The Structure of Saccharomyces cerevisiae Arginyltransferase 1 (ATE1)

Van, Verna; Ejimogu, Nna-Emeka; Bui, Toan S.; Smith, Aaron T.

doi:10.1016/j.jmb.2022.167816

The Structure of Saccharomyces cerevisiae Arginyltransferase 1 (ATE1)

Journal Article · 01 November 2022 · J. Mol. Biol.

DOI:https://doi.org/10.1016/j.jmb.2022.167816· OSTI ID:1901017

Van, Verna; Ejimogu, Nna-Emeka; Bui, Toan S.; Smith, Aaron T.

Research Organization:: Advanced Photon Source (APS), Argonne National Laboratory (ANL), Argonne, IL (US)

Sponsoring Organization:: DOE - Office Of Science; NIH

OSTI ID:: 1901017

Journal Information:: J. Mol. Biol., Journal Name: J. Mol. Biol. Journal Issue: (21) Vol. 434

Country of Publication:: United States

Language:: ENGLISH

References (70)

Degradation of a cohesin subunit by the N-end rule pathway is essential for chromosome stability Rao, Hai; Uhlmann, Frank; Nasmyth, Kim Nature, Vol. 410, Issue 6831 https://doi.org/10.1038/35073627	journal	April 2001
Uniqueness of ab initio shape determination in small-angle scattering Volkov, Vladimir V.; Svergun, Dmitri I. Journal of Applied Crystallography, Vol. 36, Issue 3, p. 860-864 https://doi.org/10.1107/S0021889803000268	journal	April 2003
Glycosylation in Cellular Mechanisms of Health and Disease Ohtsubo, Kazuaki; Marth, Jamey D. Cell, Vol. 126, Issue 5 https://doi.org/10.1016/j.cell.2006.08.019	journal	September 2006
Global Analysis of Posttranslational Protein Arginylation Wong, Catherine C. L.; Xu, Tao; Rai, Reena PLoS Biology, Vol. 5, Issue 10 https://doi.org/10.1371/journal.pbio.0050258	journal	September 2007
Impaired neurogenesis and cardiovascular development in mice lacking the E3 ubiquitin ligases UBR1 and UBR2 of the N-end rule pathway An, Jee Young; Seo, Jai Wha; Tasaki, Takafumi Proceedings of the National Academy of Sciences, Vol. 103, Issue 16 https://doi.org/10.1073/pnas.0601700103	journal	April 2006
Control of mammalian G protein signaling by N-terminal acetylation and the N-end rule pathway Park, S. -E.; Kim, J. -M.; Seok, O. -H. Science, Vol. 347, Issue 6227 https://doi.org/10.1126/science.aaa3844	journal	March 2015
Cloning and functional analysis of the arginyl-tRNA-protein transferase gene ATE1 of Saccharomyces cerevisiae. Balzi, E.; Choder, M.; Chen, W. N. Journal of Biological Chemistry, Vol. 265, Issue 13 https://doi.org/10.1016/S0021-9258(19)39136-7	journal	May 1990
PHENIX: a comprehensive Python-based system for macromolecular structure solution Adams, Paul D.; Afonine, Pavel V.; Bunkóczi, Gábor Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 2, p. 213-221 https://doi.org/10.1107/S0907444909052925	journal	January 2010
Posttranslational arginylation enzyme Ate1 affects DNA mutagenesis by regulating stress response Kumar, Akhilesh; Birnbaum, Michael D.; Patel, Devang M. Cell Death & Disease, Vol. 7, Issue 9 https://doi.org/10.1038/cddis.2016.284	journal	September 2016
Jalview Version 2--a multiple sequence alignment editor and analysis workbench Waterhouse, A. M.; Procter, J. B.; Martin, D. M. A. Bioinformatics, Vol. 25, Issue 9 https://doi.org/10.1093/bioinformatics/btp033	journal	January 2009
Binding of phenylarsenoxide to Arg-tRNA protein transferase is independent of vicinal thiols Li, Jun; Pickart, Cecile M. Biochemistry, Vol. 34, Issue 48 https://doi.org/10.1021/bi00048a028	journal	December 1995
N-degron and C-degron pathways of protein degradation Varshavsky, Alexander Proceedings of the National Academy of Sciences, Vol. 116, Issue 2 https://doi.org/10.1073/pnas.1816596116	journal	January 2019
