Identification of a conserved α-helical domain at the N terminus of human DNA methyltransferase 1

Hu, Qi; Botuyan, Maria Victoria; Mer, Georges

doi:10.1016/j.jbc.2024.105775

Title: Identification of a conserved α-helical domain at the N terminus of human DNA methyltransferase 1

Journal Article · 01 March 2024 · Journal of Biological Chemistry

DOI: https://doi.org/10.1016/j.jbc.2024.105775 · OSTI ID:2326139

Hu, Qi; Botuyan, Maria Victoria; Mer, Georges

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Sponsoring Organization:: USDOE Office of Science (SC), Biological and Environmental Research (BER)

OSTI ID:: 2326139

Journal Information:: Journal of Biological Chemistry, Journal Name: Journal of Biological Chemistry Vol. 300 Journal Issue: 3; ISSN 0021-9258

Publisher:: ElsevierCopyright Statement

Country of Publication:: United States

Language:: English

References (57)

In vivo stabilization of the Dnmt1 (cytosine-5)- methyltransferase protein Ding, Feng; Chaillet, J. Richard Proceedings of the National Academy of Sciences, Vol. 99, Issue 23 https://doi.org/10.1073/pnas.232565599	journal	October 2002
The Replication Focus Targeting Sequence (RFTS) Domain Is a DNA-competitive Inhibitor of Dnmt1 Syeda, Farisa; Fagan, Rebecca L.; Wean, Matthew Journal of Biological Chemistry, Vol. 286, Issue 17 https://doi.org/10.1074/jbc.M110.209882	journal	April 2011
Alignment of Biological Macromolecules in Novel Nonionic Liquid Crystalline Media for NMR Experiments Rückert, Markus; Otting, Gottfried Journal of the American Chemical Society, Vol. 122, Issue 32 https://doi.org/10.1021/ja001068h	journal	August 2000
Regulation of SNAIL1 and E-cadherin function by DNMT1 in a DNA methylation-independent context Espada, Jesús; Peinado, Hector; Lopez-Serra, Lidia Nucleic Acids Research, Vol. 39, Issue 21 https://doi.org/10.1093/nar/gkr658	journal	August 2011
DNA methylation: an epigenetic mark of cellular memory Kim, Mirang; Costello, Joseph Experimental & Molecular Medicine, Vol. 49, Issue 4 https://doi.org/10.1038/emm.2017.10	journal	April 2017
Determination of protein oligomeric structure from small-angle X-ray scattering: Determination of Protein Oligomeric Structure from SAXS Korasick, David A.; Tanner, John J. Protein Science, Vol. 27, Issue 4 https://doi.org/10.1002/pro.3376	journal	February 2018
Accurate prediction of protein structures and interactions using a three-track neural network Baek, Minkyung; DiMaio, Frank; Anishchenko, Ivan Science, Vol. 373, Issue 6557 https://doi.org/10.1126/science.abj8754	journal	July 2021
NMR: prediction of molecular alignment from structure using the PALES software Zweckstetter, Markus Nature Protocols, Vol. 3, Issue 4 https://doi.org/10.1038/nprot.2008.36	journal	March 2008
DNMT1 reads heterochromatic H4K20me3 to reinforce LINE-1 DNA methylation Ren, Wendan; Fan, Huitao; Grimm, Sara A. Nature Communications, Vol. 12, Issue 1 https://doi.org/10.1038/s41467-021-22665-4	journal	May 2021
Defects of mutant DNMT1 are linked to a spectrum of neurological disorders Baets, Jonathan; Duan, Xiaohui; Wu, Yanhong Brain, Vol. 138, Issue 4 https://doi.org/10.1093/brain/awv010	journal	February 2015
NMR spectroscopy: a multifaceted approach to macromolecular structure Ferentz, Ann E.; Wagner, Gerhard Quarterly Reviews of Biophysics, Vol. 33, Issue 1 https://doi.org/10.1017/S0033583500003589	journal	February 2000
Structural Basis for the Recognition of DNA Repair Proteins UNG2, XPA, and RAD52 by Replication Factor RPA Mer, Georges; Bochkarev, Alexey; Gupta, Rajesh Cell, Vol. 103, Issue 3 https://doi.org/10.1016/S0092-8674(00)00136-7	journal	October 2000
