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Title: Structural basis for the evolution of cyclic phosphodiesterase activity in the U6 snRNA exoribonuclease Usb1

Abstract

U6 snRNA undergoes post-transcriptional 3' end modification prior to incorporation into the active site of spliceosomes. The responsible exoribonuclease is Usb1, which removes nucleotides from the 3' end of U6 and, in humans, leaves a 2',3' cyclic phosphate that is recognized by the Lsm2–8 complex. Saccharomycescerevisiae Usb1 has additional 2',3' cyclic phosphodiesterase (CPDase) activity, which converts the cyclic phosphate into a 3' phosphate group. Here we investigate the molecular basis for the evolution of Usb1 CPDase activity. We examine the structure and function of Usb1 from Kluyveromyces marxianus, which shares 25 and 19% sequence identity to the S. cerevisiae and Homo sapiens orthologs of Usb1, respectively. We show that K. marxianus Usb1 enzyme has CPDase activity and determined its structure, free and bound to the substrate analog uridine 5'-monophosphate. We find that the origin of CPDase activity is related to a loop structure that is conserved in yeast and forms a distinct penultimate (n – 1) nucleotide binding site. These data provide structural and mechanistic insight into the evolutionary divergence of Usb1 catalysis.

Authors:
 [1];  [1];  [1];  [1]; ORCiD logo [1]
  1. Univ. of Wisconsin, Madison, WI (United States)
Publication Date:
Research Org.:
Argonne National Lab. (ANL), Argonne, IL (United States)
Sponsoring Org.:
USDOE; National Institutes of Health (NIH)
OSTI Identifier:
1603143
Resource Type:
Accepted Manuscript
Journal Name:
Nucleic Acids Research
Additional Journal Information:
Journal Volume: 48; Journal Issue: 3; Journal ID: ISSN 0305-1048
Publisher:
Oxford University Press
Country of Publication:
United States
Language:
ENGLISH
Subject:
59 BASIC BIOLOGICAL SCIENCES

Citation Formats

Nomura, Yuichiro, Montemayor, Eric J., Virta, Johanna M., Hayes, Samuel M., and Butcher, Samuel E. Structural basis for the evolution of cyclic phosphodiesterase activity in the U6 snRNA exoribonuclease Usb1. United States: N. p., 2019. Web. https://doi.org/10.1093/nar/gkz1177.
Nomura, Yuichiro, Montemayor, Eric J., Virta, Johanna M., Hayes, Samuel M., & Butcher, Samuel E. Structural basis for the evolution of cyclic phosphodiesterase activity in the U6 snRNA exoribonuclease Usb1. United States. https://doi.org/10.1093/nar/gkz1177
Nomura, Yuichiro, Montemayor, Eric J., Virta, Johanna M., Hayes, Samuel M., and Butcher, Samuel E. Fri . "Structural basis for the evolution of cyclic phosphodiesterase activity in the U6 snRNA exoribonuclease Usb1". United States. https://doi.org/10.1093/nar/gkz1177. https://www.osti.gov/servlets/purl/1603143.
@article{osti_1603143,
title = {Structural basis for the evolution of cyclic phosphodiesterase activity in the U6 snRNA exoribonuclease Usb1},
author = {Nomura, Yuichiro and Montemayor, Eric J. and Virta, Johanna M. and Hayes, Samuel M. and Butcher, Samuel E.},
abstractNote = {U6 snRNA undergoes post-transcriptional 3' end modification prior to incorporation into the active site of spliceosomes. The responsible exoribonuclease is Usb1, which removes nucleotides from the 3' end of U6 and, in humans, leaves a 2',3' cyclic phosphate that is recognized by the Lsm2–8 complex. Saccharomycescerevisiae Usb1 has additional 2',3' cyclic phosphodiesterase (CPDase) activity, which converts the cyclic phosphate into a 3' phosphate group. Here we investigate the molecular basis for the evolution of Usb1 CPDase activity. We examine the structure and function of Usb1 from Kluyveromyces marxianus, which shares 25 and 19% sequence identity to the S. cerevisiae and Homo sapiens orthologs of Usb1, respectively. We show that K. marxianus Usb1 enzyme has CPDase activity and determined its structure, free and bound to the substrate analog uridine 5'-monophosphate. We find that the origin of CPDase activity is related to a loop structure that is conserved in yeast and forms a distinct penultimate (n – 1) nucleotide binding site. These data provide structural and mechanistic insight into the evolutionary divergence of Usb1 catalysis.},
doi = {10.1093/nar/gkz1177},
journal = {Nucleic Acids Research},
number = 3,
volume = 48,
place = {United States},
year = {2019},
month = {12}
}