A soluble amino acid incorporating system Kaji, Akira; Kaji, Hideko; Novelli, G. David Biochemical and Biophysical Research Communications, Vol. 10, Issue 5 https://doi.org/10.1016/0006-291X(63)90546-1	journal	March 1963
Arginyltransferase suppresses cell tumorigenic potential and inversely correlates with metastases in human cancers Rai, R.; Zhang, F.; Colavita, K. Oncogene, Vol. 35, Issue 31 https://doi.org/10.1038/onc.2015.473	journal	December 2015
Scatter : software for the analysis of nano- and mesoscale small-angle scattering Förster, S.; Apostol, L.; Bras, W. Journal of Applied Crystallography, Vol. 43, Issue 3 https://doi.org/10.1107/S0021889810008289	journal	April 2010
Arginyltransferase (Ate1) regulates the RGS7 protein level and the sensitivity of light-evoked ON-bipolar responses Fina, Marie E.; Wang, Junling; Nikonov, Sergei S. Scientific Reports, Vol. 11, Issue 1 https://doi.org/10.1038/s41598-021-88628-3	journal	April 2021
Arginyltransferase ATE1 Catalyzes Midchain Arginylation of Proteins at Side Chain Carboxylates In Vivo Wang, Junling; Han, Xuemei; Wong, Catherine C. L. Chemistry & Biology, Vol. 21, Issue 3 https://doi.org/10.1016/j.chembiol.2013.12.017	journal	March 2014
ATE1-Mediated Post-Translational Arginylation Is an Essential Regulator of Eukaryotic Cellular Homeostasis Van, Verna; Smith, Aaron T. ACS Chemical Biology, Vol. 15, Issue 12 https://doi.org/10.1021/acschembio.0c00677	journal	November 2020
Dali server: conservation mapping in 3D Holm, Liisa; Rosenstrï¿½m, Pï¿½ivi Nucleic Acids Research, Vol. 38, Issue suppl_2 https://doi.org/10.1093/nar/gkq366	journal	May 2010
AlphaFold Protein Structure Database: massively expanding the structural coverage of protein-sequence space with high-accuracy models Varadi, Mihaly; Anyango, Stephen; Deshpande, Mandar Nucleic Acids Research, Vol. 50, Issue D1 https://doi.org/10.1093/nar/gkab1061	journal	November 2021
The N-end rule pathway and regulation by proteolysis Varshavsky, Alexander Protein Science, Vol. 20, Issue 8 https://doi.org/10.1002/pro.666	journal	July 2011
N-Terminal Acetylation of Cellular Proteins Creates Specific Degradation Signals Hwang, C. -S.; Shemorry, A.; Varshavsky, A. Science, Vol. 327, Issue 5968 https://doi.org/10.1126/science.1183147	journal	January 2010
Arginylation Regulates Intracellular Actin Polymer Level by Modulating Actin Properties and Binding of Capping and Severing Proteins Saha, Sougata; Mundia, Maureen M.; Zhang, Fangliang Molecular Biology of the Cell, Vol. 21, Issue 8 https://doi.org/10.1091/mbc.e09-09-0829	journal	April 2010
Sequence logos: a new way to display consensus sequences Schneider, Thomas D.; Stephens, R. Michael Nucleic Acids Research, Vol. 18, Issue 20 https://doi.org/10.1093/nar/18.20.6097	journal	January 1990
Comparative Biology of Oxygen Sensing in Plants and Animals Holdsworth, Michael J.; Gibbs, Daniel J. Current Biology, Vol. 30, Issue 8 https://doi.org/10.1016/j.cub.2020.03.021	journal	April 2020
The N-end rule: functions, mysteries, uses. Varshavsky, A. Proceedings of the National Academy of Sciences, Vol. 93, Issue 22 https://doi.org/10.1073/pnas.93.22.12142	journal	October 1996
Clustal W and Clustal X version 2.0 Larkin, M. A.; Blackshields, G.; Brown, N. P. Bioinformatics, Vol. 23, Issue 21, p. 2947-2948 https://doi.org/10.1093/bioinformatics/btm404	journal	September 2007
