2Q16
Structure of the E. coli inosine triphosphate pyrophosphatase RgdB in complex with ITP
Summary for 2Q16
| Entry DOI | 10.2210/pdb2q16/pdb |
| Related | 1K7K 2PYU |
| Descriptor | HAM1 protein homolog, CALCIUM ION, SODIUM ION, ... (6 entities in total) |
| Functional Keywords | itp pyrophosphatase x-ray structure enzyme mechanism substrate, hydrolase |
| Biological source | Escherichia coli |
| Total number of polymer chains | 2 |
| Total formula weight | 48259.46 |
| Authors | Singer, A.U.,Lam, R.,Proudfoot, M.,Skarina, T.,Savchenko, A.,Yakunin, A.F. (deposition date: 2007-05-23, release date: 2008-02-19, Last modification date: 2024-02-21) |
| Primary citation | Savchenko, A.,Proudfoot, M.,Skarina, T.,Singer, A.,Litvinova, O.,Sanishvili, R.,Brown, G.,Chirgadze, N.,Yakunin, A.F. Molecular basis of the antimutagenic activity of the house-cleaning inosine triphosphate pyrophosphatase RdgB from Escherichia coli. J.Mol.Biol., 374:1091-1103, 2007 Cited by PubMed Abstract: Inosine triphosphate pyrophosphatases, which are ubiquitous house-cleaning enzymes, hydrolyze noncanonical nucleoside triphosphates (inosine triphosphate (ITP) and xanthosine triphosphate (XTP)) and prevent the incorporation of hypoxanthine or xanthine into nascent DNA or RNA. Here we present the 1.5-A-resolution crystal structure of the inosine triphosphate pyrophosphatase RdgB from Escherichia coli in a free state and in complex with a substrate (ITP+Ca(2+)) or a product (inosine monophosphate (IMP)). ITP binding to RdgB induced a large displacement of the alpha1 helix, closing the enzyme active site. This positions the conserved Lys13 close to the bridging oxygen between the alpha- and beta-phosphates of the substrate, weakening the P(alpha)-O bond. On the other side of the substrate, the conserved Asp69 is proposed to act as a base coordinating the catalytic water molecule. Our data provide insight into the molecular mechanisms of the substrate selectivity and catalysis of RdgB and other ITPases. PubMed: 17976651DOI: 10.1016/j.jmb.2007.10.012 PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (1.95 Å) |
Structure validation
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