title: Structure and function of the bacterial decapping enzyme NudC.
abstract: RNA capping and decapping are thought to be distinctive features of eukaryotes. The redox cofactor NAD was recently discovered to be attached to small regulatory RNAs in bacteria in a cap-like manner, and Nudix hydrolase NudC was found to act as a NAD-decapping enzyme in vitro and in vivo. Here, crystal structures of Escherichia coli NudC in complex with substrate NAD and with cleavage product NMN reveal the catalytic residues lining the binding pocket and principles underlying molecular recognition of substrate and product. Biochemical mutation analysis identifies the conserved Nudix motif as the catalytic center of the enzyme, which needs to be homodimeric, as the catalytic pocket is composed of amino acids from both monomers. NudC is single-strand specific and has a purine preference for the 5'-terminal nucleotide. The enzyme strongly prefers NAD-linked RNA (NAD-RNA) over NAD and binds to a diverse set of cellular RNAs in an unspecific manner.
authors.affiliation: Institute of Pharmacy and Molecular Biotechnology, Heidelberg University, Heidelberg, Germany.
authors.forename: Katharina
authors.initials: K
authors.lastname: Höfer
authors.affiliation: Structural Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York, USA.
authors.forename: Sisi
authors.initials: S
authors.lastname: Li
authors.affiliation: Institute of Pharmacy and Molecular Biotechnology, Heidelberg University, Heidelberg, Germany.
authors.forename: Florian
authors.initials: F
authors.lastname: Abele
authors.affiliation: Institute of Pharmacy and Molecular Biotechnology, Heidelberg University, Heidelberg, Germany.
authors.forename: Jens
authors.initials: J
authors.lastname: Frindert
authors.affiliation: Institute of Pharmacy and Molecular Biotechnology, Heidelberg University, Heidelberg, Germany.
authors.forename: Jasmin
authors.initials: J
authors.lastname: Schlotthauer
authors.affiliation: Institute of Pharmacy and Molecular Biotechnology, Heidelberg University, Heidelberg, Germany.
authors.forename: Julia
authors.initials: J
authors.lastname: Grawenhoff
authors.affiliation: Shanghai Center for Plant Stress Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China.
authors.forename: Jiamu
authors.identifier: 0000-0002-1337-0786
authors.initials: J
authors.lastname: Du
authors.affiliation: Structural Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York, USA.
authors.forename: Dinshaw J
authors.initials: DJ
authors.lastname: Patel
authors.affiliation: Institute of Pharmacy and Molecular Biotechnology, Heidelberg University, Heidelberg, Germany.
authors.forename: Andres
authors.initials: A
authors.lastname: Jäschke
mesh_terms: D055162:Biocatalysis; D018360:Crystallography, X-Ray; D004926:Escherichia coli / Q000201:enzymology*; D008958:Models, Molecular; D011487:Protein Conformation; D011755:Pyrophosphatases / Q000737:chemistry* / Q000378:metabolism*; D000096964:Nudix Hydrolases
chemical_list: D011755:Pyrophosphatases; D000096964:Nudix Hydrolases