7WW5

Crystal structure of MutT-8-oxo-dGTP complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.57 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.187 

Starting Model: experimental
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Literature

Visualization of mutagenic nucleotide processing by Escherichia coli MutT, a Nudix hydrolase.

Nakamura, T.Yamagata, Y.

(2022) Proc Natl Acad Sci U S A 119: e2203118119-e2203118119

  • DOI: https://doi.org/10.1073/pnas.2203118119
  • Primary Citation of Related Structures:  
    7WW5, 7WW6, 7WW7, 7WW8, 7WW9, 7WWA, 7X9H, 7X9I, 7X9J, 7X9K, 7X9L, 7X9N, 7X9O

  • PubMed Abstract: 

    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 β-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.


  • Organizational Affiliation

    Graduate School of Pharmaceutical Sciences, Kumamoto University, Kumamoto, 862-0973, Japan.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
7,8-dihydro-8-oxoguanine-triphosphatase129Escherichia coliMutation(s): 0 
EC: 3.6.1.55 (PDB Primary Data), 3.6.1 (PDB Primary Data)
UniProt
Find proteins for P08337 (Escherichia coli (strain K12))
Explore P08337 
Go to UniProtKB:  P08337
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP08337
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.57 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.187 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 37.87α = 90
b = 55.89β = 90
c = 59.41γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministry of Education, Culture, Sports, Science and Technology (Japan)Japan--

Revision History  (Full details and data files)

  • Version 1.0: 2022-06-01
    Type: Initial release
  • Version 1.1: 2023-11-29
    Changes: Data collection, Refinement description