Structural and mechanistic basis of mammalian Nudt12 RNA deNADding

  • Nat Chem Biol. 2019 Jun;15(6):575-582. doi: 10.1038/s41589-019-0293-7.
Ewa Grudzien-Nogalska  #  1 ,  Yixuan Wu  #  2 ,  Xinfu Jiao  1 ,  Huijuan Cui  1 ,  Maria K Mateyak  1 ,  Ronald P Hart  1 ,  Liang Tong  3 ,  Megerditch Kiledjian  4
Affiliations
  • 1. Department Cell Biology and Neuroscience, Rutgers University, Piscataway, NJ, USA.
  • 2. Department Biological Sciences, Columbia University, New York, NY, USA.
  • 3. Department Biological Sciences, Columbia University, New York, NY, USA. [email protected].
  • 4. Department Cell Biology and Neuroscience, Rutgers University, Piscataway, NJ, USA. [email protected].
  • # Contributed equally.
PMID: 31101919 DOI: 10.1038/s41589-019-0293-7
Abstract

We recently demonstrated that mammalian cells harbor nicotinamide adenine dinucleotide (NAD)-capped messenger RNAs that are hydrolyzed by the DXO deNADding enzyme. Here, we report that the Nudix protein Nudt12 is a second mammalian deNADding enzyme structurally and mechanistically distinct from DXO and targeting different RNAs. The crystal structure of mouse Nudt12 in complex with the deNADding product AMP and three Mg2+ ions at 1.6 Å resolution provides insights into the molecular basis of the deNADding activity in the NAD pyrophosphate. Disruption of the Nudt12 gene stabilizes transfected NAD-capped RNA in cells, and its endogenous NAD-capped mRNA targets are enriched in those encoding proteins involved in cellular energetics. Furthermore, exposure of cells to nutrient or environmental stress manifests changes in NAD-capped RNA levels that are selectively responsive to Nudt12 or DXO, respectively, indicating an association of deNADding to cellular metabolism.