5WY1

Crystal structure of mouse DNA methyltransferase 1 (T1505A mutant)

  • Classification: TRANSFERASE
  • Organism(s): Mus musculus
  • Expression System: Spodoptera frugiperda
  • Mutation(s): Yes 

  • Deposited: 2017-01-10 Released: 2017-05-24 
  • Deposition Author(s): Kanada, K., Takeshita, K., Suetake, I., Tajima, S., Nakagawa, A.
  • Funding Organization(s): Japan Society for the Promotion of Science, Japan Science and Technology Agency, Japan Society for the Promotion of Science/the Ministry of Education, Culture, Sports, Science and Technology, the National Project on Protein Structural and Functional Analyses

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.27 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.203 
  • R-Value Observed: 0.206 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Conserved threonine 1505 in the catalytic domain stabilizes mouse DNA methyltransferase 1

Kanada, K.Takeshita, K.Suetake, I.Tajima, S.Nakagawa, A.

(2017) J Biochem 162: 271-278

  • DOI: https://doi.org/10.1093/jb/mvx024
  • Primary Citation of Related Structures:  
    5WY1

  • PubMed Abstract: 

    In mammals, DNA methyltransferase 1 (DNMT1) is responsible for propagating the DNA methylation pattern into the next generation through selective methylation of hemi-methylated CpG that emerges just after replication, a process known as maintenance methylation. The T1505, which is conserved among DNMT1s of vertebrates, in the catalytic domain of mouse DNMT1 forms the hydrogen bond with the W1512, which is also conserved among vertebrates and one of the essential residues in recognition of the 5-methylcytosine in hemi-methylated CpGs. However, importance of the hydrogen bond between T1505 and W1512 is unknown. In this study, we determined the crystal structure of mouse DNMT1(291-1620) that replaced T1505 with alanine (DNMT1(291-1620)T1505A) and examined its DNA methylation activity in vitro. Although the mutation lost the hydrogen bond between T1505 and W1512, the overall structure of DNMT1(291-1620)T1505A remained almost identical with that of the wild type. Structural stability and DNA methylation activity of DNMT1(291-1620)T1505A under physiological temperature were lower than those of DNMT1(291-1620). T1505 is crucial on the DNA methylation activity of DNMT1 through stabilizing its structure during ongoing round of DNA methylation.


  • Organizational Affiliation

    The Laboratory of Supramolecular Crystallography, Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DNA (cytosine-5)-methyltransferase 11,330Mus musculusMutation(s): 1 
Gene Names: Dnmt1DnmtMet1Uim
EC: 2.1.1.37
UniProt
Find proteins for P13864 (Mus musculus)
Explore P13864 
Go to UniProtKB:  P13864
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP13864
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.27 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.203 
  • R-Value Observed: 0.206 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 134.998α = 90
b = 97.804β = 90
c = 130.319γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data scaling
PDB_EXTRACTdata extraction
Cootmodel building
MOLREPphasing
HKL-2000data reduction

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan Society for the Promotion of ScienceJapanJP23770145
Japan Science and Technology AgencyJapan--
Japan Society for the Promotion of ScienceJapanJP24570153
Japan Society for the Promotion of ScienceJapanJP22370053
Japan Society for the Promotion of Science/the Ministry of Education, Culture, Sports, Science and TechnologyJapanJP 25291025
the National Project on Protein Structural and Functional AnalysesJapan--

Revision History  (Full details and data files)

  • Version 1.0: 2017-05-24
    Type: Initial release
  • Version 1.1: 2017-10-18
    Changes: Database references
  • Version 1.2: 2023-11-22
    Changes: Data collection, Database references, Refinement description