7x9k

From Proteopedia

Crystal structure of MutT-8-oxo-dGTP complex: Reaction for 2 hr using 10 mM Mn2+

PDB ID 7x9k

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Structural highlights

7x9k is a 1 chain structure with sequence from Escherichia coli. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 1.81Å
Ligands:	, , , , , , ,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

MUTT_ECOLI Involved in the GO system responsible for removing an oxidatively damaged form of guanine (7,8-dihydro-8-oxoguanine) from DNA and the nucleotide pool. 8-oxo-dGTP is inserted opposite dA and dC residues of template DNA with almost equal efficiency thus leading to A.T to G.C transversions. MutT specifically degrades 8-oxo-dGTP to the monophosphate.^[1] ^[2]

Publication Abstract from PubMed

Escherichia coli MutT prevents mutations by hydrolyzing mutagenic 8-oxo-2'-deoxyguanosine 5'-triphosphate (8-oxo-dGTP) in the presence of Mg2+ or Mn2+ ions. MutT is one of the most studied enzymes in the nucleoside diphosphate-linked moiety X (Nudix) hydrolase superfamily, which is widely distributed in living organisms. However, the catalytic mechanisms of most Nudix hydrolases, including two- or three-metal-ion mechanisms, are still unclear because these mechanisms are proposed using the structures mimicking the reaction states, such as substrate analog complexes. Here, we visualized the hydrolytic reaction process of MutT by time-resolved X-ray crystallography using a biological substrate, 8-oxo-dGTP, and an active metal ion, Mn2+. The reaction was initiated by soaking MutT crystals in a MnCl2 solution and stopped by freezing the crystals at various time points. In total, five types of intermediate structures were refined by investigating the time course of the electron densities in the active site as well as the anomalous signal intensities of Mn2+ ions. The structures and electron densities show that three Mn2+ ions bind to the Nudix motif of MutT and align the substrate 8-oxo-dGTP for catalysis. Accompanied by the coordination of the three Mn2+ ions, a water molecule, bound to a catalytic base, forms a binuclear Mn2+ center for nucleophilic substitution at the beta-phosphorus of 8-oxo-dGTP. The reaction condition using Mg2+ also captured a structure in complex with three Mg2+ ions. This study provides the structural details essential for understanding the three-metal-ion mechanism of Nudix hydrolases and proposes that some of the Nudix hydrolases share this mechanism.

Visualization of mutagenic nucleotide processing by Escherichia coli MutT, a Nudix hydrolase.,Nakamura T, Yamagata Y Proc Natl Acad Sci U S A. 2022 May 24;119(21):e2203118119. doi: , 10.1073/pnas.2203118119. Epub 2022 May 20. PMID:35594391^[3]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Maki H, Sekiguchi M. MutT protein specifically hydrolyses a potent mutagenic substrate for DNA synthesis. Nature. 1992 Jan 16;355(6357):273-5. PMID:1309939 doi:http://dx.doi.org/10.1038/355273a0
↑ Ito R, Hayakawa H, Sekiguchi M, Ishibashi T. Multiple enzyme activities of Escherichia coli MutT protein for sanitization of DNA and RNA precursor pools. Biochemistry. 2005 May 3;44(17):6670-4. PMID:15850400 doi:http://dx.doi.org/10.1021/bi047550k
↑ Nakamura T, Yamagata Y. Visualization of mutagenic nucleotide processing by Escherichia coli MutT, a Nudix hydrolase. Proc Natl Acad Sci U S A. 2022 May 24;119(21):e2203118119. PMID:35594391 doi:10.1073/pnas.2203118119