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Xiaodong Cheng

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Publications

TOP 3
Yiwei Liu; Xing Zhang; Robert Blumenthal; Xiaodong Cheng
A common mode of recognition for methylated CpG.
Hideharu Hashimoto; Xing Zhang; Xiaodong Cheng
Selective excision of 5-carboxylcytosine by a thymine DNA glycosylase mutant.
Yiwei Liu; Hiroyuki Sasaki; Hidehiro Toh; Xing Zhang; Xiaodong Cheng
An atomic model of Zfp57 recognition of CpG methylation within a specific DNA sequence.

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All Publications

2013: Yiwei Liu; Xing Zhang; Robert Blumenthal; Xiaodong Cheng
A common mode of recognition for methylated CpG.
Trends in biochemical sciences 2013;38(4):177-83.
2013: Hideharu Hashimoto; Xing Zhang; Xiaodong Cheng
Selective excision of 5-carboxylcytosine by a thymine DNA glycosylase mutant.
Journal of molecular biology 2013;425(6):971-6.
2012: Yiwei Liu; Hiroyuki Sasaki; Hidehiro Toh; Xing Zhang; Xiaodong Cheng
An atomic model of Zfp57 recognition of CpG methylation within a specific DNA sequence.
Genes & development 2012;26(21):2374-9.
2012: Hideharu Hashimoto; Samuel Hong; Xing Zhang; Ashok S Bhagwat; Xiaodong Cheng
Excision of 5-hydroxymethyluracil and 5-carboxylcytosine by the thymine DNA glycosylase domain: its structural basis and implications for active DNA demethylation.
Nucleic acids research 2012;40(20):10203-14.
2012: John Horton; Megumu Yamada Mabuchi; Richard J Roberts; Mala Samaranayake; Xing Zhang; Yu Zheng; Devora Cohen-Karni; Rose M Griggs; Xiaodong Cheng
Structure and cleavage activity of the tetrameric MspJI DNA modification-dependent restriction endonuclease.
Nucleic acids research 2012;40(19):9763-73.
2012: Hideharu Hashimoto; Xing Zhang; Xiaodong Cheng
Excision of thymine and 5-hydroxymethyluracil by the MBD4 DNA glycosylase domain: structural basis and implications for active DNA demethylation.
Nucleic acids research 2012;40(17):8276-84.
2012: Hideharu Hashimoto; Shelley B Howerton; Yiwei Liu; Anup K Upadhyay; Paula M Vertino; Xing Zhang; Yanqi Chang; Xiaodong Cheng
Recognition and potential mechanisms for replication and erasure of cytosine hydroxymethylation.
Nucleic acids research 2012;40(11):4841-9.
2012: Anup K Upadhyay; Young-Sup Yoon; Xing Zhang; Yanqi Chang; Ji Woong Han; Ruogu Hu; Donatella Labella; Antonello Mai; dante rotili; Xiaodong Cheng
An analog of BIX-01294 selectively inhibits a family of histone H3 lysine 9 Jumonji demethylases.
Journal of molecular biology 2012;416(3):319-27.
2011: Keith E Szulwach; Anup K Upadhyay; Aparna Vasanthakumar; Hao Wu; Allan Levey; Xuekun Li; Yujing Li; Chun-Xiao Song; Qiang Chang; Xiaodong Cheng; Qing Dai; Marla Gearing; Lucy A Godley; Chuan He; Hasan Irier; Peng Jin
5-hmC-mediated epigenetic dynamics during postnatal neurodevelopment and aging.
Nature neuroscience 2011;14(12):1607-16.
2011: Anup K Upadhyay; Xing Zhang; John Horton; Xiaodong Cheng
Coordinated methyl-lysine erasure: structural and functional linkage of a Jumonji demethylase domain and a reader domain.
Current opinion in structural biology 2011;21(6):750-60.
2011: Jing Zhao; Yan Bai; Joseph T Barbieri; Xiaodong Cheng; Lupei Du; Yuhong Du; John Horton; Fadlo R Khuri; Minyong Li; Bin Lou; Anup K Upadhyay; Binghe Wang; Lixin Zhang; Xing Zhang; Haian Fu
Discovery and structural characterization of a small molecule 14-3-3 protein-protein interaction inhibitor.
Proceedings of the National Academy of Sciences of the United States of America 2011;108(39):16212-6.
2011: Yanqi Chang; Or Gozani; John Horton; Dan Levy; Junmin Peng; Xing Zhang; Xiaodong Cheng
Structural basis of SETD6-mediated regulation of the NF-kB network via methyl-lysine signaling.
