Crystal structure of the BRPF2 PWWP domain in complex with DNA reveals a different binding mode than

Zhang, Mengmeng; Lei, Ming; Qin, Su; Dong, Aiping; Yang, Ally; Li, Yanjun; Loppnau, Peter; Hughes, Timothy R.; Min, Jinrong; Liu, Yanli

doi:10.1016/j.bbagrm.2021.194688

Crystal structure of the BRPF2 PWWP domain in complex with DNA reveals a different binding mode than

Journal Article · 01 March 2021 · BBA - Gene Regul. Mech.

DOI:https://doi.org/10.1016/j.bbagrm.2021.194688· OSTI ID:1772763

Zhang, Mengmeng; Lei, Ming; Qin, Su; Dong, Aiping; Yang, Ally; Li, Yanjun; Loppnau, Peter; Hughes, Timothy R.; Min, Jinrong; Liu, Yanli

Research Organization:: Argonne National Lab. (ANL), Argonne, IL (United States). Advanced Photon Source (APS)

Sponsoring Organization:: DOE - Office Of Science; FOREIGN

OSTI ID:: 1772763

Journal Information:: BBA - Gene Regul. Mech., Vol. 1864, Issue (3)

Country of Publication:: United States

Language:: ENGLISH

References (34)

Hepatoma-Derived Growth Factor Belongs to a Gene Family in Mice Showing Significant Homology in the Amino Terminus Izumoto, Yoshitaka; Kuroda, Toshifumi; Harada, Hiroshi Biochemical and Biophysical Research Communications, Vol. 238, Issue 1 https://doi.org/10.1006/bbrc.1997.7233	journal	September 1997
WHSC1, a 90 kb SET Domain-Containing Gene, Expressed in Early Development and Homologous to a Drosophila Dysmorphy Gene Maps in the Wolf-Hirschhorn Syndrome Critical Region and is Fused to IgH in t(1;14) Multiple Myeloma Stec, I.; Wright, T. J.; van Ommen, G. -J. B. Human Molecular Genetics, Vol. 7, Issue 7 https://doi.org/10.1093/hmg/7.7.1071	journal	July 1998
Structure and function of the nucleosome-binding PWWP domain Qin, Su; Min, Jinrong Trends in Biochemical Sciences, Vol. 39, Issue 11 https://doi.org/10.1016/j.tibs.2014.09.001	journal	November 2014
The Tudor domain ‘Royal Family’: Tudor, plant Agenet, Chromo, PWWP and MBT domains Maurer-Stroh, Sebastian; Dickens, Nicholas J.; Hughes-Davies, Luke Trends in Biochemical Sciences, Vol. 28, Issue 2 https://doi.org/10.1016/S0968-0004(03)00004-5	journal	February 2003
The PWWP Domain of Dnmt3a and Dnmt3b Is Required for Directing DNA Methylation to the Major Satellite Repeats at Pericentric Heterochromatin Chen, T.; Tsujimoto, N.; Li, E. Molecular and Cellular Biology, Vol. 24, Issue 20 https://doi.org/10.1128/MCB.24.20.9048-9058.2004	journal	September 2004
High resolution structure of the HDGF PWWP domain: A potential DNA binding domain Lukasik, S. M. Protein Science, Vol. 15, Issue 2 https://doi.org/10.1110/ps.051751706	journal	February 2006
Human Mismatch Repair Protein MSH6 Contains a PWWP Domain That Targets Double Stranded DNA ^† Laguri, Cédric; Duband-Goulet, Isabelle; Friedrich, Nikolas Biochemistry, Vol. 47, Issue 23 https://doi.org/10.1021/bi7024639	journal	June 2008
Solution structure of the Pdp1 PWWP domain reveals its unique binding sites for methylated H4K20 and DNA Qiu, Yu; Zhang, Wen; Zhao, Chen Biochemical Journal, Vol. 442, Issue 3 https://doi.org/10.1042/BJ20111885	journal	February 2012
Crystal structure of human BS69 Bromo-ZnF-PWWP reveals its role in H3K36me3 nucleosome binding Wang, Juncheng; Qin, Su; Li, Fudong Cell Research, Vol. 24, Issue 7 https://doi.org/10.1038/cr.2014.38	journal	March 2014
Structure and function of histone methylation binding proteinsThis paper is one of a selection of papers published in this Special Issue, entitled CSBMCB’s 51st Annual Meeting – Epigenetics and Chromatin Dynamics, and has undergone the Journal’s usual peer review process. Adams-Cioaba, Melanie A.; Min, Jinrong Biochemistry and Cell Biology, Vol. 87, Issue 1 https://doi.org/10.1139/O08-129	journal	February 2009
Readout of Epigenetic Modifications Patel, Dinshaw J.; Wang, Zhanxin Annual Review of Biochemistry, Vol. 82, Issue 1 https://doi.org/10.1146/annurev-biochem-072711-165700	journal	June 2013
Structure and function of histone methylation-binding proteins in plants Liu, Yanli; Min, Jinrong Biochemical Journal, Vol. 473, Issue 12 https://doi.org/10.1042/BCJ20160123	journal	June 2016
The multidomain protein Brpf1 binds histones and is required for Hox gene expression and segmental identity Laue, K.; Daujat, S.; Crump, J. G. Development, Vol. 135, Issue 11 https://doi.org/10.1242/dev.017160	journal	April 2008
Regulation of Set9-Mediated H4K20 Methylation by a PWWP Domain Protein Wang, Yu; Reddy, Bharat; Thompson, James Molecular Cell, Vol. 33, Issue 4 https://doi.org/10.1016/j.molcel.2009.02.002	journal	February 2009
ZMYND11 links histone H3.3K36me3 to transcription elongation and tumour suppression Wen, Hong; Li, Yuanyuan; Xi, Yuanxin Nature, Vol. 508, Issue 7495 https://doi.org/10.1038/nature13045	journal	March 2014
