The structure of the Thermococcus gammatolerans McrB N-terminal domain reveals a new mode of substrate recognition and specificity among McrB homologs
Abstract
McrBC is a two-component, modification-dependent restriction system that cleaves foreign DNA-containing methylated cytosines. Previous crystallographic studies have shown that Escherichia coli McrB uses a base-flipping mechanism to recognize these modified substrates with high affinity. The side chains stabilizing both the flipped base and the distorted duplex are poorly conserved among McrB homologs, suggesting that other mechanisms may exist for binding modified DNA. In this paper we present the structures of the Thermococcus gammatolerans McrB DNA-binding domain (TgΔ185) both alone and in complex with a methylated DNA substrate at 1.68 and 2.27 Å resolution, respectively. The structures reveal that TgΔ185 consists of a YT521-B homology (YTH) domain, which is commonly found in eukaryotic proteins that bind methylated RNA and is structurally unrelated to the E. coli McrB DNA-binding domain. Structural superposition and co-crystallization further show that TgΔ185 shares a conserved aromatic cage with other YTH domains, which forms the binding pocket for a flipped-out base. Mutational analysis of this aromatic cage supports its role in conferring specificity for the methylated adenines, whereas an extended basic surface present in TgΔ185 facilitates its preferential binding to duplex DNA rather than RNA. Together, these findings establish a new binding mode and specificity among McrBmore »
- Publication Date:
- Research Org.:
- Argonne National Lab. (ANL), Argonne, IL (United States). Advanced Photon Source (APS)
- Sponsoring Org.:
- USDOE Office of Science (SC); National Institutes of Health (NIH)
- OSTI Identifier:
- 1593451
- Grant/Contract Number:
- AC02-06CH11357; GM120242; P41 GM103403; S10 RR029205
- Resource Type:
- Accepted Manuscript
- Journal Name:
- Journal of Biological Chemistry
- Additional Journal Information:
- Journal Volume: 295; Journal Issue: 3; Journal ID: ISSN 0021-9258
- Publisher:
- American Society for Biochemistry and Molecular Biology
- Country of Publication:
- United States
- Language:
- ENGLISH
- Subject:
- 59 BASIC BIOLOGICAL SCIENCES; 37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CHEMISTRY; X-ray crystallography; DNA binding protein; protein-nucleic acid interaction; protein structure; RNA-protein interaction; structural biology; 6-methyladenosine; DNA binding; McrB; restriction system; YTH domain
Citation Formats
Hosford, Christopher J., Bui, Anthony Q., and Chappie, Joshua S. The structure of the Thermococcus gammatolerans McrB N-terminal domain reveals a new mode of substrate recognition and specificity among McrB homologs. United States: N. p., 2019.
Web. doi:10.1074/jbc.RA119.010188.
Hosford, Christopher J., Bui, Anthony Q., & Chappie, Joshua S. The structure of the Thermococcus gammatolerans McrB N-terminal domain reveals a new mode of substrate recognition and specificity among McrB homologs. United States. https://doi.org/10.1074/jbc.RA119.010188
Hosford, Christopher J., Bui, Anthony Q., and Chappie, Joshua S. Tue .
"The structure of the Thermococcus gammatolerans McrB N-terminal domain reveals a new mode of substrate recognition and specificity among McrB homologs". United States. https://doi.org/10.1074/jbc.RA119.010188. https://www.osti.gov/servlets/purl/1593451.