Nucleic acids research 2011;39(15):6380-9.
2011: Yanqi Chang; John Horton; Mark T Bedford; Xing Zhang; Xiaodong Cheng
Structural insights for MPP8 chromodomain interaction with histone H3 lysine 9: potential effect of phosphorylation on methyl-lysine binding.
Journal of molecular biology 2011;408(5):807-14.
2011: John Horton; Anup K Upadhyay; Hideharu Hashimoto; Xing Zhang; Xiaodong Cheng
Structural basis for human PHF2 Jumonji domain interaction with metal ions.
Journal of molecular biology 2011;406(1):1-8.
2011: Yanqi Chang; Mark T Bedford; Alexsandra Espejo; Jia Fang; Mikiko Fukuda; John R Horton; Victoria Izumi; Kenji Kokura; John M Koomen; Yoichi Shinkai; Lidong Sun; Xing Zhang; Xiaodong Cheng
MPP8 mediates the interactions between DNA methyltransferase Dnmt3a and H3K9 methyltransferase GLP/G9a.
Nature communications 2011;2():533.
2011: Xiaodong Cheng; Robert M Blumenthal
Introduction--Epiphanies in epigenetics.
Progress in molecular biology and translational science 2011;101():1-21.
2011: Xiaodong Cheng; Robert M Blumenthal
We would like to thank those who made this volume possible. Preface.
Progress in molecular biology and translational science 2011;101():xiii-xiv.
2011: Pierre-Olivier Estève; Yanqi Chang; Mala Samaranayake; Anup K Upadhyay; John R Horton; George R Feehery; Xiaodong Cheng; Sriharsa Pradhan
A methylation and phosphorylation switch between an adjacent lysine and serine determines human DNMT1 stability.
Nature structural & molecular biology 2011;18(1):42-8.
2011: Anup K Upadhyay; Xiaodong Cheng
Dynamics of histone lysine methylation: structures of methyl writers and erasers.
Progress in drug research. Fortschritte der Arzneimittelforschung. Progrès des recherches pharmaceutiques 2011;67():107-24.
2011: Dan Levy; Alex J Kuo; Yanqi Chang; Uwe Schaefer; Christopher Kitson; Peggie Cheung; Alexsandra Espejo; Barry M Zee; Chih Long Liu; Stephanie Tangsombatvisit; Ruth I Tennen; Andrew Y Kuo; Song Tanjing; Regina Cheung; Katrin F Chua; Paul J Utz; Xiaobing Shi; Rab Prinjha; Kevin Lee; Benjamin A Garcia; Mark T Bedford; Alexander Tarakhovsky; Xiaodong Cheng; Or Gozani
Lysine methylation of the NF-κB subunit RelA by SETD6 couples activity of the histone methyltransferase GLP at chromatin to tonic repression of NF-κB signaling.
Nature immunology 2011;12(1):29-36.
2010: Hideharu Hashimoto; Paula M Vertino; Xiaodong Cheng
Molecular coupling of DNA methylation and histone methylation.
Epigenomics 2010;2(5):657-69.
2010: Chung-Fan Lee; Derick S-C Ou; SB Lee; Liang-Hao Chang; Ruo-Kai Lin; Ying-Shiuan Li; Anup K Upadhyay; Xiaodong Cheng; Yi-Ching Wang; Han-Shui Hsu; Michael Hsiao; Cheng-Wen Wu; Li-Jung Juan
hNaa10p contributes to tumorigenesis by facilitating DNMT1-mediated tumor suppressor gene silencing.
The Journal of clinical investigation 2010;120(8):2920-30.
2010: Yanqi Chang; Thota Ganesh; John Horton; Astrid Spannhoff; Jin Liu; Aiming Sun; Xing Zhang; Mark T Bedford; Yoichi Shinkai; James P Snyder; Xiaodong Cheng
Adding a lysine mimic in the design of potent inhibitors of histone lysine methyltransferases.
Journal of molecular biology 2010;400(1):1-7.
2010: Robert Collins; Xiaodong Cheng
A case study in cross-talk: the histone lysine methyltransferases G9a and GLP.
Nucleic acids research 2010;38(11):3503-11.
2010: Xiaodong Cheng; Robert Blumenthal
Coordinated chromatin control: structural and functional linkage of DNA and histone methylation.
Biochemistry 2010;49(14):2999-3008.
2010: John Horton; Anup K Upadhyay; Hank H Qi; Xing Zhang; Yang Shi; Xiaodong Cheng
Enzymatic and structural insights for substrate specificity of a family of jumonji histone lysine demethylases.
