The human pseudouridine synthase PUS7 recognizes RNA with an extended multi-domain binding surface

Guegueniat, Julia; Halabelian, Levon; Zeng, Hong; Dong, Aiping; Li, Yanjun; Wu, Hong; Arrowsmith, Cheryl H; Kothe, Ute

doi:10.1093/nar/gkab934

The human pseudouridine synthase PUS7 recognizes RNA with an extended multi-domain binding surface

Journal Article · 01 November 2021 · Nucleic Acids Res.

DOI:https://doi.org/10.1093/nar/gkab934· OSTI ID:1836684

Guegueniat, Julia; Halabelian, Levon; Zeng, Hong; Dong, Aiping; Li, Yanjun; Wu, Hong; Arrowsmith, Cheryl H; Kothe, Ute

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

Sponsoring Organization:: DOE - Office Of Science; FOREIGN

OSTI ID:: 1836684

Journal Information:: Nucleic Acids Res., Vol. 49, Issue (20)

Country of Publication:: United States

Language:: ENGLISH

References (41)

Cracking the epitranscriptome Schwartz, Schraga RNA, Vol. 22, Issue 2 https://doi.org/10.1261/rna.054502.115	journal	January 2016
MODOMICS: a database of RNA modification pathways. 2017 update Boccaletto, Pietro; Machnicka, Magdalena A.; Purta, Elzbieta Nucleic Acids Research, Vol. 46, Issue D1 https://doi.org/10.1093/nar/gkx1030	journal	November 2017
RNA modifications and structures cooperate to guide RNA–protein interactions Lewis, Cole J. T.; Pan, Tao; Kalsotra, Auinash Nature Reviews Molecular Cell Biology, Vol. 18, Issue 3 https://doi.org/10.1038/nrm.2016.163	journal	February 2017
Pseudouridine profiling reveals regulated mRNA pseudouridylation in yeast and human cells Carlile, Thomas M.; Rojas-Duran, Maria F.; Zinshteyn, Boris Nature, Vol. 515, Issue 7525 https://doi.org/10.1038/nature13802	journal	September 2014
Transcriptome-Wide Mapping of Pseudouridines: Pseudouridine Synthases Modify Specific mRNAs in S. cerevisiae Lovejoy, Alexander F.; Riordan, Daniel P.; Brown, Patrick O. PLoS ONE, Vol. 9, Issue 10 https://doi.org/10.1371/journal.pone.0110799	journal	October 2014
Transcriptome-wide Mapping Reveals Widespread Dynamic-Regulated Pseudouridylation of ncRNA and mRNA Schwartz, Schraga; Bernstein, Douglas A.; Mumbach, Maxwell R. Cell, Vol. 159, Issue 1 https://doi.org/10.1016/j.cell.2014.08.028	journal	September 2014
Pseudouridine: Still mysterious, but never a fake (uridine)! Spenkuch, Felix; Motorin, Yuri; Helm, Mark RNA Biology, Vol. 11, Issue 12 https://doi.org/10.4161/15476286.2014.992278	journal	December 2014
RNA-Guided RNA modification: functional organization of the archaeal H/ACA RNP Baker, Daniel L.; Youssef, Osama A.; Chastkofsky, Michael I. R. Genes & Development, Vol. 19, Issue 10 https://doi.org/10.1101/gad.1309605	journal	May 2005
Pseudouridine Synthases Hamma, Tomoko; Ferré-D'Amaré, Adrian R. Chemistry & Biology, Vol. 13, Issue 11 https://doi.org/10.1016/j.chembiol.2006.09.009	journal	November 2006
Eukaryotic stand-alone pseudouridine synthases – RNA modifying enzymes and emerging regulators of gene expression? Rintala-Dempsey, Anne C.; Kothe, Ute RNA Biology, Vol. 14, Issue 9 https://doi.org/10.1080/15476286.2016.1276150	journal	February 2017
Expression, purification, crystallization and preliminary diffraction studies of the tRNA pseudouridine synthase TruD from Escherichia coli Ericsson, Ulrika B.; Andersson, Martin E.; Engvall, Benita Acta Crystallographica Section D Biological Crystallography, Vol. 60, Issue 4 https://doi.org/10.1107/S0907444904003506	journal	March 2004