Structure of the Dnmt1 Reader Module Complexed with a Unique Two-Mono-Ubiquitin Mark on Histone H3 Reveals the Basis for DNA Methylation Maintenance Ishiyama, Satoshi; Nishiyama, Atsuya; Saeki, Yasushi Molecular Cell, Vol. 68, Issue 2 https://doi.org/10.1016/j.molcel.2017.09.037	journal	October 2017
Highly accurate protein structure prediction with AlphaFold Jumper, John; Evans, Richard; Pritzel, Alexander Nature https://doi.org/10.1038/s41586-021-03819-2	journal	July 2021
Crystal Structure of Human DNA Methyltransferase 1 Zhang, Zhi-Min; Liu, Shuo; Lin, Krystal Journal of Molecular Biology, Vol. 427, Issue 15 https://doi.org/10.1016/j.jmb.2015.06.001	journal	July 2015
The Xplor-NIH NMR molecular structure determination package Schwieters, Charles D.; Kuszewski, John J.; Tjandra, Nico Journal of Magnetic Resonance, Vol. 160, Issue 1 https://doi.org/10.1016/S1090-7807(02)00014-9	journal	January 2003
Using Xplor–NIH for NMR molecular structure determination Schwieters, C.; Kuszewski, J.; Mariusclore, G. Progress in Nuclear Magnetic Resonance Spectroscopy, Vol. 48, Issue 1 https://doi.org/10.1016/j.pnmrs.2005.10.001	journal	March 2006
The Amino-Terminus of Mouse DNA Methyltransferase 1 Forms an Independent Domain and Binds to DNA with the Sequence Involving PCNA Binding Motif Suetake, Isao; Hayata, Daichika; Tajima, Shoji The Journal of Biochemistry, Vol. 140, Issue 6 https://doi.org/10.1093/jb/mvj210	journal	December 2006
Biochemical Studies and Molecular Dynamic Simulations Reveal the Molecular Basis of Conformational Changes in DNA Methyltransferase-1 Ye, Fei; Kong, Xiangqian; Zhang, Hao ACS Chemical Biology, Vol. 13, Issue 3 https://doi.org/10.1021/acschembio.7b00890	journal	January 2018
DALI shines a light on remote homologs: One hundred discoveries Holm, Liisa; Laiho, Aleksi; Törönen, Petri Protein Science, Vol. 32, Issue 1 https://doi.org/10.1002/pro.4519	journal	December 2022
Function and information content of DNA methylation Schübeler, Dirk Nature, Vol. 517, Issue 7534 https://doi.org/10.1038/nature14192	journal	January 2015
DNMT1 binds HDAC2 and a new co-repressor, DMAP1, to form a complex at replication foci Rountree, Michael R.; Bachman, Kurtis E.; Baylin, Stephen B. Nature Genetics, Vol. 25, Issue 3 https://doi.org/10.1038/77023	journal	July 2000
DNA methylation and DNA methyltransferases Edwards, John R.; Yarychkivska, Olya; Boulard, Mathieu Epigenetics & Chromatin, Vol. 10, Issue 1 https://doi.org/10.1186/s13072-017-0130-8	journal	May 2017
Protein folding intermediates: native-state hydrogen exchange Bai, Y.; Sosnick, T.; Mayne, L. Science, Vol. 269, Issue 5221 https://doi.org/10.1126/science.7618079	journal	July 1995
DNMT1 mutation hot spot causes varied phenotypes of HSAN1 with dementia and hearing loss Klein, Christopher J.; Bird, Tom; Ertekin-Taner, Nilufer Neurology, Vol. 80, Issue 9 https://doi.org/10.1212/WNL.0b013e318284076d	journal	February 2013
Characterization of Dnmt1 Binding and DNA Methylation on Nucleosomes and Nucleosomal Arrays Schrader, Anna; Gross, Thomas; Thalhammer, Verena PLOS ONE, Vol. 10, Issue 10 https://doi.org/10.1371/journal.pone.0140076	journal	October 2015
New concepts in DNA methylation Jeltsch, Albert; Jurkowska, Renata Z. Trends in Biochemical Sciences, Vol. 39, Issue 7 https://doi.org/10.1016/j.tibs.2014.05.002	journal	July 2014
FoXS: a web server for rapid computation and fitting of SAXS profiles Schneidman-Duhovny, D.; Hammel, M.; Sali, A. Nucleic Acids Research, Vol. 38, Issue Web Server https://doi.org/10.1093/nar/gkq461	journal	May 2010