Nature structural & molecular biology 2010;17(1):38-43.
2009: Zhen Qian; John Horton; Xiaodong Cheng; Stefan Lutz
Structural redesign of lipase B from Candida antarctica by circular permutation and incremental truncation.
Journal of molecular biology 2009;393(1):191-201.
2009: Tiyu Gao; Robert E Collins; John Horton; Xing Zhang; Rongguang Zhang; Arunkumar Dhayalan; Raluca Tamas; Albert Jeltsch; Xiaodong Cheng
The ankyrin repeat domain of Huntingtin interacting protein 14 contains a surface aromatic cage, a potential site for methyl-lysine binding.
Proteins 2009;76(3):772-7.
2009: Yanqi Chang; Xing Zhang; John Horton; Anup K Upadhyay; Astrid Spannhoff; Jin Liu; James P Snyder; Mark T Bedford; Xiaodong Cheng
Structural basis for G9a-like protein lysine methyltransferase inhibition by BIX-01294.
Nature structural & molecular biology 2009;16(3):312-7.
2009: Hideharu Hashimoto; John Horton; Xing Zhang; Xiaodong Cheng
UHRF1, a modular multi-domain protein, regulates replication-coupled crosstalk between DNA methylation and histone modifications.
Epigenetics : official journal of the DNA Methylation Society 2009;4(1):8-14.
2008: Renata Z Jurkowska; Nils Anspach; Claus Urbanke; Da Jia; Richard Reinhardt; Wolfgang Nellen; Xiaodong Cheng; Albert Jeltsch
Formation of nucleoprotein filaments by mammalian DNA methyltransferase Dnmt3a in complex with regulator Dnmt3L.
Nucleic acids research 2008;36(21):6656-63.
2008: Hideharu Hashimoto; John Horton; Xing Zhang; Magnolia Bostick; Steven E Jacobsen; Xiaodong Cheng
The SRA domain of UHRF1 flips 5-methylcytosine out of the DNA helix.
Nature 2008;455(7214):826-9.
2008: Philipp Rathert; Arunkumar Dhayalan; Marie Murakami; Xing Zhang; Raluca Tamas; Renata Jurkowska; Yasuhiko Komatsu; Yoichi Shinkai; Xiaodong Cheng; Albert Jeltsch
Protein lysine methyltransferase G9a acts on non-histone targets.
Nature chemical biology 2008;4(6):344-6.
2008: Krithika Subramanian; Da Jia; Priya Kapoor-Vazirani; Doris R Powell; Robert E Collins; Dipali Sharma; Junmin Peng; Xiaodong Cheng; Paula M Vertino
Regulation of estrogen receptor alpha by the SET7 lysine methyltransferase.
Molecular cell 2008;30(3):336-47.
2008: Xiaodong Cheng; Robert Blumenthal
Mammalian DNA methyltransferases: a structural perspective.
Structure (London, England : 1993) 2008;16(3):341-50.
2008: Robert E Collins; Jeffrey P Northrop; John Horton; David Y Lee; Xing Zhang; Michael R Stallcup; Xiaodong Cheng
The ankyrin repeats of G9a and GLP histone methyltransferases are mono- and dimethyllysine binding modules.
Nature structural & molecular biology 2008;15(3):245-50.
2008: Arunkumar Dhayalan; Tomasz P Jurkowski; Heike Laser; Richard Reinhardt; Da Jia; Xiaodong Cheng; Albert Jeltsch
Mapping of protein-protein interaction sites by the 'absence of interference' approach.
Journal of molecular biology 2008;376(4):1091-9.
2008: Philipp Rathert; Xing Zhang; Christian Freund; Xiaodong Cheng; Albert Jeltsch
Analysis of the substrate specificity of the Dim-5 histone lysine methyltransferase using peptide arrays.
Chemistry & biology 2008;15(1):5-11.
2007: Tanesha C Osborne; Obiamaka Obianyo; Xing Zhang; Xiaodong Cheng; Paul R Thompson
Protein arginine methyltransferase 1: positively charged residues in substrate peptides distal to the site of methylation are important for substrate binding and catalysis.
Biochemistry 2007;46(46):13370-81.
2007: Philipp Rathert; Xiaodong Cheng; Albert Jeltsch
Continuous enzymatic assay for histone lysine methyltransferases.
BioTechniques 2007;43(5):602, 604, 606 passim.