@article{osti_1593451,
title = {The structure of the Thermococcus gammatolerans McrB N-terminal domain reveals a new mode of substrate recognition and specificity among McrB homologs},
author = {Hosford, Christopher J. and Bui, Anthony Q. and Chappie, Joshua S.},
abstractNote = {McrBC is a two-component, modification-dependent restriction system that cleaves foreign DNA-containing methylated cytosines. Previous crystallographic studies have shown that Escherichia coli McrB uses a base-flipping mechanism to recognize these modified substrates with high affinity. The side chains stabilizing both the flipped base and the distorted duplex are poorly conserved among McrB homologs, suggesting that other mechanisms may exist for binding modified DNA. In this paper we present the structures of the Thermococcus gammatolerans McrB DNA-binding domain (TgΔ185) both alone and in complex with a methylated DNA substrate at 1.68 and 2.27 Å resolution, respectively. The structures reveal that TgΔ185 consists of a YT521-B homology (YTH) domain, which is commonly found in eukaryotic proteins that bind methylated RNA and is structurally unrelated to the E. coli McrB DNA-binding domain. Structural superposition and co-crystallization further show that TgΔ185 shares a conserved aromatic cage with other YTH domains, which forms the binding pocket for a flipped-out base. Mutational analysis of this aromatic cage supports its role in conferring specificity for the methylated adenines, whereas an extended basic surface present in TgΔ185 facilitates its preferential binding to duplex DNA rather than RNA. Together, these findings establish a new binding mode and specificity among McrB homologs and expand the biological roles of YTH domains.},
doi = {10.1074/jbc.RA119.010188},
journal = {Journal of Biological Chemistry},
number = 3,
volume = 295,
place = {United States},
year = {Tue Dec 10 00:00:00 EST 2019},
month = {Tue Dec 10 00:00:00 EST 2019}
}
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Works referenced in this record:
Bacteriophage resistance mechanisms
journal, March 2010
- Labrie, Simon J.; Samson, Julie E.; Moineau, Sylvain
- Nature Reviews Microbiology, Vol. 8, Issue 5
Nucleoside triphosphate-dependent restriction enzymes
journal, September 2001
- Dryden, D. T. F.
- Nucleic Acids Research, Vol. 29, Issue 18
Epigenetics: A Landscape Takes Shape
journal, February 2007
- Goldberg, Aaron D.; Allis, C. David; Bernstein, Emily
- Cell, Vol. 128, Issue 4
Hypomethylation of an Expanded FMR1 Allele Is Not Associated with a Global DNA Methylation Defect
journal, November 1999
- Burman, Robert W.; Yates, Phillip A.; Green, Lindsay D.
- The American Journal of Human Genetics, Vol. 65, Issue 5
A Mutational Analysis of the PD...D/EXK Motif Suggests That McrC Harbors the Catalytic Center for DNA Cleavage by the GTP-Dependent Restriction Enzyme McrBC from Escherichia coli †
journal, April 2002
- Pieper, Uwe; Pingoud, Alfred
- Biochemistry, Vol. 41, Issue 16
Control of Organ-specific Demethylation by an Element of the T-cell Receptor-α Locus Control Region
journal, January 2000
- Santoso, Buyung; Ortiz, Benjamin D.; Winoto, Astar
- Journal of Biological Chemistry, Vol. 275, Issue 3
DNA N6-methyladenine in metazoans: functional epigenetic mark or bystander?
journal, June 2017
- Luo, Guan-Zheng; He, Chuan
- Nature Structural & Molecular Biology, Vol. 24, Issue 6
The GTP-binding Domain of McrB: More Than Just a Variation on a Common Theme?
journal, September 1999
- Pieper, Uwe; Schweitzer, Thomas; Groll, Detlef H.
- Journal of Molecular Biology, Vol. 292, Issue 3
Structural basis for selective binding of m6A RNA by the YTHDC1 YTH domain
journal, September 2014
- Xu, Chao; Wang, Xiao; Liu, Ke
- Nature Chemical Biology, Vol. 10, Issue 11
The McrBC endonuclease translocates DNA in a reaction dependent on GTP hydrolysis 1 1Edited by J. Karn
journal, July 1999
- Panne, Daniel; Raleigh, Elisabeth A.; Bickle, Thomas A.
- Journal of Molecular Biology, Vol. 290, Issue 1
Understanding m6A Function Through Uncovering the Diversity Roles of YTH Domain-Containing Proteins
journal, January 2019
- Zhao, Y. L.; Liu, Y. H.; Wu, R. F.
