The crystal structure of mouse DNMT1 (731-1602) mutant - N1248A

Experimental Data Snapshot

  • Resolution: 2.10 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.201 

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Biochemical Studies and Molecular Dynamic Simulations Reveal the Molecular Basis of Conformational Changes in DNA Methyltransferase-1.

Ye, F.Kong, X.Zhang, H.Liu, Y.Shao, Z.Jin, J.Cai, Y.Zhang, R.Li, L.Zhang, Y.W.Liu, Y.C.Zhang, C.Xie, W.Yu, K.Ding, H.Zhao, K.Chen, S.Jiang, H.Baylin, S.B.Luo, C.

(2018) ACS Chem Biol 13: 772-781

  • DOI: https://doi.org/10.1021/acschembio.7b00890
  • Primary Citation of Related Structures:  
    5GUT, 5GUV

  • PubMed Abstract: 

    DNA methyltransferase-1 (DNMT1) plays a crucial role in the maintenance of genomic methylation patterns. The crystal structure of DNMT1 was determined in two different states in which the helix that follows the catalytic loop was either kinked (designated helix-kinked) or well folded (designated helix-straight state). Here, we show that the proper structural transition between these two states is required for DNMT1 activity. The mutations of N1248A and R1279D, which did not affect interactions between DNMT1 and substrates or cofactors, allosterically reduced enzymatic activities in vitro by decreasing k cat / K m for AdoMet. The crystallographic data combined with molecular dynamic (MD) simulations indicated that the N1248A and R1279D mutants bias the catalytic helix to either the kinked or straight conformation. In addition, genetic complementation assays for the two mutants suggested that disturbing the conformational transition reduced DNMT1 activity in cells, which could act additively with existing DNMT inhibitors to decrease DNA methylation. Collectively, our studies provide molecular insights into conformational changes of the catalytic helix, which is essential for DNMT1 catalytic activity, and thus aid in better understanding the relationship between DNMT1 dynamic switching and enzymatic activity.

  • Organizational Affiliation

    College of Life Sciences , Zhejiang Sci-Tech University , Hangzhou 310018 , China.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DNA (cytosine-5)-methyltransferase 1872Mus musculusMutation(s): 1 
Gene Names: Dnmt1DnmtMet1Uim
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
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on SAH

Download Ideal Coordinates CCD File 
C14 H20 N6 O5 S
Query on SO4

Download Ideal Coordinates CCD File 
E [auth A]
F [auth A]
G [auth A]
H [auth A]
I [auth A]
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
L [auth A],
M [auth A],
N [auth A]
O4 S
Query on ZN

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A]
Binding Affinity Annotations 
IDSourceBinding Affinity
SAH BindingDB:  5GUT IC50: min: 71, max: 4000 (nM) from 8 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 2.10 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.201 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 75.424α = 90
b = 78.554β = 90
c = 164.544γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Natural Science Foundation of ChinaChina81402849
National Natural Science Foundation of ChinaChina21472208
National Natural Science Foundation of ChinaChina21210003

Revision History  (Full details and data files)

  • Version 1.0: 2017-09-06
    Type: Initial release
  • Version 1.1: 2019-03-13
    Changes: Data collection, Database references
  • Version 1.2: 2023-11-08
    Changes: Data collection, Database references, Derived calculations, Refinement description