2007: Da Jia; Renata Z Jurkowska; Xing Zhang; Albert Jeltsch; Xiaodong Cheng
Structure of Dnmt3a bound to Dnmt3L suggests a model for de novo DNA methylation.
Nature 2007;449(7159):248-51.
2007: Fei Lan; Robert E Collins; Rossella De Cegli; Roman Alpatov; John Horton; Xiaobing Shi; Or Gozani; Xiaodong Cheng; Yang Shi
Recognition of unmethylated histone H3 lysine 4 links BHC80 to LSD1-mediated gene repression.
Nature 2007;448(7154):718-22.
2007: Steen K T Ooi; Chen Qiu; Emily Bernstein; Keqin Li; Da Jia; Zhe Yang; Hediye Erdjument-Bromage; Paul Tempst; Shau-Ping Lin; C David Allis; Xiaodong Cheng; Timothy H Bestor
DNMT3L connects unmethylated lysine 4 of histone H3 to de novo methylation of DNA.
Nature 2007;448(7154):714-7.
2007: Kirsten Liebert; John Horton; Sanjay Chahar; Marcella Orwick; Xiaodong Cheng; Albert Jeltsch
Two alternative conformations of S-adenosyl-L-homocysteine bound to Escherichia coli DNA adenine methyltransferase and the implication of conformational changes in regulating the catalytic cycle.
The Journal of biological chemistry 2007;282(31):22848-55.
2007: Ken Higashimoto; Peter Kuhn; Dhaval Desai; Xiaodong Cheng; Wei Xu
Phosphorylation-mediated inactivation of coactivator-associated arginine methyltransferase 1.
Proceedings of the National Academy of Sciences of the United States of America 2007;104(30):12318-23.
2007: David Y Lee; Irina Ianculescu; Daniel J Purcell; Xing Zhang; Xiaodong Cheng; Michael R Stallcup
Surface-scanning mutational analysis of protein arginine methyltransferase 1: roles of specific amino acids in methyltransferase substrate specificity, oligomerization, and coactivator function.
Molecular endocrinology (Baltimore, Md.) 2007;21(6):1381-93.
2007: John Horton; Stuart J Elgar; Seema I Khan; Xing Zhang; Paul A Wade; Xiaodong Cheng
Structure of the SANT domain from the Xenopus chromatin remodeling factor ISWI.
Proteins 2007;67(4):1198-202.
2007: Xiaodong Cheng; Xing Zhang
Structural dynamics of protein lysine methylation and demethylation.
Mutation research 2007;618(1-2):102-15.
2007: Hong Wu; John Horton; Kevin Battaile; Abdellah Allali-Hassani; Fernando Martin; Hong Zeng; Peter Loppnau; Masoud Vedadi; Alexey Bochkarev; Alexander N Plotnikov; Xiaodong Cheng
Structural basis of allele variation of human thiopurine-S-methyltransferase.
Proteins 2007;67(1):198-208.
2006: Robert E Collins; Xiaodong Cheng
Structural and biochemical advances in mammalian RNAi.
Journal of cellular biochemistry 2006;99(5):1251-66.
2006: Jeffrey Mercante; Kazushi Suzuki; Xiaodong Cheng; Paul Babitzke; Tony Romeo
Comprehensive alanine-scanning mutagenesis of Escherichia coli CsrA defines two subdomains of critical functional importance.
The Journal of biological chemistry 2006;281(42):31832-42.
2006: John Horton; Kirsten Liebert; Miklos Bekes; Albert Jeltsch; Xiaodong Cheng
Structure and substrate recognition of the Escherichia coli DNA adenine methyltransferase.
Journal of molecular biology 2006;358(2):559-70.
2006: Francisca E Reyes-Turcu; John Horton; James E Mullally; Annie Heroux; Xiaodong Cheng; Keith Wilkinson
The ubiquitin binding domain ZnF UBP recognizes the C-terminal diglycine motif of unanchored ubiquitin.
Cell 2006;124(6):1197-208.
2006: John Horton; Xing Zhang; Robert Maunus; Zhe Yang; Geoffrey G Wilson; Richard J Roberts; Xiaodong Cheng
DNA nicking by HinP1I endonuclease: bending, base flipping and minor groove expansion.
Nucleic acids research 2006;34(3):939-48.
2005: Robert E Collins; Xiaodong Cheng
Structural domains in RNAi.
FEBS letters 2005;579(26):5841-9.
2005: John Horton; Ken Sawada; Masahiro Nishibori; Xiaodong Cheng
Structural basis for inhibition of histamine N-methyltransferase by diverse drugs.