- Molecular Biotechnology, Vol. 61, Issue 5
RNA-Methylation-Dependent RNA Processing Controls the Speed of the Circadian Clock
journal, November 2013
- Fustin, Jean-Michel; Doi, Masao; Yamaguchi, Yoshiaki
- Cell, Vol. 155, Issue 4
Dali server: conservation mapping in 3D
journal, May 2010
- Holm, Liisa; Rosenstr�m, P�ivi
- Nucleic Acids Research, Vol. 38, Issue suppl_2
A Type IV Modification Dependent Restriction Nuclease that Targets Glucosylated Hydroxymethyl Cytosine Modified DNAs
journal, February 2007
- Bair, Catherine L.; Black, Lindsay W.
- Journal of Molecular Biology, Vol. 366, Issue 3
Crystal structure of the YTH domain of YTHDF2 reveals mechanism for recognition of N6-methyladenosine
journal, November 2014
- Zhu, Tingting; Roundtree, Ian A.; Wang, Ping
- Cell Research, Vol. 24, Issue 12
DNA methyltransferases and epigenetic regulation in bacteria
journal, July 2016
- Adhikari, Satish; Curtis, Patrick D.
- FEMS Microbiology Reviews, Vol. 40, Issue 5
Anomalous diffraction in crystallographic phase evaluation
journal, February 2014
- Hendrickson, Wayne A.
- Quarterly Reviews of Biophysics, Vol. 47, Issue 1
DNA base repair – recognition and initiation of catalysis
journal, November 2009
- Dalhus, Bjørn; Laerdahl, Jon K.; Backe, Paul H.
- FEMS Microbiology Reviews, Vol. 33, Issue 6
Characterization of Natronobacterium magadii phage ΦCh1, a unique archaeal phage containing DNA and RNA
journal, January 1997
- Witte, Angela; Baranyi, Ulrike; Klein, Reinhard
- Molecular Microbiology, Vol. 23, Issue 3
A rapid, PCR based test for differential molecular diagnosis of Prader-Willi and Angelman syndromes.
journal, June 1998
- Chotai, K. A.; Payne, S. J.
- Journal of Medical Genetics, Vol. 35, Issue 6
Molecular basis for the recognition of methylated adenines in RNA by the eukaryotic YTH domain
journal, September 2014
- Luo, S.; Tong, L.
- Proceedings of the National Academy of Sciences, Vol. 111, Issue 38
N6-Methyladenine DNA Modification in the Human Genome
journal, July 2018
- Xiao, Chuan-Le; Zhu, Song; He, Minghui
- Molecular Cell, Vol. 71, Issue 2
The Phyre2 web portal for protein modeling, prediction and analysis
journal, May 2015
- Kelley, Lawrence A.; Mezulis, Stefans; Yates, Christopher M.
- Nature Protocols, Vol. 10, Issue 6
Structure of the YTH domain of human YTHDF2 in complex with an m6A mononucleotide reveals an aromatic cage for m6A recognition
journal, November 2014
- Li, Fudong; Zhao, Debiao; Wu, Jihui
- Cell Research, Vol. 24, Issue 12
The McrBC restriction endonuclease assembles into a ring structure in the presence of G nucleotides
journal, June 2001
- Panne, D.
- The EMBO Journal, Vol. 20, Issue 12
McrBC: a multisubunit GTP-dependent restriction endonuclease
journal, May 1992
- Sutherland, Ellen; Coe, Linda; Raleigh, Elisabeth A.
- Journal of Molecular Biology, Vol. 225, Issue 2
Nucleic Acid Modifications in Regulation of Gene Expression
journal, January 2016
- Chen, Kai; Zhao, Boxuan Simen; He, Chuan
- Cell Chemical Biology, Vol. 23, Issue 1
The GTP-Dependent Restriction Enzyme McrBC from Escherichia coli Forms High-Molecular Mass Complexes with DNA and Produces a Cleavage Pattern with a Characteristic 10-Base Pair Repeat †
journal, April 2002
- Pieper, Uwe; Groll, Detlef H.; Wünsch, Sandra
- Biochemistry, Vol. 41, Issue 16
The crystal structure of the Helicobacter pylori LlaJI.R1 N-terminal domain provides a model for site-specific DNA binding
journal, June 2018
- Hosford, Christopher J.; Chappie, Joshua S.
