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

Fei Ye, Xiangqian Kong, Hao Zhang, Yan Liu, Zhiyuan Shao, Jia Jin, Yi Cai, Rukang Zhang, Linjuan Li, Yang Zhang, Yu Chih Liu, Chenhua Zhang, Wenbing Xie, Kunqian Yu, Hong Ding, Kehao Zhao, Shijie Chen, Hualiang Jiang, Stephen B Baylin, Cheng Luo

Research output: Contribution to journalArticle

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.

Original languageEnglish (US)
Pages (from-to)772-781
Number of pages10
JournalACS Chemical Biology
Volume13
Issue number3
DOIs
StatePublished - Mar 16 2018

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ASJC Scopus subject areas

  • Biochemistry
  • Molecular Medicine

Cite this

Ye, F., Kong, X., Zhang, H., Liu, Y., Shao, Z., Jin, J., Cai, Y., Zhang, R., Li, L., Zhang, Y., Liu, Y. C., Zhang, C., Xie, W., Yu, K., Ding, H., Zhao, K., Chen, S., Jiang, H., Baylin, S. B., & Luo, C. (2018). Biochemical Studies and Molecular Dynamic Simulations Reveal the Molecular Basis of Conformational Changes in DNA Methyltransferase-1. ACS Chemical Biology, 13(3), 772-781. https://doi.org/10.1021/acschembio.7b00890