X-ray structure of tRNA pseudouridine synthase TruD reveals an inserted domain with a novel fold Ericsson, Ulrika B.; Nordlund, Pär; Hallberg, B. Martin FEBS Letters, Vol. 565, Issue 1-3 https://doi.org/10.1016/j.febslet.2004.03.085	journal	April 2004
A novel unanticipated type of pseudouridine synthase with homologs in bacteria, archaea, and eukarya Kaya, Yusuf; Ofengand, James RNA, Vol. 9, Issue 6 https://doi.org/10.1261/rna.5230603	journal	June 2003
Crystal Structure of TruD, a Novel Pseudouridine Synthase with a New Protein Fold Kaya, Yusuf; Del Campo, Mark; Ofengand, James Journal of Biological Chemistry, Vol. 279, Issue 18 https://doi.org/10.1074/jbc.C400072200	journal	April 2004
Crystal structure of the highly divergent pseudouridine synthase TruD reveals a circular permutation of a conserved fold Hoang, Charmaine; FerrÉ-D’AmarÉ, Adrian R. RNA, Vol. 10, Issue 7 https://doi.org/10.1261/rna.7240504	journal	June 2004
Pseudouridylation (Psi) of U2 snRNA in S.cerevisiae is catalyzed by an RNA-independent mechanism Ma, X. The EMBO Journal, Vol. 22, Issue 8 https://doi.org/10.1093/emboj/cdg191	journal	April 2003
The Pseudouridine Synthases Proceed through a Glycal Intermediate Veerareddygari, Govardhan Reddy; Singh, Sanjay K.; Mueller, Eugene G. Journal of the American Chemical Society, Vol. 138, Issue 25 https://doi.org/10.1021/jacs.6b04491	journal	June 2016
Different Mechanisms for Pseudouridine Formation in Yeast 5S and 5.8S rRNAs Decatur, Wayne A.; Schnare, Murray N. Molecular and Cellular Biology, Vol. 28, Issue 10 https://doi.org/10.1128/MCB.01574-07	journal	May 2008
ψ35 in the Branch Site Recognition Region of U2 Small Nuclear RNA Is Important for Pre-mRNA Splicing in Saccharomyces cerevisiae Yang, Chunxing; McPheeters, David S.; Yu, Yi-Tao Journal of Biological Chemistry, Vol. 280, Issue 8 https://doi.org/10.1074/jbc.M413288200	journal	February 2005
Pseudouridines in and near the branch site recognition region of U2 snRNA are required for snRNP biogenesis and pre-mRNA splicing in Xenopus oocytes Zhao, Xinliang; Yu, Yi-Tao RNA, Vol. 10, Issue 4 https://doi.org/10.1261/rna.5159504	journal	March 2004
U2 snRNA is inducibly pseudouridylated at novel sites by Pus7p and snR81 RNP: Inducible U2 pseudouridylation Wu, Guowei; Xiao, Mu; Yang, Chunxing The EMBO Journal, Vol. 30, Issue 1 https://doi.org/10.1038/emboj.2010.316	journal	December 2010
The Saccharomyces cerevisiae U2 snRNA:pseudouridine-synthase Pus7p is a novel multisite–multisubstrate RNA:Ψ-synthase also acting on tRNAs Behm-Ansmant, Isabelle; Urban, Alan; Ma, Xiaoju RNA, Vol. 9, Issue 11 https://doi.org/10.1261/rna.5520403	journal	October 2003
Chemical pulldown reveals dynamic pseudouridylation of the mammalian transcriptome Li, Xiaoyu; Zhu, Ping; Ma, Shiqing Nature Chemical Biology, Vol. 11, Issue 8 https://doi.org/10.1038/nchembio.1836	journal	June 2015
Pseudouridine synthase 7 impacts Candida albicans rRNA processing and morphological plasticity Pickerill, Ethan S.; Kurtz, Rebecca P.; Tharp, Aaron Yeast, Vol. 36, Issue 11 https://doi.org/10.1002/yea.3436	journal	August 2019
A novel PUS7 mutation causes intellectual disability with autistic and aggressive behaviors Darvish, Hossein; Azcona, Luis J.; Alehabib, Elham Neurology Genetics, Vol. 5, Issue 5 https://doi.org/10.1212/NXG.0000000000000356	journal	September 2019
PUS7 mutations impair pseudouridylation in humans and cause intellectual disability and microcephaly Shaheen, Ranad; Tasak, Monika; Maddirevula, Sateesh Human Genetics, Vol. 138, Issue 3 https://doi.org/10.1007/s00439-019-01980-3	journal	February 2019