ATSAS 3.0 : expanded functionality and new tools for small-angle scattering data analysis Manalastas-Cantos, Karen; Konarev, Petr V.; Hajizadeh, Nelly R. Journal of Applied Crystallography, Vol. 54, Issue 1 https://doi.org/10.1107/S1600576720013412	journal	February 2021
Structure and Functional Diversity of GCN5-Related N-Acetyltransferases (GNAT) Salah Ud-Din, Abu; Tikhomirova, Alexandra; Roujeinikova, Anna International Journal of Molecular Sciences, Vol. 17, Issue 7 https://doi.org/10.3390/ijms17071018	journal	June 2016
Automatic generation of protein structure cartoons with Pro-origami Stivala, A.; Wybrow, M.; Wirth, A. Bioinformatics, Vol. 27, Issue 23 https://doi.org/10.1093/bioinformatics/btr575	journal	October 2011
Spotlight on protein N-terminal acetylation Ree, Rasmus; Varland, Sylvia; Arnesen, Thomas Experimental & Molecular Medicine, Vol. 50, Issue 7, p. 1-13 https://doi.org/10.1038/s12276-018-0116-z	journal	July 2018
Determination of the regularization parameter in indirect-transform methods using perceptual criteria Svergun, D. I. Journal of Applied Crystallography, Vol. 25, Issue 4, p. 495-503 https://doi.org/10.1107/S0021889892001663	journal	August 1992
Scattering Curves of Ordered Mesoscopic Materials Förster, S.; Timmann, A.; Konrad, M. The Journal of Physical Chemistry B, Vol. 109, Issue 4 https://doi.org/10.1021/jp0467494	journal	February 2005
An Essential Role of N-Terminal Arginylation in Cardiovascular Development Kwon, Yong Tae; Kashina, Anna S.; Davydov, Ilia V. Science, Vol. 297, Issue 5578 https://doi.org/10.1126/science.1069531	journal	July 2002
Proteomic analysis of post-translational modifications Mann, Matthias; Jensen, Ole N. Nature Biotechnology, Vol. 21, Issue 3 https://doi.org/10.1038/nbt0303-255	journal	March 2003
FoXS, FoXSDock and MultiFoXS: Single-state and multi-state structural modeling of proteins and their complexes based on SAXS profiles Schneidman-Duhovny, Dina; Hammel, Michal; Tainer, John A. Nucleic Acids Research, Vol. 44, Issue W1 https://doi.org/10.1093/nar/gkw389	journal	May 2016
A reactive nucleophile proximal to vicinal thiols is an evolutionarily conserved feature in the mechanism of Arg aminoacyl-tRNA protein transferase Berleth, Erica S.; Li, Jun; Braunscheidel, Julie A. Archives of Biochemistry and Biophysics, Vol. 298, Issue 2 https://doi.org/10.1016/0003-9861(92)90441-X	journal	November 1992
An Arginyl-Transfer Ribonucleic Acid Protein Transferase from Cereal Embryos Manahan, Charles O.; App, Alva A. Plant Physiology, Vol. 52, Issue 1 https://doi.org/10.1104/pp.52.1.13	journal	July 1973
Crystal structure of the Ate1 arginyl-tRNA-protein transferase and arginylation of N-degron substrates Kim, Bong Heon; Kim, Min Kyung; Oh, Sun Joo Proceedings of the National Academy of Sciences, Vol. 119, Issue 31 https://doi.org/10.1073/pnas.2209597119	journal	July 2022
Protein Posttranslational Signatures Identified in COVID-19 Patient Plasma Vedula, Pavan; Tang, Hsin-Yao; Speicher, David W. Frontiers in Cell and Developmental Biology, Vol. 10 https://doi.org/10.3389/fcell.2022.807149	journal	February 2022
WebLogo: A Sequence Logo Generator Crooks, Gavin E.; Hon, Gary; Chandonia, John-Marc Genome Research, Vol. 14, Issue 6, p. 1188-1190 https://doi.org/10.1101/gr.849004	journal	May 2004
Coot model-building tools for molecular graphics Emsley, Paul; Cowtan, Kevin Acta Crystallographica Section D Biological Crystallography, Vol. 60, Issue 12, p. 2126-2132 https://doi.org/10.1107/S0907444904019158	journal	November 2004
