5OTN

Crystal structure of zebrafish MTH1 in complex with O6-methyl-dGMP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.99 Å
  • R-Value Free: 0.133 
  • R-Value Work: 0.121 
  • R-Value Observed: 0.121 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

MutT homologue 1 (MTH1) catalyzes the hydrolysis of mutagenic O6-methyl-dGTP.

Jemth, A.S.Gustafsson, R.Brautigam, L.Henriksson, L.Vallin, K.S.A.Sarno, A.Almlof, I.Homan, E.Rasti, A.Warpman Berglund, U.Stenmark, P.Helleday, T.

(2018) Nucleic Acids Res 46: 10888-10904

  • DOI: 10.1093/nar/gky896
  • Primary Citation of Related Structures:  
    5OTM, 5OTN

  • PubMed Abstract: 
  • Nucleotides in the free pool are more susceptible to nonenzymatic methylation than those protected in the DNA double helix. Methylated nucleotides like O6-methyl-dGTP can be mutagenic and toxic if incorporated into DNA. Removal of methylated nucleotides from the nucleotide pool may therefore be important to maintain genome integrity ...

    Nucleotides in the free pool are more susceptible to nonenzymatic methylation than those protected in the DNA double helix. Methylated nucleotides like O6-methyl-dGTP can be mutagenic and toxic if incorporated into DNA. Removal of methylated nucleotides from the nucleotide pool may therefore be important to maintain genome integrity. We show that MutT homologue 1 (MTH1) efficiently catalyzes the hydrolysis of O6-methyl-dGTP with a catalytic efficiency similar to that for 8-oxo-dGTP. O6-methyl-dGTP activity is exclusive to MTH1 among human NUDIX proteins and conserved through evolution but not found in bacterial MutT. We present a high resolution crystal structure of human and zebrafish MTH1 in complex with O6-methyl-dGMP. By microinjecting fertilized zebrafish eggs with O6-methyl-dGTP and inhibiting MTH1 we demonstrate that survival is dependent on active MTH1 in vivo. O6-methyl-dG levels are higher in DNA extracted from zebrafish embryos microinjected with O6-methyl-dGTP and inhibition of O6-methylguanine-DNA methyl transferase (MGMT) increases the toxicity of O6-methyl-dGTP demonstrating that O6-methyl-dGTP is incorporated into DNA. MTH1 deficiency sensitizes human cells to the alkylating agent Temozolomide, a sensitization that is more pronounced upon MGMT inhibition. These results expand the cellular MTH1 function and suggests MTH1 also is important for removal of methylated nucleotides from the nucleotide pool.


    Organizational Affiliation

    Sheffield Cancer Centre, Department of Oncology and Metabolism, University of Sheffield, Sheffield S10 2RX, UK.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Nudix (Nucleoside diphosphate linked moiety X)-type motif 1A159Danio rerioMutation(s): 0 
Gene Names: nudt1
Find proteins for Q7ZWC3 (Danio rerio)
Explore Q7ZWC3 
Go to UniProtKB:  Q7ZWC3
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
6OG
Query on 6OG

Download CCD File 
A
6-O-METHYL GUANOSINE-5'-MONOPHOSPHATE
C11 H16 N5 O7 P
GFRAHVJOXXMIDI-RRKCRQDMSA-N
 Ligand Interaction
GOL
Query on GOL

Download CCD File 
A
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO

Download CCD File 
A
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

Download CCD File 
A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.99 Å
  • R-Value Free: 0.133 
  • R-Value Work: 0.121 
  • R-Value Observed: 0.121 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 44.528α = 90
b = 55.379β = 90
c = 65.92γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Swedish Research CouncilSweden--
Knut and Alice Wallenberg FoundationSweden--
Wenner-Gren FoundationSweden--
Ake Wiberg FoundationSweden--
Swedish Foundation for Strategic ResearchSweden--
Swedish Pain Relief FoundationSweden--
Torsten and Ragnar Soderberg FoundationSweden--
Swedish Childrens Cancer FoundationSweden--
Swedish Cancer SocietySweden--

Revision History 

  • Version 1.0: 2018-09-05
    Type: Initial release
  • Version 1.1: 2018-10-17
    Changes: Data collection, Database references
  • Version 1.2: 2018-10-24
    Changes: Data collection, Database references
  • Version 1.3: 2018-11-28
    Changes: Data collection, Database references