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Works referenced in this record:

Proteome survey reveals modularity of the yeast cell machinery
journal, January 2006

  • Gavin, Anne-Claude; Aloy, Patrick; Grandi, Paola
  • Nature, Vol. 440, Issue 7084
  • DOI: 10.1038/nature04532

Human Mpn1 promotes post-transcriptional processing and stability of U6atac
journal, July 2015


HKL2MAP : a graphical user interface for macromolecular phasing with SHELX programs
journal, September 2004


Advances in automated data analysis and processing within autoPROC , combined with improved characterisation, mitigation and visualisation of the anisotropy of diffraction limits using STARANISO
journal, July 2018

  • Vonrhein, Clemens; Tickle, Ian J.; Flensburg, Claus
  • Acta Crystallographica Section A Foundations and Advances, Vol. 74, Issue a1
  • DOI: 10.1107/S010876731809640X

Aberrant 3′ oligoadenylation of spliceosomal U6 small nuclear RNA in poikiloderma with neutropenia
journal, February 2013


Refinement of Macromolecular Structures by the Maximum-Likelihood Method
journal, May 1997

  • Murshudov, G. N.; Vagin, A. A.; Dodson, E. J.
  • Acta Crystallographica Section D Biological Crystallography, Vol. 53, Issue 3
  • DOI: 10.1107/S0907444996012255

Ribonuclease A
journal, May 1998


High-Quality Binary Protein Interaction Map of the Yeast Interactome Network
journal, October 2008


Overview of the CCP 4 suite and current developments
journal, March 2011

  • Winn, Martyn D.; Ballard, Charles C.; Cowtan, Kevin D.
  • Acta Crystallographica Section D Biological Crystallography, Vol. 67, Issue 4
  • DOI: 10.1107/S0907444910045749

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
  • DOI: 10.1107/S0108767307043930

Structural and mechanistic basis for preferential deadenylation of U6 snRNA by Usb1
journal, September 2018

  • Nomura, Yuichiro; Roston, Daniel; Montemayor, Eric J.
  • Nucleic Acids Research, Vol. 46, Issue 21
  • DOI: 10.1093/nar/gky812

Determinants of ligand binding and catalytic activity in the myelin enzyme 2′,3′-cyclic nucleotide 3′-phosphodiesterase
journal, November 2015

  • Raasakka, Arne; Myllykoski, Matti; Laulumaa, Saara
  • Scientific Reports, Vol. 5, Issue 1
  • DOI: 10.1038/srep16520

Heavy-atom derivatization
journal, October 2003

  • Garman, Elspeth; Murray, James W.
  • Acta Crystallographica Section D Biological Crystallography, Vol. 59, Issue 11
  • DOI: 10.1107/S0907444903012794

Molecular evidence for an ancient duplication of the entire yeast genome
journal, June 1997

  • Wolfe, Kenneth H.; Shields, Denis C.
  • Nature, Vol. 387, Issue 6634
  • DOI: 10.1038/42711

AKAP18 Contains a Phosphoesterase Domain that Binds AMP
journal, February 2008

  • Gold, Matthew G.; Smith, F. Donelson; Scott, John D.
  • Journal of Molecular Biology, Vol. 375, Issue 5
  • DOI: 10.1016/j.jmb.2007.11.037

3'-cyclic phosphorylation of U6 snRNA leads to recruitment of recycling factor p110 through LSm proteins
journal, June 2008


