5OTM | pdb_00005otm

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

PDB DOI: https://doi.org/10.2210/pdb5OTM/pdb

Classification: HYDROLASE
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2017-08-22 Released: 2018-09-05
Deposition Author(s): Gustafsson, R., Henriksson, L., Jemth, A.-S., Brautigam, L., Carreras Puigvert, J., Homan, E., Warpman Berglund, U., Helleday, T., Stenmark, P.
Funding Organization(s): Swedish Research Council, Knut and Alice Wallenberg Foundation, Wenner-Gren Foundation, Ake Wiberg Foundation, Swedish Foundation for Strategic Research, Swedish Pain Relief Foundation, Torsten and Ragnar Soderberg Foundation, Swedish Childrens Cancer Foundation, Swedish Cancer Society

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free:
0.247 (Depositor), 0.254 (DCC)
R-Value Work:
0.196 (Depositor), 0.207 (DCC)
R-Value Observed:
0.199 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.4 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

PubMed: 30304478 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1093/nar/gky896
Primary Citation 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. 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

Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, S-171 76 Stockholm, Sweden.

Macromolecule Content

Total Structure Weight: 38.06 kDa
Atom Count: 2,898
Modeled Residue Count: 314
Deposited Residue Count: 318
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
7,8-dihydro-8-oxoguanine triphosphatase	A, B	159	Homo sapiens	Mutation(s): 0 Gene Names: NUDT1, MTH1 EC: 3.6.1.55 (PDB Primary Data), 3.6.1.56 (PDB Primary Data), 3.6.1 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P36639 (Homo sapiens) Explore P36639 Go to UniProtKB: P36639
PHAROS: P36639 GTEx: ENSG00000106268
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P36639
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
6OG (Subject of Investigation/LOI) Query on 6OG Download:Ideal Coordinates CCD File SDF format, chain M [auth B] SDF format, chain H [auth A] MOL2 format, chain M [auth B] MOL2 format, chain H [auth A] mmCIF format, chain M [auth B] mmCIF format, chain H [auth A]	H [auth A], M [auth B]	6-O-METHYL GUANOSINE-5'-MONOPHOSPHATE C₁₁ H₁₆ N₅ O₇ P GFRAHVJOXXMIDI-RRKCRQDMSA-N		Interactions Focus chain H [auth A] Focus chain M [auth B] Interactions & Density Focus chain H [auth A] Focus chain M [auth B]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain L [auth B] SDF format, chain K [auth B] SDF format, chain J [auth B] SDF format, chain I [auth B] SDF format, chain F [auth A] SDF format, chain E [auth A] SDF format, chain D [auth A] SDF format, chain C [auth A] MOL2 format, chain L [auth B] MOL2 format, chain K [auth B] MOL2 format, chain J [auth B] MOL2 format, chain I [auth B] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] MOL2 format, chain C [auth A] mmCIF format, chain L [auth B] mmCIF format, chain K [auth B] mmCIF format, chain J [auth B] mmCIF format, chain I [auth B] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A] mmCIF format, chain D [auth A] mmCIF format, chain C [auth A]	C [auth A] D [auth A] E [auth A] F [auth A] I [auth B] C [auth A], D [auth A], E [auth A], F [auth A], I [auth B], J [auth B], K [auth B], L [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B]
ACT Query on ACT Download:Ideal Coordinates CCD File SDF format, chain G [auth A] MOL2 format, chain G [auth A] mmCIF format, chain G [auth A]	G [auth A]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain G [auth A] Interactions & Density Focus chain G [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.247 (Depositor), 0.254 (DCC)
R-Value Work: 0.196 (Depositor), 0.207 (DCC)
R-Value Observed: 0.199 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 59.581	α = 90
b = 67.237	β = 90
c = 79.025	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2018-09-05

Deposition Author(s):

Carreras Puigvert, J.

Funding Organization	Location	Grant Number
Swedish Research Council	Sweden	--
Knut and Alice Wallenberg Foundation	Sweden	--
Wenner-Gren Foundation	Sweden	--
Ake Wiberg Foundation	Sweden	--
Swedish Foundation for Strategic Research	Sweden	--
Swedish Pain Relief Foundation	Sweden	--
Torsten and Ragnar Soderberg Foundation	Sweden	--
Swedish Childrens Cancer Foundation	Sweden	--
Swedish Cancer Society	Sweden	--

Revision History (Full details and data files)

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
Version 1.4: 2024-01-17
Changes: Data collection, Database references, Refinement description