3W5W
Mn2+-GMP complex of nanoRNase (Nrn) from Bacteroides fragilis
Summary for 3W5W
| Entry DOI | 10.2210/pdb3w5w/pdb |
| Related | 3DMA |
| Descriptor | Putative exopolyphosphatase-related protein, GUANOSINE-5'-MONOPHOSPHATE, MANGANESE (II) ION, ... (4 entities in total) |
| Functional Keywords | dhh phosphatase, dhha1 motif, phosphatase, hydrolase |
| Biological source | Bacteroides fragilis |
| Total number of polymer chains | 1 |
| Total formula weight | 40753.20 |
| Authors | Uemura, Y.,Nakagawa, N.,Wakamatsu, T.,Montelione, G.T.,Hunt, J.F.,Masui, R.,Kuramitsu, S. (deposition date: 2013-02-07, release date: 2013-07-10, Last modification date: 2023-11-08) |
| Primary citation | Uemura, Y.,Nakagawa, N.,Wakamatsu, T.,Kim, K.,Montelione, G.T.,Hunt, J.F.,Kuramitsu, S.,Masui, R. Crystal structure of the ligand-binding form of nanoRNase from Bacteroides fragilis, a member of the DHH/DHHA1 phosphoesterase family of proteins. Febs Lett., 587:2669-2674, 2013 Cited by PubMed Abstract: NanoRNase (Nrn) specifically degrades nucleoside 3',5'-bisphosphate and the very short RNA, nanoRNA, during the final step of mRNA degradation. The crystal structure of Nrn in complex with a reaction product GMP was determined. The overall structure consists of two domains that are interconnected by a flexible loop and form a cleft. Two Mn²⁺ ions are coordinated by conserved residues in the DHH motif of the N-terminal domain. GMP binds near the DHHA1 motif region in the C-terminal domain. Our structure enables us to predict the substrate-bound form of Nrn as well as other DHH/DHHA1 phosphoesterase family proteins. PubMed: 23851074DOI: 10.1016/j.febslet.2013.06.053 PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (2.95 Å) |
Structure validation
Download full validation report