Arginyl-tRNA-protein transferase 1 contributes to governing optimal stability of the human immunodeficiency virus type 1 core Kishimoto, Naoki; Okano, Ryosuke; Akita, Ayano Retrovirology, Vol. 18, Issue 1 https://doi.org/10.1186/s12977-021-00574-0	journal	September 2021
Protein arginylation targets alpha synuclein, facilitates normal brain health, and prevents neurodegeneration Wang, Junling; Han, Xuemei; Leu, Nicolae Adrian Scientific Reports, Vol. 7, Issue 1 https://doi.org/10.1038/s41598-017-11713-z	journal	September 2017
Unique roles of iron and zinc binding to the yeast Fe–S cluster scaffold assembly protein “Isu1” Lewis, Brianne E.; Mason, Zachary; Rodrigues, Andria V. Metallomics, Vol. 11, Issue 11 https://doi.org/10.1039/C9MT00172G	journal	January 2019
Small molecule inhibitors of arginyltransferase regulate arginylation-dependent protein degradation, cell motility, and angiogenesis Saha, Sougata; Wang, Junling; Buckley, Brian Biochemical Pharmacology, Vol. 83, Issue 7 https://doi.org/10.1016/j.bcp.2012.01.012	journal	April 2012
UCSF Chimera?A visualization system for exploratory research and analysis Pettersen, Eric F.; Goddard, Thomas D.; Huang, Conrad C. Journal of Computational Chemistry, Vol. 25, Issue 13 https://doi.org/10.1002/jcc.20084	journal	January 2004
Protein Posttranslational Modifications: The Chemistry of Proteome Diversifications Walsh, Christopher T.; Garneau-Tsodikova, Sylvie; Gatto, Gregory J. Angewandte Chemie International Edition, Vol. 44, Issue 45 https://doi.org/10.1002/anie.200501023	journal	November 2005
Amino acid substitution matrices from protein blocks. Henikoff, S.; Henikoff, J. G. Proceedings of the National Academy of Sciences, Vol. 89, Issue 22, p. 10915-10919 https://doi.org/10.1073/pnas.89.22.10915	journal	November 1992
xia2 : an expert system for macromolecular crystallography data reduction Winter, G. Journal of Applied Crystallography, Vol. 43, Issue 1 https://doi.org/10.1107/S0021889809045701	journal	December 2009
Heme biosynthesis depends on previously unrecognized acquisition of iron-sulfur cofactors in human amino-levulinic acid dehydratase Liu, Gang; Sil, Debangsu; Maio, Nunziata Nature Communications, Vol. 11, Issue 1 https://doi.org/10.1038/s41467-020-20145-9	journal	December 2020
Liat1, an arginyltransferase-binding protein whose evolution among primates involved changes in the numbers of its 10-residue repeats Brower, Christopher S.; Rosen, Connor E.; Jones, Richard H. Proceedings of the National Academy of Sciences, Vol. 111, Issue 46 https://doi.org/10.1073/pnas.1419587111	journal	November 2014
A soluble amino acid-incorporating system from rat liver Kaji, Hideko; Novelli, G. D.; Kaji, Akira Biochimica et Biophysica Acta (BBA) - Specialized Section on Nucleic Acids and Related Subjects, Vol. 76 https://doi.org/10.1016/0926-6550(63)90070-7	journal	January 1963
Historical review: the field of protein methylation Paik, Woon Ki; Paik, David C.; Kim, Sangduk Trends in Biochemical Sciences, Vol. 32, Issue 3 https://doi.org/10.1016/j.tibs.2007.01.006	journal	March 2007
In vivo half-life of a protein is a function of its amino-terminal residue Bachmair, A.; Finley, D.; Varshavsky, A. Science, Vol. 234, Issue 4773 https://doi.org/10.1126/science.3018930	journal	October 1986
Automated matching of high- and low-resolution structural models Kozin, M. B.; Svergun, D. I. Journal of Applied Crystallography, Vol. 34, Issue 1, p. 33-41 https://doi.org/10.1107/S0021889800014126	journal	February 2001
