5IW5
Crystal structure of E. coli NudC in complex with NMN
Summary for 5IW5
| Entry DOI | 10.2210/pdb5iw5/pdb |
| Related | 5IW4 |
| Descriptor | NADH pyrophosphatase, ZINC ION, BETA-NICOTINAMIDE RIBOSE MONOPHOSPHATE, ... (4 entities in total) |
| Functional Keywords | nmn, rna, capping, nudix, hydrolase |
| Biological source | Escherichia coli B354 |
| Total number of polymer chains | 2 |
| Total formula weight | 60425.31 |
| Authors | Li, S.,Du, J.,Patel, D.J. (deposition date: 2016-03-22, release date: 2016-07-13, Last modification date: 2023-11-08) |
| Primary citation | Hofer, K.,Li, S.,Abele, F.,Frindert, J.,Schlotthauer, J.,Grawenhoff, J.,Du, J.,Patel, D.J.,Jaschke, A. Structure and function of the bacterial decapping enzyme NudC Nat.Chem.Biol., 12:730-734, 2016 Cited by PubMed 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. PubMed: 27428510DOI: 10.1038/nchembio.2132 PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (2.7 Å) |
Structure validation
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