1K7K

crystal structure of RdgB- inosine triphosphate pyrophosphatase from E. coli

Summary for 1K7K

• Entry DOI: 10.2210/pdb1k7k/pdb
• Descriptor: Hypothetical protein yggV (2 entities in total)
• Functional Keywords: mad, his-tag, large groove, disordered se-met, structural genomics, putative ribosomal protein, psi, protein structure initiative, midwest center for structural genomics, mcsg, unknown function
• Biological source: Escherichia coli
• Total number of polymer chains: 1
• Total formula weight: 23871.47

Authors

Sanishvili, R.,Joachimiak, A.,Edwards, A.,Savchenko, A.,Skarina, T.,Midwest Center for Structural Genomics (MCSG) (deposition date: 2001-10-19, release date: 2002-08-14, Last modification date: 2024-11-13)

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

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: 17976651
DOI: 10.1016/j.jmb.2007.10.012

Experimental method

X-RAY DIFFRACTION (1.5 Å)