Journal of molecular biology 2005;353(2):334-44.
2005: humaira gowher; Xing Zhang; Xiaodong Cheng; Albert Jeltsch
Avidin plate assay system for enzymatic characterization of a histone lysine methyltransferase.
Analytical biochemistry 2005;342(2):287-91.
2005: John Horton; Kirsten Liebert; Stanley Hattman; Albert Jeltsch; Xiaodong Cheng
Transition from nonspecific to specific DNA interactions along the substrate-recognition pathway of dam methyltransferase.
Cell 2005;121(3):349-61.
2005: Robert E Collins; Makoto Tachibana; Hisashi Tamaru; Kristina Smith; Da Jia; Xing Zhang; Eric U Selker; Yoichi Shinkai; Xiaodong Cheng
In vitro and in vivo analyses of a Phe/Tyr switch controlling product specificity of histone lysine methyltransferases.
The Journal of biological chemistry 2005;280(7):5563-70.
2005: Juan Carlos Amor; Jennifer Swails; Xinjun Zhu; Craig R Roy; Hiroki Nagai; Alyssa Ingmundson; Xiaodong Cheng; Richard A Kahn
The structure of RalF, an ADP-ribosylation factor guanine nucleotide exchange factor from Legionella pneumophila, reveals the presence of a cap over the active site.
The Journal of biological chemistry 2005;280(2):1392-400.
2005: Shane C Dillon; Xing Zhang; Raymond C Trievel; Xiaodong Cheng
The SET-domain protein superfamily: protein lysine methyltransferases.
Genome biology 2005;6(8):227.
2005: Xiaodong Cheng; Robert E Collins; Xing Zhang
Structural and sequence motifs of protein (histone) methylation enzymes.
Annual review of biophysics and biomolecular structure 2005;34():267-94.
2005: Zhe Yang; John Horton; Robert Maunus; Geoffrey G Wilson; Richard J Roberts; Xiaodong Cheng
Structure of HinP1I endonuclease reveals a striking similarity to the monomeric restriction enzyme MspI.
Nucleic acids research 2005;33(6):1892-901.
2004: Ken Sawada; Zhe Yang; John Horton; Robert E Collins; Xing Zhang; Xiaodong Cheng
Structure of the conserved core of the yeast Dot1p, a nucleosomal histone H3 lysine 79 methyltransferase.
The Journal of biological chemistry 2004;279(41):43296-306.
2004: Zhe Yang; Lance Shipman; Meng Zhang; Brian P Anton; Richard J Roberts; Xiaodong Cheng
Structural characterization and comparative phylogenetic analysis of Escherichia coli HemK, a protein (N5)-glutamine methyltransferase.
Journal of molecular biology 2004;340(4):695-706.
2004: Aiping Dong; Lan Zhou; Xing Zhang; Shawn Stickel; Richard J Roberts; Xiaodong Cheng
Structure of the Q237W mutant of HhaI DNA methyltransferase: an insight into protein-protein interactions.
Biological chemistry 2004;385(5):373-9.
2004: James P Jackson; Lianna Johnson; Zuzana Jasencakova; Xing Zhang; Laura PerezBurgos; Prim B Singh; Xiaodong Cheng; Ingo Schubert; Thomas Jenuwein; Steven E Jacobsen
Dimethylation of histone H3 lysine 9 is a critical mark for DNA methylation and gene silencing in Arabidopsis thaliana.
Chromosoma 2004;112(6):308-15.
2004: John Horton; Gary Ratner; Nilesh K Banavali; Niu Huang; Yongseok Choi; Martin A Maier; Victor E Marquez; Alexander D. Mackerell; Xiaodong Cheng
Caught in the act: visualization of an intermediate in the DNA base-flipping pathway induced by HhaI methyltransferase.
Nucleic acids research 2004;32(13):3877-86.
2003: Zhe Yang; John Horton; Lan Zhou; Xu Jia Zhang; Aiping Dong; Xing Zhang; Samuel L Schlagman; Valeri G Kossykh; Stanley Hattman; Xiaodong Cheng
Structure of the bacteriophage T4 DNA adenine methyltransferase.
Nature structural biology 2003;10(10):849-55.
2003: Xing Zhang; Zhe Yang; Seema I Khan; John Horton; Hisashi Tamaru; Eric U Selker; Xiaodong Cheng
Structural basis for the product specificity of histone lysine methyltransferases.
Molecular cell 2003;12(1):177-85.
