Human DNMT1 transition state structure

Quan Du, Zhen Wang, Vern L. Schramm

Research output: Contribution to journalArticle

24 Citations (Scopus)

Abstract

Human DNA methyltransferase 1 (DNMT1) maintains the epigenetic state of DNA by replicating CpG methylation signatures from parent to daughter strands, producing heritable methylation patterns through cell divisions. The proposed catalytic mechanism of DNMT1 involves nucleophilic attack of Cys1226 to cytosine (Cyt) C6, methyl transfer from S-adenosyl-L-methionine (SAM) to Cyt C5, and proton abstraction from C5 to form methylated CpG in DNA. Here, we report the subangstrom geometric and electrostatic structure of the major transition state (TS) of the reaction catalyzed by human DNMT1. Experimental kinetic isotope effects were used to guide quantum mechanical calculations to solve the TS structure. Methyl transfer occurs after Cys1226 attack to Cyt C6, and the methyl transfer step is chemically rate-limiting for DNMT1. Electrostatic potential maps were compared for the TS and ground states, providing the electronic basis for interactions between the protein and reactants at the TS. Understanding the TS of DNMT1 demonstrates the possibility of using similar analysis to gain subangstrom geometric insight into the complex reactions of epigenetic modifications.

Original languageEnglish (US)
Pages (from-to)2916-2921
Number of pages6
JournalProceedings of the National Academy of Sciences of the United States of America
Volume113
Issue number11
DOIs
StatePublished - Mar 15 2016

Fingerprint

Methyltransferases
Cytosine
DNA
Static Electricity
Epigenomics
Methylation
Catalytic DNA
S-Adenosylmethionine
Isotopes
Cell Division
Protons
Proteins

Keywords

  • 5-methylcytosine
  • CpG methylation
  • DNA methyltransferase
  • S-adenosyl-L-methionine
  • Transition state

ASJC Scopus subject areas

  • General

Cite this

Human DNMT1 transition state structure. / Du, Quan; Wang, Zhen; Schramm, Vern L.

In: Proceedings of the National Academy of Sciences of the United States of America, Vol. 113, No. 11, 15.03.2016, p. 2916-2921.

Research output: Contribution to journalArticle

@article{bfc3f4814ba44c548a8f0a2a2b8379fd,
title = "Human DNMT1 transition state structure",
abstract = "Human DNA methyltransferase 1 (DNMT1) maintains the epigenetic state of DNA by replicating CpG methylation signatures from parent to daughter strands, producing heritable methylation patterns through cell divisions. The proposed catalytic mechanism of DNMT1 involves nucleophilic attack of Cys1226 to cytosine (Cyt) C6, methyl transfer from S-adenosyl-L-methionine (SAM) to Cyt C5, and proton abstraction from C5 to form methylated CpG in DNA. Here, we report the subangstrom geometric and electrostatic structure of the major transition state (TS) of the reaction catalyzed by human DNMT1. Experimental kinetic isotope effects were used to guide quantum mechanical calculations to solve the TS structure. Methyl transfer occurs after Cys1226 attack to Cyt C6, and the methyl transfer step is chemically rate-limiting for DNMT1. Electrostatic potential maps were compared for the TS and ground states, providing the electronic basis for interactions between the protein and reactants at the TS. Understanding the TS of DNMT1 demonstrates the possibility of using similar analysis to gain subangstrom geometric insight into the complex reactions of epigenetic modifications.",
keywords = "5-methylcytosine, CpG methylation, DNA methyltransferase, S-adenosyl-L-methionine, Transition state",
author = "Quan Du and Zhen Wang and Schramm, {Vern L.}",
year = "2016",
month = "3",
day = "15",
doi = "10.1073/pnas.1522491113",
language = "English (US)",
volume = "113",
pages = "2916--2921",
journal = "Proceedings of the National Academy of Sciences of the United States of America",
issn = "0027-8424",
number = "11",

}

TY - JOUR

T1 - Human DNMT1 transition state structure

AU - Du, Quan

AU - Wang, Zhen

AU - Schramm, Vern L.

PY - 2016/3/15

Y1 - 2016/3/15

N2 - Human DNA methyltransferase 1 (DNMT1) maintains the epigenetic state of DNA by replicating CpG methylation signatures from parent to daughter strands, producing heritable methylation patterns through cell divisions. The proposed catalytic mechanism of DNMT1 involves nucleophilic attack of Cys1226 to cytosine (Cyt) C6, methyl transfer from S-adenosyl-L-methionine (SAM) to Cyt C5, and proton abstraction from C5 to form methylated CpG in DNA. Here, we report the subangstrom geometric and electrostatic structure of the major transition state (TS) of the reaction catalyzed by human DNMT1. Experimental kinetic isotope effects were used to guide quantum mechanical calculations to solve the TS structure. Methyl transfer occurs after Cys1226 attack to Cyt C6, and the methyl transfer step is chemically rate-limiting for DNMT1. Electrostatic potential maps were compared for the TS and ground states, providing the electronic basis for interactions between the protein and reactants at the TS. Understanding the TS of DNMT1 demonstrates the possibility of using similar analysis to gain subangstrom geometric insight into the complex reactions of epigenetic modifications.

AB - Human DNA methyltransferase 1 (DNMT1) maintains the epigenetic state of DNA by replicating CpG methylation signatures from parent to daughter strands, producing heritable methylation patterns through cell divisions. The proposed catalytic mechanism of DNMT1 involves nucleophilic attack of Cys1226 to cytosine (Cyt) C6, methyl transfer from S-adenosyl-L-methionine (SAM) to Cyt C5, and proton abstraction from C5 to form methylated CpG in DNA. Here, we report the subangstrom geometric and electrostatic structure of the major transition state (TS) of the reaction catalyzed by human DNMT1. Experimental kinetic isotope effects were used to guide quantum mechanical calculations to solve the TS structure. Methyl transfer occurs after Cys1226 attack to Cyt C6, and the methyl transfer step is chemically rate-limiting for DNMT1. Electrostatic potential maps were compared for the TS and ground states, providing the electronic basis for interactions between the protein and reactants at the TS. Understanding the TS of DNMT1 demonstrates the possibility of using similar analysis to gain subangstrom geometric insight into the complex reactions of epigenetic modifications.

KW - 5-methylcytosine

KW - CpG methylation

KW - DNA methyltransferase

KW - S-adenosyl-L-methionine

KW - Transition state

UR - http://www.scopus.com/inward/record.url?scp=84961778159&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=84961778159&partnerID=8YFLogxK

U2 - 10.1073/pnas.1522491113

DO - 10.1073/pnas.1522491113

M3 - Article

VL - 113

SP - 2916

EP - 2921

JO - Proceedings of the National Academy of Sciences of the United States of America

JF - Proceedings of the National Academy of Sciences of the United States of America

SN - 0027-8424

IS - 11

ER -