- Journal of Biological Chemistry, Vol. 293, Issue 30
Structural and Functional Characterization of the Proteins Responsible for N 6 -Methyladenosine Modification and Recognition
journal, March 2016
- Liu, Ke; Ding, Yumin; Ye, Weiyuan
- Current Protein & Peptide Science, Vol. 17, Issue 4
Structural Basis for the Discriminative Recognition of N 6 -Methyladenosine RNA by the Human YT521-B Homology Domain Family of Proteins
journal, August 2015
- Xu, Chao; Liu, Ke; Ahmed, Hazem
- Journal of Biological Chemistry, Vol. 290, Issue 41
Atomic Structures of the Human Immunophilin FKBP-12 Complexes with FK506 and Rapamycin
journal, January 1993
- Van Duyne, Gregory D.; Standaert, Robert F.; Karplus, P. Andrew
- Journal of Molecular Biology, Vol. 229, Issue 1
Topology of the human and mouse m6A RNA methylomes revealed by m6A-seq
journal, April 2012
- Dominissini, Dan; Moshitch-Moshkovitz, Sharon; Schwartz, Schraga
- Nature, Vol. 485, Issue 7397
UCSF Chimera?A visualization system for exploratory research and analysis
journal, January 2004
- Pettersen, Eric F.; Goddard, Thomas D.; Huang, Conrad C.
- Journal of Computational Chemistry, Vol. 25, Issue 13
Methyl-specific DNA binding by McrBC, a modification-dependent restriction enzyme
journal, May 2000
- Stewart, Fiona J.; Panne, Daniel; Bickle, Thomas A.
- Journal of Molecular Biology, Vol. 298, Issue 4
In vivo genetic exchange of a functional domain from a type II A methylase between lactococcal plasmid pTR2030 and a virulent bacteriophage.
journal, January 1991
- Hill, C.; Miller, L. A.; Klaenhammer, T. R.
- Journal of Bacteriology, Vol. 173, Issue 14
Solution structure of the YTH domain in complex with N6-methyladenosine RNA: a reader of methylated RNA
journal, November 2014
- Theler, Dominik; Dominguez, Cyril; Blatter, Markus
- Nucleic Acids Research, Vol. 42, Issue 22
Biosynthesis and Function of Modified Bases in Bacteria and Their Viruses
journal, May 2016
- Weigele, Peter; Raleigh, Elisabeth A.
- Chemical Reviews, Vol. 116, Issue 20
Conflicts Targeting Epigenetic Systems and Their Resolution by Cell Death: Novel Concepts for Methyl-Specific and Other Restriction Systems
journal, November 2010
- Ishikawa, K.; Fukuda, E.; Kobayashi, I.
- DNA Research, Vol. 17, Issue 6
Complex restriction enzymes: NTP-driven molecular motors
journal, November 2002
- Bourniquel, Aude A.; Bickle, Thomas A.
- Biochimie, Vol. 84, Issue 11
Rapid Separation of Protein‐Bound DNA from Free DNA Using Nitrocellulose Filters
journal, October 1996
- Papoulas, Ophelia
- Current Protocols in Molecular Biology, Vol. 36, Issue 1
Defining the Location and Function of Domains of McrB by Deletion Mutagenesis
journal, January 1999
- Pieper, Uwe; Schweitzer, Thomas; Groll, Detlef H.
- Biological Chemistry, Vol. 380, Issue 10
Characterization of PvuRts1I endonuclease as a tool to investigate genomic 5–hydroxymethylcytosine
journal, March 2011
- Szwagierczak, Aleksandra; Brachmann, Andreas; Schmidt, Christine S.
