3ZR1 | pdb_00003zr1

Crystal structure of human MTH1

• PDB DOI: https://doi.org/10.2210/pdb3ZR1/pdb

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


• Deposited: 2011-06-13 Released: 2011-07-27 
• Deposition Author(s): Svensson, L.M., Jemth, A., Desroses, M., Loseva, O., Helleday, T., Hogbom, M., Stenmark, P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.245 (Depositor), 0.252 (DCC) 
• R-Value Work: 
  0.191 (Depositor), 0.198 (DCC) 
• R-Value Observed: 
  0.193 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure of Human Mth1 and the 8-Oxo-Dgmp Product Complex.

Svensson, L.M., Jemth, A., Desroses, M., Loseva, O., Helleday, T., Hogbom, M., Stenmark, P.

(2011) FEBS Lett 585: 2617

• PubMed: 21787772 
• DOI: https://doi.org/10.1016/j.febslet.2011.07.017
• Primary Citation Related Structures: 
  3ZR0, 3ZR1


• PubMed Abstract: 
  

  MTH1 hydrolyzes oxidized nucleotide triphosphates, thereby preventing them from being incorporated into DNA. We here present the structures of human MTH1 (1.9Å) and its complex with the product 8-oxo-dGMP (1.8Å). Unexpectedly MTH1 binds the nucleotide in the anti conformation with no direct interaction between the 8-oxo group and the protein. We suggest that the specificity depends on the stabilization of an enol tautomer of the 8-oxo form of dGTP. The binding of the product induces no major structural changes. The structures reveal the mode of nucleotide binding in MTH1 and provide the structural basis for inhibitor design.

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Organizational Affiliation: 
• Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 36.45 kDa 
• Atom Count: 2,680 
• Modeled Residue Count: 305 
• Deposited Residue Count: 312 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
7,8-DIHYDRO-8-OXOGUANINE TRIPHOSPHATASE	A, B	156	Homo sapiens	Mutation(s): 0  Gene Names: NUDT1 EC: 3.6.1 (PDB Primary Data), 3.6.1.56 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P36639 (Homo sapiens) Explore P36639  Go to UniProtKB:  P36639
PHAROS:  P36639 GTEx:  ENSG00000106268

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	D [auth A], E [auth A], F [auth A], H [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
ACT	C [auth A], G [auth B]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.245 (Depositor), 0.252 (DCC) 
• R-Value Work:  0.191 (Depositor), 0.198 (DCC) 
• R-Value Observed: 0.193 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 59.52	α = 90
b = 67.08	β = 90
c = 80.13	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
BALBES	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-07-27 
Deposition Author(s): Svensson, L.M., Jemth, A., Desroses, M., Loseva, O., Helleday, T., Hogbom, M., Stenmark, P.

Revision History  

• Version 1.0: 2011-07-27
  Type: Initial release
  
• Version 1.1: 2011-08-24
  Changes: Database references
• Version 1.2: 2023-12-20
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description