Biological Assembly 1  

 3D View: Structure | 1D-3D View | Validation Report

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 17.97 kDa 
• Atom Count: 1266 
• Modelled Residue Count: 156 
• Deposited Residue Count: 156 
• Unique protein chains: 1

1IRY

Solution structure of the hMTH1, a nucleotide pool sanitization enzyme

• PDB DOI: 10.2210/pdb1IRY/pdb

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


• Deposited: 2001-10-25 Released: 2003-12-23 
• Deposition Author(s): Mishima, M., Itoh, N., Sakai, Y., Kamiya, H., Nakabeppu, Y., Shirakawa, M.

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 100 
• Conformers Submitted: 30 
• Selection Criteria: structures with the lowest energy 

Literature

Structure of human MTH1, a Nudix family hydrolase that selectively degrades oxidized purine nucleoside triphosphates

Mishima, M., Sakai, Y., Itoh, N., Kamiya, H., Furuichi, M., Takahashi, M., Yamagata, Y., Iwai, S., Nakabeppu, Y., Shirakawa, M.

(2004) J Biol Chem 279: 33806-33815

• PubMed: 15133035 
• DOI: 10.1074/jbc.M402393200
• Primary Citation of Related Structures:  
  1IRY


• PubMed Abstract: 
  

Oxygen radicals generated through normal cellular respiration processes can cause mutations in genomic and mitochondrial DNA. Human MTH1 hydrolyzes oxidized purine nucleoside triphosphates, such as 8-oxo-dGTP and 2-hydroxy-dATP, to monophosphates, thereby preventing the misincorporation of these oxidized nucleotides during replication. Here we present the solution structure of MTH1 solved by multidimensional heteronuclear NMR spectroscopy. The protein adopts a fold similar to that of Escherichia coli MutT, despite the low sequence similarity between these proteins outside the conserved Nudix motif. The substrate-binding pocket of MTH1, deduced from chemical shift perturbation experiments, is located at essentially the same position as in MutT; however, a pocket-forming helix is largely displaced in MTH1 (approximately 9 A) such that the shape of the pocket differs between the two proteins. Detailed analysis of the pocket-forming residues enabled us to identify Asn33 as one of the key residues in MTH1 for discriminating the oxidized form of purine, and mutation of this residue modifies the substrate specificity. We also show that MTH1 catalyzes hydrolysis of 8-oxo-dGTP through nucleophilic substitution of water at the beta-phosphate.

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Organizational Affiliation: 

Graduate School of Biological Sciences, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0101, Japan.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
hMTH1	A	156	Homo sapiens	Mutation(s): 0  Gene Names: hMTH1, NUDT1, MTH1 EC: 3.1.6 (PDB Primary Data), 3.6.1.56 (UniProt), 3.6.1 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P36639 (Homo sapiens) Explore P36639  Go to UniProtKB:  P36639
PHAROS:  P36639

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 100 
• Conformers Submitted: 30 
• Selection Criteria: structures with the lowest energy 
• OLDERADO: 1IRY Olderado

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2001-10-25 
• Released Date: 2003-12-23 
Deposition Author(s): Mishima, M., Itoh, N., Sakai, Y., Kamiya, H., Nakabeppu, Y., Shirakawa, M.

Revision History  

• Version 1.0: 2003-12-23
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2022-02-23
  Changes: Data collection, Database references, Derived calculations