3EF5
Structure of the RNA pyrophosphohydrolase BdRppH in complex with dGTP
Summary for 3EF5
| Entry DOI | 10.2210/pdb3ef5/pdb |
| Related | 3EES 3EEU |
| Descriptor | Probable pyrophosphohydrolase, 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE (3 entities in total) |
| Functional Keywords | nudix, rna pyrophosphohydrolase, hydrolase |
| Biological source | Bdellovibrio bacteriovorus |
| Total number of polymer chains | 2 |
| Total formula weight | 36282.99 |
| Authors | Messing, S.A.,Gabelli, S.B.,Amzel, L.M. (deposition date: 2008-09-08, release date: 2009-03-24, Last modification date: 2024-02-21) |
| Primary citation | Messing, S.A.,Gabelli, S.B.,Liu, Q.,Celesnik, H.,Belasco, J.G.,Pineiro, S.A.,Amzel, L.M. Structure and Biological Function of the RNA Pyrophosphohydrolase BdRppH from Bdellovibrio bacteriovorus. Structure, 17:472-481, 2009 Cited by PubMed Abstract: Until recently, the mechanism of mRNA decay in bacteria was thought to be different from that of eukaryotes. This paradigm changed with the discovery that RppH (ORF176/NudH/YgdP), an Escherichia coli enzyme that belongs to the Nudix superfamily, is an RNA pyrophosphohydrolase that initiates mRNA decay by cleaving pyrophosphate from the 5'-triphosphate. Here we report the 1.9 Angstroms resolution structure of the Nudix hydrolase BdRppH from Bdellovibrio bacteriovorus, a bacterium that feeds on other Gram-negative bacteria. Based on the structure of the enzyme alone and in complex with GTP-Mg2+, we propose a mode of RNA binding similar to that of the nuclear decapping enzyme from Xenopus laevis, X29. In additional experiments, we show that BdRppH can indeed function in vitro and in vivo as an RNA pyrophosphohydrolase. These findings set the basis for the identification of possible decapping enzymes in other bacteria. PubMed: 19278661DOI: 10.1016/j.str.2008.12.022 PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (2.6 Å) |
Structure validation
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