- Nucleic Acids Research, Vol. 39, Issue 12
A short history of SHELX
journal, December 2007
- Sheldrick, George M.
- Acta Crystallographica Section A Foundations of Crystallography, Vol. 64, Issue 1, p. 112-122
McrB: a prokaryotic protein specifically recognizing DNA containing modified cytosine residues.
journal, June 1995
- Krüger, T.; Wild, C.; Noyer-Weidner, M.
- The EMBO Journal, Vol. 14, Issue 11
N6-methyladenosine-dependent regulation of messenger RNA stability
journal, November 2013
- Wang, Xiao; Lu, Zhike; Gomez, Adrian
- Nature, Vol. 505, Issue 7481
SNDV, a Novel Virus of the Extremely Thermophilic and Acidophilic Archaeon Sulfolobus
journal, July 2000
- Arnold, Hans Peter; Ziese, Ulrike; Zillig, Wolfram
- Virology, Vol. 272, Issue 2
High-Resolution Mapping Reveals a Conserved, Widespread, Dynamic mRNA Methylation Program in Yeast Meiosis
journal, December 2013
- Schwartz, Schraga; Agarwala, Sudeep D.; Mumbach, Maxwell R.
- Cell, Vol. 155, Issue 6
A novel RNA-binding mode of the YTH domain reveals the mechanism for recognition of determinant of selective removal by Mmi1
journal, December 2015
- Wang, Chongyuan; Zhu, Yuwei; Bao, Hongyu
- Nucleic Acids Research, Vol. 44, Issue 2
Features and development of Coot
journal, March 2010
- Emsley, P.; Lohkamp, B.; Scott, W. G.
- Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 4
A novel nucleoid-associated protein specific to the actinobacteria
journal, February 2013
- Swiercz, Julia P.; Nanji, Tamiza; Gloyd, Melanie
- Nucleic Acids Research, Vol. 41, Issue 7
PHENIX: a comprehensive Python-based system for macromolecular structure solution
journal, January 2010
- Adams, Paul D.; Afonine, Pavel V.; Bunkóczi, Gábor
- Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 2, p. 213-221
The Recognition of Methylated DNA by the GTP-Dependent Restriction Endonuclease McrBC Resides in the N-Terminal Domain of Mcr B
journal, January 1997
- Gast, Frank-Ulrich; Brinkmann, Thilo; Pieper, Uwe
- Biological Chemistry, Vol. 378, Issue 9
Thermococcus gammatolerans sp. nov., a hyperthermophilic archaeon from a deep-sea hydrothermal vent that resists ionizing radiation
journal, May 2003
- Jolivet, E.
- INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, Vol. 53, Issue 3
Improvements to the APBS biomolecular solvation software suite: Improvements to the APBS Software Suite
journal, October 2017
- Jurrus, Elizabeth; Engel, Dave; Star, Keith
- Protein Science, Vol. 27, Issue 1
Comparative characterization of the PvuRts1I family of restriction enzymes and their application in mapping genomic 5-hydroxymethylcytosine
journal, August 2011
- Wang, Hua; Guan, Shengxi; Quimby, Aine
- Nucleic Acids Research, Vol. 39, Issue 21
The YTH Domain Is a Novel RNA Binding Domain
journal, February 2010
- Zhang, Zhaiyi; Theler, Dominik; Kaminska, Katarzyna H.
- Journal of Biological Chemistry, Vol. 285, Issue 19
The other face of restriction: modification-dependent enzymes
journal, August 2013
- Loenen, Wil A. M.; Raleigh, Elisabeth A.
- Nucleic Acids Research, Vol. 42, Issue 1
A Nonhereditary, Host-Induced Variation of Bacterial Viruses1
journal, January 1952
- Luria, S. E.; Human, Mary L.
- Journal of Bacteriology, Vol. 64, Issue 4
Genome-scale DNA methylation analysis
journal, February 2010
- Fouse, Shaun D.; Nagarajan, Raman P.; Costello, Joseph F.