2003: Heidi L Schubert; Robert Blumenthal; Xiaodong Cheng
Many paths to methyltransfer: a chronicle of convergence.
Trends in biochemical sciences 2003;28(6):329-35.
2003: Xing Zhang; Xiaodong Cheng
Structure of the predominant protein arginine methyltransferase PRMT1 and analysis of its binding to substrate peptides.
Structure (London, England : 1993) 2003;11(5):509-20.
2003: Hisashi Tamaru; Xing Zhang; Debra McMillen; Prim B Singh; Jun-ichi Nakayama; Shiv I S Grewal; C David Allis; Xiaodong Cheng; Eric U Selker
Trimethylated lysine 9 of histone H3 is a mark for DNA methylation in Neurospora crassa.
Nature genetics 2003;34(1):75-9.
2003: Peiying Wu; Chen Qiu; anjum sohail; Xing Zhang; Ashok S Bhagwat; Xiaodong Cheng
Mismatch repair in methylated DNA. Structure and activity of the mismatch-specific thymine glycosylase domain of methyl-CpG-binding protein MBD4.
The Journal of biological chemistry 2003;278(7):5285-91.
2002: Sarah E Whitehead; Kevin W Jones; Xing Zhang; Xiaodong Cheng; Rebecca M Terns; Michael P Terns
Determinants of the interaction of the spinal muscular atrophy disease protein SMN with the dimethylarginine-modified box H/ACA small nucleolar ribonucleoprotein GAR1.
The Journal of biological chemistry 2002;277(50):48087-93.
2002: Jinrong Min; Xing Zhang; Xiaodong Cheng; Shiv I S Grewal; Rui-Ming Xu
Structure of the SET domain histone lysine methyltransferase Clr4.
Nature structural biology 2002;9(11):828-32.
2002: Xing Zhang; Hisashi Tamaru; Seema I Khan; John Horton; Lisa J Keefe; Eric U Selker; Xiaodong Cheng
Structure of the Neurospora SET domain protein DIM-5, a histone H3 lysine methyltransferase.
Cell 2002;111(1):117-27.
2002: Lan Zhou; Xiaodong Cheng; B A Connolly; Mark J Dickman; Paul Hurd; David P Hornby
Zebularine: a novel DNA methylation inhibitor that forms a covalent complex with DNA methyltransferases.
Journal of molecular biology 2002;321(4):591-9.
2002: Young-Ho Lee; Stephen S Koh; Xing Zhang; Xiaodong Cheng; Michael R Stallcup
Synergy among nuclear receptor coactivators: selective requirement for protein methyltransferase and acetyltransferase activities.
Molecular and cellular biology 2002;22(11):3621-32.
2002: Deanna M Green; Kavita A Marfatia; Emily B Crafton; Xing Zhang; Xiaodong Cheng; Anita H Corbett
Nab2p is required for poly(A) RNA export in Saccharomyces cerevisiae and is regulated by arginine methylation via Hmt1p.
The Journal of biological chemistry 2002;277(10):7752-60.
2002: Chen Qiu; Ken Sawada; Xing Zhang; Xiaodong Cheng
The PWWP domain of mammalian DNA methyltransferase Dnmt3b defines a new family of DNA-binding folds.
Nature structural biology 2002;9(3):217-24.
2002: Xiaodong Cheng; Robert Blumenthal
Cytosines do it, thymines do it, even pseudouridines do it--base flipping by an enzyme that acts on RNA.
Structure (London, England : 1993) 2002;10(2):127-9.
2001: Juan Carlos Amor; John Horton; Xinjun Zhu; Yuhuan Wang; C Sullards; D Ringe; Xiaodong Cheng; Richard A Kahn
Structures of yeast ARF2 and ARL1: distinct roles for the N terminus in the structure and function of ARF family GTPases.
The Journal of biological chemistry 2001;276(45):42477-84.
2001: Xiaodong Cheng; Richard J Roberts
AdoMet-dependent methylation, DNA methyltransferases and base flipping.
Nucleic acids research 2001;29(18):3784-95.
2001: John Horton; Ken Sawada; M Nishibori; Xing Zhang; Xiaodong Cheng
Two polymorphic forms of human histamine methyltransferase: structural, thermal, and kinetic comparisons.
Structure (London, England : 1993) 2001;9(9):837-49.
2001: Robert Blumenthal; Xiaodong Cheng
A Taq attack displaces bases.
Nature structural biology 2001;8(2):101-3.
2001: A Dong; Jeffrey A Yoder; Xing Zhang; L Zhou; Timothy H Bestor; Xiaodong Cheng
Structure of human DNMT2, an enigmatic DNA methyltransferase homolog that displays denaturant-resistant binding to DNA.