Structural basis for activation of DNMT1 Kikuchi, Amika; Onoda, Hiroki; Yamaguchi, Kosuke Nature Communications, Vol. 13, Issue 1 https://doi.org/10.1038/s41467-022-34779-4	journal	November 2022
New developments in the ATSAS program package for small-angle scattering data analysis Petoukhov, Maxim V.; Franke, Daniel; Shkumatov, Alexander V. Journal of Applied Crystallography, Vol. 45, Issue 2 https://doi.org/10.1107/S0021889812007662	journal	March 2012
Structural Dynamics of PMP-D2: An Experimental and Theoretical Study^, Mer, Georges; Dejaegere, Annick; Stote, Roland The Journal of Physical Chemistry, Vol. 100, Issue 7 https://doi.org/10.1021/jp9528368	journal	January 1996
Backbone Dynamics of a Free and a Phosphopeptide-Complexed Src Homology 2 Domain Studied by 15N NMR Relaxation Farrow, Neil A.; Muhandiram, Ranjith; Singer, Alex U. Biochemistry, Vol. 33, Issue 19 https://doi.org/10.1021/bi00185a040	journal	May 1994
TALOS+: a hybrid method for predicting protein backbone torsion angles from NMR chemical shifts Shen, Yang; Delaglio, Frank; Cornilescu, Gabriel Journal of Biomolecular NMR, Vol. 44, Issue 4 https://doi.org/10.1007/s10858-009-9333-z	journal	June 2009
Non-CG Methylation in the Human Genome He, Yupeng; Ecker, Joseph R. Annual Review of Genomics and Human Genetics, Vol. 16, Issue 1 https://doi.org/10.1146/annurev-genom-090413-025437	journal	August 2015
Structural Modeling Using Solution Small-Angle X-ray Scattering (SAXS) Gräwert, Tobias W.; Svergun, Dmitri I. Journal of Molecular Biology, Vol. 432, Issue 9 https://doi.org/10.1016/j.jmb.2020.01.030	journal	April 2020
Improvements to the APBS biomolecular solvation software suite: Improvements to the APBS Software Suite Jurrus, Elizabeth; Engel, Dave; Star, Keith Protein Science, Vol. 27, Issue 1 https://doi.org/10.1002/pro.3280	journal	October 2017
Dali: a network tool for protein structure comparison Holm, Liisa; Sander, Chris Trends in Biochemical Sciences, Vol. 20, Issue 11 https://doi.org/10.1016/S0968-0004(00)89105-7	journal	November 1995
Structural and mechanistic insights into UHRF1-mediated DNMT1 activation in the maintenance DNA methylation Li, Tao; Wang, Linsheng; Du, Yongming Nucleic Acids Research, Vol. 46, Issue 6 https://doi.org/10.1093/nar/gky104	journal	February 2018
Inhibition of Histone Deacetylases Promotes Ubiquitin-Dependent Proteasomal Degradation of DNA Methyltransferase 1 in Human Breast Cancer Cells Zhou, Qun; Agoston, Agoston T.; Atadja, Peter Molecular Cancer Research, Vol. 6, Issue 5 https://doi.org/10.1158/1541-7786.MCR-07-0330	journal	May 2008
NMRPipe: A multidimensional spectral processing system based on UNIX pipes Delaglio, Frank; Grzesiek, Stephan; Vuister, GeertenW. Journal of Biomolecular NMR, Vol. 6, Issue 3 https://doi.org/10.1007/BF00197809	journal	November 1995
Direct Measurement of Distances and Angles in Biomolecules by NMR in a Dilute Liquid Crystalline Medium Tjandra, N. Science, Vol. 278, Issue 5340 https://doi.org/10.1126/science.278.5340.1111	journal	November 1997
Structural insight into maintenance methylation by mouse DNA methyltransferase 1 (Dnmt1) Takeshita, K.; Suetake, I.; Yamashita, E. Proceedings of the National Academy of Sciences, Vol. 108, Issue 22 https://doi.org/10.1073/pnas.1019629108	journal	April 2011
Validation of Protein Structure from Anisotropic Carbonyl Chemical Shifts in a Dilute Liquid Crystalline Phase Cornilescu, Gabriel; Marquardt, John L.; Ottiger, Marcel Journal of the American Chemical Society, Vol. 120, Issue 27 https://doi.org/10.1021/ja9812610	journal	July 1998