Structural basis for high-affinity binding of LEDGF PWWP to mononucleosomes Eidahl, Jocelyn O.; Crowe, Brandon L.; North, Justin A. Nucleic Acids Research, Vol. 41, Issue 6 https://doi.org/10.1093/nar/gkt074	journal	February 2013
Nucleosomal DNA binding drives the recognition of H3K36-methylated nucleosomes by the PSIP1-PWWP domain van Nuland, Rick; van Schaik, Frederik MA; Simonis, Marieke Epigenetics & Chromatin, Vol. 6, Issue 1 https://doi.org/10.1186/1756-8935-6-12	journal	January 2013
The HRP3 PWWP domain recognizes the minor groove of double-stranded DNA and recruits HRP3 to chromatin Tian, Wei; Yan, Peiqiang; Xu, Ning Nucleic Acids Research, Vol. 47, Issue 10 https://doi.org/10.1093/nar/gkz294	journal	April 2019
Structure of H3K36-methylated nucleosome–PWWP complex reveals multivalent cross-gyre binding Wang, Haibo; Farnung, Lucas; Dienemann, Christian Nature Structural & Molecular Biology, Vol. 27, Issue 1 https://doi.org/10.1038/s41594-019-0345-4	journal	December 2019
A PWWP Domain of Histone-Lysine N -Methyltransferase NSD2 Binds to Dimethylated Lys-36 of Histone H3 and Regulates NSD2 Function at Chromatin Sankaran, Saumya M.; Wilkinson, Alex W.; Elias, Joshua E. Journal of Biological Chemistry, Vol. 291, Issue 16 https://doi.org/10.1074/jbc.M116.720748	journal	February 2016
Domain swapping and SMYD1 interactions with the PWWP domain of human hepatoma-derived growth factor Chen, Li-Ying; Huang, Yen-Chieh; Huang, Shih-Tsung Scientific Reports, Vol. 8, Issue 1 https://doi.org/10.1038/s41598-017-18510-8	journal	January 2018
Variation in Homeodomain DNA Binding Revealed by High-Resolution Analysis of Sequence Preferences Berger, Michael F.; Badis, Gwenael; Gehrke, Andrew R. Cell, Vol. 133, Issue 7 https://doi.org/10.1016/j.cell.2008.05.024	journal	June 2008
Sequence specificity is obtained from the majority of modular C2H2 zinc-finger arrays Lam, Kathy N.; van Bakel, Harm; Cote, Atina G. Nucleic Acids Research, Vol. 39, Issue 11 https://doi.org/10.1093/nar/gkq1303	journal	February 2011
Evaluation of methods for modeling transcription factor sequence specificity Weirauch, Matthew T.; Cote, Atina; Norel, Raquel Nature Biotechnology, Vol. 31, Issue 2 https://doi.org/10.1038/nbt.2486	journal	January 2013
A Tail-Based Mechanism Drives Nucleosome Demethylation by the LSD2/NPAC Multimeric Complex Marabelli, Chiara; Marrocco, Biagina; Pilotto, Simona Cell Reports, Vol. 27, Issue 2 https://doi.org/10.1016/j.celrep.2019.03.061	journal	April 2019
Crystal Structure of the LSD1/CoREST Histone Demethylase Bound to Its Nucleosome Substrate Kim, Sang-Ah; Zhu, Jiang; Yennawar, Neela Molecular Cell, Vol. 78, Issue 5 https://doi.org/10.1016/j.molcel.2020.04.019	journal	June 2020
Nucleosome-bound SOX2 and SOX11 structures elucidate pioneer factor function Dodonova, Svetlana O.; Zhu, Fangjie; Dienemann, Christian Nature, Vol. 580, Issue 7805 https://doi.org/10.1038/s41586-020-2195-y	journal	April 2020
Mechanisms of OCT4-SOX2 motif readout on nucleosomes Michael, Alicia K.; Grand, Ralph S.; Isbel, Luke Science, Vol. 368, Issue 6498 https://doi.org/10.1126/science.abb0074	journal	April 2020
Structural basis for recognition of histone H3K36me3 nucleosome by human de novo DNA methyltransferases 3A and 3B Rondelet, Grégoire; Dal Maso, Thomas; Willems, Luc Journal of Structural Biology, Vol. 194, Issue 3 https://doi.org/10.1016/j.jsb.2016.03.013	journal	June 2016
[20] Processing of X-ray diffraction data collected in oscillation mode Otwinowski, Zbyszek; Minor, Wladek Macromolecular Crystallography Part A, 307-326 https://doi.org/10.1016/S0076-6879(97)76066-X	book	January 1997
Phaser crystallographic software McCoy, Airlie J.; Grosse-Kunstleve, Ralf W.; Adams, Paul D. Journal of Applied Crystallography, Vol. 40, Issue 4 https://doi.org/10.1107/S0021889807021206	journal	July 2007
Features and development of Coot Emsley, P.; Lohkamp, B.; Scott, W. G. Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 4 https://doi.org/10.1107/S0907444910007493	journal	March 2010
Refinement of Macromolecular Structures by the Maximum-Likelihood Method Murshudov, G. N.; Vagin, A. A.; Dodson, E. J. Acta Crystallographica Section D Biological Crystallography, Vol. 53, Issue 3 https://doi.org/10.1107/S0907444996012255	journal	May 1997
MolProbity : all-atom structure validation for macromolecular crystallography Chen, Vincent B.; Arendall, W. Bryan; Headd, Jeffrey J. Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 1 https://doi.org/10.1107/S0907444909042073	journal	December 2009

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