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ACS Chem Biol. 2018 Mar 16;13(3):772-781. doi: 10.1021/acschembio.7b00890. Epub 2018 Feb 8.

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

Author information

1
College of Life Sciences , Zhejiang Sci-Tech University , Hangzhou 310018 , China.
2
Drug Discovery and Design Center, CAS Key Laboratory of Receptor Research, State Key Laboratory of Drug Research , Shanghai Institute of Materia Medica, Chinese Academy of Sciences , Shanghai 201203 , China.
3
Department of Oncology, The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins , The Johns Hopkins University School of Medicine , Baltimore , Maryland 21287 , United States.
4
Shanghai ChemPartner Co., LTD , Building 5, 998 Halei Road , Zhangjiang Hi-Tech Park, Pudong New Area, Shanghai 201203 , P.R. China.
5
School of Pharmacy , Shanghai University of Traditional Chinese Medicine , 1200 Cailun Road , Shanghai 201203 , China.
6
China Novartis Institutes for BioMedical Research , Shanghai 201203 , China.

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 kcat/ Km 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.

PMID:
29381856
DOI:
10.1021/acschembio.7b00890
[Indexed for MEDLINE]

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