- Epigenomics, Vol. 2, Issue 1
YTH Domain: A Family of N 6 -methyladenosine (m 6 A) Readers
journal, April 2018
- Liao, Shanhui; Sun, Hongbin; Xu, Chao
- Genomics, Proteomics & Bioinformatics, Vol. 16, Issue 2
Characterization of the 5-hydroxymethylcytosine-specific DNA restriction endonucleases
journal, March 2013
- Borgaro, J. G.; Zhu, Z.
- Nucleic Acids Research, Vol. 41, Issue 7
The recognition domain of the methyl-specific endonuclease McrBC flips out 5-methylcytosine
journal, May 2012
- Sukackaite, Rasa; Grazulis, Saulius; Tamulaitis, Gintautas
- Nucleic Acids Research, Vol. 40, Issue 15
The archaeal halophilic virus-encoded Dam-like methyltransferase M.phiCh1-I methylates adenine residues and complements dam mutants in the low salt environment of Escherichia coli
journal, March 2000
- Baranyi, U.; Klein, R.; Lubitz, W.
- Molecular Microbiology, Vol. 35, Issue 5
Recognition of modified cytosine variants by the DNA‐binding domain of methyl‐directed endonuclease McrBC
journal, September 2018
- Zagorskaitė, Evelina; Manakova, Elena; Sasnauskas, Giedrius
- FEBS Letters, Vol. 592, Issue 19
Emerging Roles of DNA Glycosylases and the Base Excision Repair Pathway
journal, September 2019
- Mullins, Elwood A.; Rodriguez, Alyssa A.; Bradley, Noah P.
- Trends in Biochemical Sciences, Vol. 44, Issue 9
IMG/M: integrated genome and metagenome comparative data analysis system
journal, October 2016
- Chen, I-Min A.; Markowitz, Victor M.; Chu, Ken
- Nucleic Acids Research, Vol. 45, Issue D1
Phaser crystallographic software
journal, July 2007
- McCoy, Airlie J.; Grosse-Kunstleve, Ralf W.; Adams, Paul D.
- Journal of Applied Crystallography, Vol. 40, Issue 4
Restriction and modification in Bacillus subtilis: sequence specificities of restriction/modification systems BsuM, BsuE, and BsuF.
journal, January 1983
- Jentsch, S.
- Journal of Bacteriology, Vol. 156, Issue 2
PARP1 exhibits enhanced association and catalytic efficiency with γH2A.X-nucleosome
journal, December 2019
- Sharma, Deepti; De Falco, Louis; Padavattan, Sivaraman
- Nature Communications, Vol. 10, Issue 1
Cavin1 intrinsically disordered domains are essential for fuzzy electrostatic interactions and caveola formation
journal, February 2021
- Tillu, Vikas A.; Rae, James; Gao, Ya
- Nature Communications, Vol. 12, Issue 1
Rapid Separation of Protein‐Bound DNA from Free DNA Using Nitrocellulose Filters: DNA‐Protein Interactions
journal, July 1988
- Papoulas, Ophelia
- Current Protocols in Molecular Biology, Vol. 3, Issue 1
Solution structure of the YTH domain in complex with N6-methyladenosine RNA: A reader of methylated RNA
text, January 2014
- Theler, Dominik; Dominguez, Cyril; Blatter, Markus
- ETH Zurich
PHENIX: a comprehensive Python-based system for macromolecular structure solution.
text, January 2010
- Adams, Paul D.; Afonine, Pavel V.; Bunkóczi, Gábor
- Apollo - University of Cambridge Repository
Recognition of modified cytosine variants by the DNA-binding domain of methyl-directed endonuclease McrBC
text, January 2018
- Zagorskaitė, Evelina; Manakova, Elena; Sasnauskas, Giedrius
- Deutsches Elektronen-Synchrotron, DESY, Hamburg
Improvements to the APBS biomolecular solvation software suite
text, January 2017
- Jurrus, Elizabeth; Engel, Dave; Star, Keith
- arXiv
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- Nature Communications, Vol. 11, Issue 1