The N-end rule pathway promotes seed germination and establishment through removal of ABA sensitivity in Arabidopsis Holman, Tara J.; Jones, Peter D.; Russell, Laurel Proceedings of the National Academy of Sciences, Vol. 106, Issue 11 https://doi.org/10.1073/pnas.0810280106	journal	March 2009
Protein kinase C catalyzes phosphorylation of guanylate cyclase in vitro. Zwiller, J.; Revel, M. O.; Malviya, A. N. Journal of Biological Chemistry, Vol. 260, Issue 3 https://doi.org/10.1016/S0021-9258(18)89593-X	journal	February 1985
Target site specificity and in vivo complexity of the mammalian arginylome Wang, Junling; Pejaver, Vikas Rao; Dann, Geoffrey P. Scientific Reports, Vol. 8, Issue 1 https://doi.org/10.1038/s41598-018-34639-6	journal	November 2018
Fe-S clusters masquerading as zinc finger proteins Pritts, Jordan D.; Michel, Sarah L. J. Journal of Inorganic Biochemistry, Vol. 230 https://doi.org/10.1016/j.jinorgbio.2022.111756	journal	May 2022
Protein Phosphorylation: A Major Switch Mechanism for Metabolic Regulation Humphrey, Sean J.; James, David E.; Mann, Matthias Trends in Endocrinology & Metabolism, Vol. 26, Issue 12 https://doi.org/10.1016/j.tem.2015.09.013	journal	December 2015
Arginylation of ß-Actin Regulates Actin Cytoskeleton and Cell Motility Karakozova, Marina; Kozak, Marina; Wong, Catherine C. L. Science, Vol. 313, Issue 5784 https://doi.org/10.1126/science.1129344	journal	July 2006
tRNAArg-Derived Fragments Can Serve as Arginine Donors for Protein Arginylation Avcilar-Kucukgoze, Irem; Gamper, Howard; Polte, Christine Cell Chemical Biology, Vol. 27, Issue 7 https://doi.org/10.1016/j.chembiol.2020.05.013	journal	July 2020
Deciphering conformational transitions of proteins by small angle X-ray scattering and normal mode analysis Panjkovich, Alejandro; Svergun, Dmitri I. Physical Chemistry Chemical Physics, Vol. 18, Issue 8 https://doi.org/10.1039/C5CP04540A	journal	January 2016
Molecular dissection of arginyltransferases guided by similarity to bacterial peptidoglycan synthases Rai, Reena; Mushegian, Arcady; Makarova, Kira EMBO reports, Vol. 7, Issue 8 https://doi.org/10.1038/sj.embor.7400747	journal	July 2006
Determination of Domain Structure of Proteins from X-Ray Solution Scattering Svergun, Dmitri I.; Petoukhov, Maxim V.; Koch, Michel H. J. Biophysical Journal, Vol. 80, Issue 6 https://doi.org/10.1016/S0006-3495(01)76260-1	journal	June 2001
The crystal structure of Klebsiella pneumoniae FeoA reveals a site for protein‐protein interactions Linkous, Richard O.; Sestok, Alexandrea E.; Smith, Aaron T. Proteins: Structure, Function, and Bioinformatics, Vol. 87, Issue 11 https://doi.org/10.1002/prot.25755	journal	June 2019
Protein-based peptide-bond formation by aminoacyl-tRNA protein transferase Watanabe, Kazunori; Toh, Yukimatsu; Suto, Kyoko Nature, Vol. 449, Issue 7164 https://doi.org/10.1038/nature06167	journal	September 2007
Histone acetylation: a switch between repressive and permissive chromatin: Second in review series on chromatin dynamics Eberharter, Anton; Becker, Peter B. EMBO reports, Vol. 3, Issue 3 https://doi.org/10.1093/embo-reports/kvf053	journal	March 2002
Cleavage and polyadenylation specificity factor 30: An RNA-binding zinc-finger protein with an unexpected 2Fe–2S cluster Shimberg, Geoffrey D.; Michalek, Jamie L.; Oluyadi, Abdulafeez A. Proceedings of the National Academy of Sciences, Vol. 113, Issue 17 https://doi.org/10.1073/pnas.1517620113	journal	April 2016

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