Variants in PUS7 Cause Intellectual Disability with Speech Delay, Microcephaly, Short Stature, and Aggressive Behavior de Brouwer, Arjan P. M.; Abou Jamra, Rami; Körtel, Nadine The American Journal of Human Genetics, Vol. 103, Issue 6 https://doi.org/10.1016/j.ajhg.2018.10.026	journal	December 2018
Family-based exome sequencing identifies rare coding variants in age-related macular degeneration Ratnapriya, Rinki; Acar, İlhan E.; Geerlings, Maartje J. Human Molecular Genetics, Vol. 29, Issue 12 https://doi.org/10.1093/hmg/ddaa057	journal	April 2020
Pseudouridylation of tRNA-Derived Fragments Steers Translational Control in Stem Cells Guzzi, Nicola; Cieśla, Maciej; Ngoc, Phuong Cao Thi Cell, Vol. 173, Issue 5 https://doi.org/10.1016/j.cell.2018.03.008	journal	May 2018
HKL -3000: the integration of data reduction and structure solution – from diffraction images to an initial model in minutes Minor, Wladek; Cymborowski, Marcin; Otwinowski, Zbyszek Acta Crystallographica Section D Biological Crystallography, Vol. 62, Issue 8 https://doi.org/10.1107/S0907444906019949	journal	July 2006
Automated main-chain model building by template matching and iterative fragment extension Terwilliger, Thomas C. Acta Crystallographica Section D Biological Crystallography, Vol. 59, Issue 1 https://doi.org/10.1107/S0907444902018036	journal	December 2002
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
MolProbity: More and better reference data for improved all-atom structure validation: PROTEIN SCIENCE.ORG Williams, Christopher J.; Headd, Jeffrey J.; Moriarty, Nigel W. Protein Science, Vol. 27, Issue 1 https://doi.org/10.1002/pro.3330	journal	November 2017
NPDock: a web server for protein–nucleic acid docking Tuszynska, Irina; Magnus, Marcin; Jonak, Katarzyna Nucleic Acids Research, Vol. 43, Issue W1 https://doi.org/10.1093/nar/gkv493	journal	May 2015
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
Solution Structure of the R3H Domain from Human Sμbp-2 Liepinsh, Edvards; Leonchiks, Ainars; Sharipo, Anatoly Journal of Molecular Biology, Vol. 326, Issue 1 https://doi.org/10.1016/S0022-2836(02)01381-5	journal	February 2003
RNA Sequence and Two-dimensional Structure Features Required for Efficient Substrate Modification by the Saccharomyces cerevisiae RNA:Ψ-Synthase Pus7p Urban, Alan; Behm-Ansmant, Isabelle; Branlant, Christiane Journal of Biological Chemistry, Vol. 284, Issue 9 https://doi.org/10.1074/jbc.M807986200	journal	February 2009
G-quadruplex structures contribute to the neuroprotective effects of angiogenin-induced tRNA fragments Ivanov, Pavel; O’Day, Elizabeth; Emara, Mohamed M. Proceedings of the National Academy of Sciences, Vol. 111, Issue 51 https://doi.org/10.1073/pnas.1407361111	journal	November 2014
Metal Cations in G-Quadruplex Folding and Stability Bhattacharyya, Debmalya; Mirihana Arachchilage, Gayan; Basu, Soumitra Frontiers in Chemistry, Vol. 4 https://doi.org/10.3389/fchem.2016.00038	journal	September 2016
Incorporation of aminoacyl-tRNA into the ribosome as seen by cryo-electron microscopy Valle, Mikel; Zavialov, Andrey; Li, Wen Nature Structural & Molecular Biology, Vol. 10, Issue 11 https://doi.org/10.1038/nsb1003	journal	October 2003
Structural Mechanism of Substrate RNA Recruitment in H/ACA RNA-Guided Pseudouridine Synthase Duan, Jingqi; Li, Ling; Lu, Jing Molecular Cell, Vol. 34, Issue 4 https://doi.org/10.1016/j.molcel.2009.05.005	journal	May 2009

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