Nucleic acids research 2001;29(2):439-48.
2000: Giedrius Vilkaitis; A Dong; Elmar Weinhold; Xiaodong Cheng; Saulius Klimasauskas
Functional roles of the conserved threonine 250 in the target recognition domain of HhaI DNA methyltransferase.
The Journal of biological chemistry 2000;275(49):38722-30.
2000: John Horton; Xiaodong Cheng
PvuII endonuclease contains two calcium ions in active sites.
Journal of molecular biology 2000;300(5):1049-56.
2000: Xing Zhang; Lan Zhou; Xiaodong Cheng
Crystal structure of the conserved core of protein arginine methyltransferase PRMT3.
The EMBO journal 2000;19(14):3509-19.
1999: Y Liu; W Gong; C C Huang; Winship Herr; Xiaodong Cheng
Crystal structure of the conserved core of the herpes simplex virus transcriptional regulatory protein VP16.
Genes & development 1999;13(13):1692-703.
1999: Margaret M O'gara; Xing Zhang; Richard J Roberts; Xiaodong Cheng
Structure of a binary complex of HhaI methyltransferase with S-adenosyl-L-methionine formed in the presence of a short non-specific DNA oligonucleotide.
Journal of molecular biology 1999;287(2):201-9.
1999: G Sheikhnejad; Adam S Brank; Judith K Christman; A Goddard; E Alvarez; H Ford; Victor E Marquez; Canio J Marasco; Janice R Sufrin; Margaret M O'gara; Xiaodong Cheng
Mechanism of inhibition of DNA (cytosine C5)-methyltransferases by oligodeoxyribonucleotides containing 5,6-dihydro-5-azacytosine.
Journal of molecular biology 1999;285(5):2021-34.
1998: John Horton; H G Nastri; Paul Riggs; Xiaodong Cheng
Asp34 of PvuII endonuclease is directly involved in DNA minor groove recognition and indirectly involved in catalysis.
Journal of molecular biology 1998;284(5):1491-504.
1998: Margaret M O'gara; John Horton; Richard J Roberts; Xiaodong Cheng
Structures of HhaI methyltransferase complexed with substrates containing mismatches at the target base.
Nature structural biology 1998;5(10):872-7.
1998: John Horton; J Bonventre; Xiaodong Cheng
How is modification of the DNA substrate recognized by the PvuII restriction endonuclease?
Biological chemistry 1998;379(4-5):451-8.
1998: Richard J Roberts; Xiaodong Cheng
Base flipping.
Annual review of biochemistry 1998;67():181-98.
1997: Margaret M O'gara; G M Adams; W Gong; R Kobayashi; Robert Blumenthal; Xiaodong Cheng
Expression, purification, mass spectrometry, crystallization and multiwavelength anomalous diffraction of selenomethionyl PvuII DNA methyltransferase (cytosine-N4-specific).
European journal of biochemistry / FEBS 1997;247(3):1009-18.
1997: S Kumar; John Horton; G D Jones; R T Walker; Richard J Roberts; Xiaodong Cheng
DNA containing 4'-thio-2'-deoxycytidine inhibits methylation by HhaI methyltransferase.
Nucleic acids research 1997;25(14):2773-83.
1997: W Gong; Margaret M O'gara; Robert Blumenthal; Xiaodong Cheng
Structure of pvu II DNA-(cytosine N4) methyltransferase, an example of domain permutation and protein fold assignment.
Nucleic acids research 1997;25(14):2702-15.
1997: Rui-Ming Xu; L Jokhan; Xiaodong Cheng; A Mayeda; Adrian R Krainer
Crystal structure of human UP1, the domain of hnRNP A1 that contains two RNA-recognition motifs.
Structure (London, England : 1993) 1997;5(4):559-70.
1997: R M Xu; C Koch; Y Liu; John Horton; D Knapp; K Nasmyth; Xiaodong Cheng
Crystal structure of the DNA-binding domain of Mbp1, a transcription factor important in cell-cycle control of DNA synthesis.
Structure (London, England : 1993) 1997;5(3):349-58.
1997: R Stephen Lloyd; Xiaodong Cheng
Mechanistic link between DNA methyltransferases and DNA repair enzymes by base flipping.
Biopolymers 1997;44(2):139-51.
1996: Margaret M O'gara; Richard J Roberts; Xiaodong Cheng
A structural basis for the preferential binding of hemimethylated DNA by HhaI DNA methyltransferase.
