 
impact factor 17.848* 
(Clarivate Analytics, 2019)

Volume 26 Issue 9, September 2016: 1062-1066   |  Open Access

LETTERS TO THE EDITOR

Structural basis of prokaryotic NAD-RNA decapping by NudC

Delin Zhang^1,*, Yexing Liu^2,*, Qiang Wang¹, Zeyuan Guan¹, Jing Wang¹, Jian Liu¹, Tingting Zou^1,3 and Ping Yin¹

¹National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research, Huazhong Agricultural University, Wuhan 430070, China
²Center for Structural Biology, School of Life Science, Tsinghua University, Beijing 100084, China
³College of Life Sciences and Technology, Huazhong Agricultural University, Wuhan 430070, China Correspondence: Ping Yin,(yinping@mail.hzau.edu.cn)

In eukaryotes, the 5′,5′-triphosphate-linked 7-methylguanosine (m7G) cap is essential for modulation of mRNA metabolism and protects the mRNA from degradation1. Removal of the cap from the 5′-terminus of the RNA is mainly carried out by decapping protein 2 (Dcp2)2,3 and scavenger decapping enzyme (DcpS)4. A distinctive feature of prokaryotic mRNA is the absence of a 5′-capped structure. Recently, nicotinamide adenine dinucleotide (NAD) or a triphosphate group has been shown to be covalently linked to the 5′-end of certain types of prokaryotic RNAs5,6 as a cap that improves stability, and NADH pyrophosphatase (NudC)6 and RNA pyrophosphohydrolase (RppH)7 are responsible for the 5′ hydrolysis of NAD or the triphosphate group, respectively, from the RNA. Interestingly, Dcp2, NudC and RppH all belong to the Nudix hydrolase superfamily, whose members act on substrates of nucleoside diphosphate linked to another moiety, X (hence the name Nudix)8. The Nudix enzymes share a conserved 23-amino acid sequence termed the Nudix motif (GX5EX7REUXEEXGU), which is required for substrate catalysis, but each uses a distinct strategy for substrate recognition. Although the molecular bases of substrate recognition by Dcp2 and RppH have been well studied9,10, the mechanism by which NudC removes the NAD cap still remains to be elucidated. Here, we report the crystal structure of Escherichia coli NudC in complex with NAD, uncovering the structural basis of NudC-mediated decapping of NAD-capped RNA.

10.1038/cr.2016.98

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