Mutations in DNMT1 cause autosomal dominant cerebellar ataxia, deafness and narcolepsy Winkelmann, Juliane; Lin, Ling; Schormair, Barbara Human Molecular Genetics, Vol. 21, Issue 10 https://doi.org/10.1093/hmg/dds035	journal	February 2012
Characterizing flexible and intrinsically unstructured biological macromolecules by SAS using the Porod-Debye law Rambo, Robert P.; Tainer, John A. Biopolymers, Vol. 95, Issue 8 https://doi.org/10.1002/bip.21638	journal	April 2011
Non-catalytic functions of DNMT1 Espada, Jesús Epigenetics, Vol. 7, Issue 2 https://doi.org/10.4161/epi.7.2.18756	journal	February 2012
Direct readout of heterochromatic H3K9me3 regulates DNMT1-mediated maintenance DNA methylation Ren, Wendan; Fan, Huitao; Grimm, Sara A. Proceedings of the National Academy of Sciences, Vol. 117, Issue 31 https://doi.org/10.1073/pnas.2009316117	journal	July 2020
MPP8 mediates the interactions between DNA methyltransferase Dnmt3a and H3K9 methyltransferase GLP/G9a Chang, Yanqi; Sun, Lidong; Kokura, Kenji Nature Communications, Vol. 2, Issue 1 https://doi.org/10.1038/ncomms1549	journal	September 2011
Structure of DNMT1-DNA Complex Reveals a Role for Autoinhibition in Maintenance DNA Methylation Song, J.; Rechkoblit, O.; Bestor, T. H. Science, Vol. 331, Issue 6020 https://doi.org/10.1126/science.1195380	journal	December 2010
Improved accuracy of 15N–1H scalar and residual dipolar couplings from gradient-enhanced IPAP-HSQC experiments on protonated proteins Yao, Lishan; Ying, Jinfa; Bax, Ad Journal of Biomolecular NMR, Vol. 43, Issue 3 https://doi.org/10.1007/s10858-009-9299-x	journal	February 2009
Increased Protein Stability Causes DNA Methyltransferase 1 Dysregulation in Breast Cancer Agoston, Agoston T.; Argani, Pedram; Yegnasubramanian, Srinivasan Journal of Biological Chemistry, Vol. 280, Issue 18 https://doi.org/10.1074/jbc.M501675200	journal	May 2005
Protein lysine methyltransferase G9a acts on non-histone targets Rathert, Philipp; Dhayalan, Arunkumar; Murakami, Marie Nature Chemical Biology, Vol. 4, Issue 6 https://doi.org/10.1038/nchembio.88	journal	April 2008
Theory and Practice of Nuclear spin Relaxation in Proteins Dayie, Kwaku T.; Wagner, Gerhard; Lefèvre, Jean-François Annual Review of Physical Chemistry, Vol. 47, Issue 1 https://doi.org/10.1146/annurev.physchem.47.1.243	journal	October 1996
Solution structure and dynamics of yeast elongin C in complex with a von hippel-lindau peptide 1 1Edited by M. F. Summers Botuyan, Maria Victoria; Mer, Georges; Yi, Gwan-Su Journal of Molecular Biology, Vol. 312, Issue 1 https://doi.org/10.1006/jmbi.2001.4938	journal	September 2001
Mutations in DNMT1 cause hereditary sensory neuropathy with dementia and hearing loss Klein, Christopher J.; Botuyan, Maria-Victoria; Wu, Yanhong Nature Genetics, Vol. 43, Issue 6 https://doi.org/10.1038/ng.830	journal	May 2011
DNA Methyltransferase 1-associated Protein (DMAP1) Is a Co-repressor That Stimulates DNA Methylation Globally and Locally at Sites of Double Strand Break Repair Lee, Gun E.; Kim, Joo Hee; Taylor, Michael Journal of Biological Chemistry, Vol. 285, Issue 48 https://doi.org/10.1074/jbc.M110.148536	journal	November 2010
Sex-specific exons control DNA methyltransferase in mammalian germ cells Mertineit, Carmen; Yoder, Jeffrey A.; Taketo, Teruko Development, Vol. 125, Issue 5 https://doi.org/10.1242/dev.125.5.889	journal	March 1998

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