Journal of molecular biology 1996;263(4):597-606.
1996: Margaret M O'gara; Saulius Klimasauskas; Richard J Roberts; Xiaodong Cheng
Enzymatic C5-cytosine methylation of DNA: mechanistic implications of new crystal structures for HhaL methyltransferase-DNA-AdoHcy complexes.
Journal of molecular biology 1996;261(5):634-45.
1996: Rui-Ming Xu; G Carmel; Jeffrey Kuret; Xiaodong Cheng
Structural basis for selectivity of the isoquinoline sulfonamide family of protein kinase inhibitors.
Proceedings of the National Academy of Sciences of the United States of America 1996;93(13):6308-13.
1996: Xiaodong Cheng; Robert Blumenthal
Finding a basis for flipping bases.
Structure (London, England : 1993) 1996;4(6):639-45.
1995: T Malone; Robert Blumenthal; Xiaodong Cheng
Structure-guided analysis reveals nine sequence motifs conserved among DNA amino-methyltransferases, and suggests a catalytic mechanism for these enzymes.
Journal of molecular biology 1995;253(4):618-32.
1995: Xiaodong Cheng; K Balendiran; Schildkraut Ira; J E Anderson
Crystal structure of the PvuII restriction endonuclease.
Gene 1995;157(1-2):139-40.
1995: Margaret M O'gara; K McCloy; T Malone; Xiaodong Cheng
Structure-based sequence alignment of three AdoMet-dependent DNA methyltransferases.
Gene 1995;157(1-2):135-8.
1995: G Schluckebier; Margaret M O'gara; Wolfram Saenger; Xiaodong Cheng
Universal catalytic domain structure of AdoMet-dependent methyltransferases.
Journal of molecular biology 1995;247(1):16-20.
1995: Rui-Ming Xu; G Carmel; R M Sweet; Jeffrey Kuret; Xiaodong Cheng
Crystal structure of casein kinase-1, a phosphate-directed protein kinase.
The EMBO journal 1995;14(5):1015-23.
1995: Xiaodong Cheng
DNA modification by methyltransferases.
Current opinion in structural biology 1995;5(1):4-10.
1995: Xiaodong Cheng
Structure and function of DNA methyltransferases.
Annual review of biophysics and biomolecular structure 1995;24():293-318.
1994: Xiaodong Cheng; K Balendiran; Schildkraut Ira; J E Anderson
Structure of PvuII endonuclease with cognate DNA.
The EMBO journal 1994;13(17):3927-35.
1994: Xiaodong Cheng; X Zhang; J W Pflugrath; F W Studier
The structure of bacteriophage T7 lysozyme, a zinc amidase and an inhibitor of T7 RNA polymerase.
Proceedings of the National Academy of Sciences of the United States of America 1994;91(9):4034-8.
1994: G Carmel; B Leichus; Xiaodong Cheng; S D Patterson; U Mirza; Brian T Chait; Jeffrey Kuret
Expression, purification, crystallization, and preliminary x-ray analysis of casein kinase-1 from Schizosaccharomyces pombe.
The Journal of biological chemistry 1994;269(10):7304-9.
1994: Saulius Klimasauskas; S Kumar; Richard J Roberts; Xiaodong Cheng
HhaI methyltransferase flips its target base out of the DNA helix.
Cell 1994;76(2):357-69.
1994: S Kumar; Xiaodong Cheng; Saulius Klimasauskas; S Mi; J Posfai; Richard J Roberts; G G Wilson
The DNA (cytosine-5) methyltransferases.
Nucleic acids research 1994;22(1):1-10.
1993: Xiaodong Cheng; S Kumar; J Posfai; J W Pflugrath; Richard J Roberts
Crystal structure of the HhaI DNA methyltransferase complexed with S-adenosyl-L-methionine.
Cell 1993;74(2):299-307.
1993: Xiaodong Cheng; S Kumar; Saulius Klimasauskas; Richard J Roberts
Crystal structure of the HhaI DNA methyltransferase.
Cold Spring Harbor symposia on quantitative biology 1993;58():331-8.
1992: S Kumar; Xiaodong Cheng; J W Pflugrath; Richard J Roberts
Purification, crystallization, and preliminary X-ray diffraction analysis of an M.HhaI-AdoMet complex.
Biochemistry 1992;31(36):8648-53.
1991: Xiaodong Cheng; B P Schoenborn
Neutron diffraction study of carbonmonoxymyoglobin.
Journal of molecular biology 1991;220(2):381-99.