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
  • DOI: 10.1107/S0907444910007493

Crystallographic Analysis of the Reaction Cycle of 2′,3′-Cyclic Nucleotide 3′-Phosphodiesterase, a Unique Member of the 2H Phosphoesterase Family
journal, November 2013

  • Myllykoski, Matti; Raasakka, Arne; Lehtimäki, Mari
  • Journal of Molecular Biology, Vol. 425, Issue 22
  • DOI: 10.1016/j.jmb.2013.06.012

Energetics of Catalysis by Ribonucleases: Fate of the 2',3'-Cyclic Phosphodiester Intermediate
journal, June 1994

  • Thompson, James E.; Venegas, Fernando D.; Raines, Ronald T.
  • Biochemistry, Vol. 33, Issue 23
  • DOI: 10.1021/bi00189a047

Mpn1, Mutated in Poikiloderma with Neutropenia Protein 1, Is a Conserved 3′-to-5′ RNA Exonuclease Processing U6 Small Nuclear RNA
journal, October 2012


Towards automated crystallographic structure refinement with phenix.refine
journal, March 2012

  • Afonine, Pavel V.; Grosse-Kunstleve, Ralf W.; Echols, Nathaniel
  • Acta Crystallographica Section D Biological Crystallography, Vol. 68, Issue 4
  • DOI: 10.1107/S0907444912001308

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
  • DOI: 10.1107/S0907444909052925

Structure and mechanism of E. coli RNA 2′,3′-cyclic phosphodiesterase
journal, September 2014


The life of U6 small nuclear RNA, from cradle to grave
journal, January 2018


Architecture of the U6 snRNP reveals specific recognition of 3′-end processed U6 snRNA
journal, May 2018

  • Montemayor, Eric J.; Didychuk, Allison L.; Yake, Allyson D.
  • Nature Communications, Vol. 9, Issue 1
  • DOI: 10.1038/s41467-018-04145-4

How good are my data and what is the resolution?
journal, June 2013

  • Evans, Philip R.; Murshudov, Garib N.
  • Acta Crystallographica Section D Biological Crystallography, Vol. 69, Issue 7
  • DOI: 10.1107/S0907444913000061

Myelin 2′,3′-Cyclic Nucleotide 3′-Phosphodiesterase: Active-Site Ligand Binding and Molecular Conformation
journal, February 2012


Mammalian U6 small nuclear RNA undergoes 3' end modifications within the spliceosome.
journal, March 1993

  • Tazi, J.; Forne, T.; Jeanteur, P.
  • Molecular and Cellular Biology, Vol. 13, Issue 3
  • DOI: 10.1128/MCB.13.3.1641

Tobacco etch virus protease: mechanism of autolysis and rational design of stable mutants with wild-type catalytic proficiency
journal, December 2001

  • Kapust, Rachel B.; Tözsér, József; Fox, Jeffrey D.
  • Protein Engineering, Design and Selection, Vol. 14, Issue 12
  • DOI: 10.1093/protein/14.12.993

Cryo-electron microscopy snapshots of the spliceosome: structural insights into a dynamic ribonucleoprotein machine
journal, October 2017

  • Fica, Sebastian M.; Nagai, Kiyoshi
  • Nature Structural & Molecular Biology, Vol. 24, Issue 10
  • DOI: 10.1038/nsmb.3463

The structure of Pyrococcus horikoshii 2′-5′ RNA ligase at 1.94 Å resolution reveals a possible open form with a wider active-site cleft
journal, November 2006

  • Gao, Yong-Gui; Yao, Min; Okada, Ayuko
  • Acta Crystallographica Section F Structural Biology and Crystallization Communications, Vol. 62, Issue 12
  • DOI: 10.1107/S1744309106046616

π-Stacking Interactions: ALIVE AND WELL IN PROTEINS
journal, June 1998

  • McGaughey, Georgia B.; Gagné, Marc; Rappé, Anthony K.
  • Journal of Biological Chemistry, Vol. 273, Issue 25
  • DOI: 10.1074/jbc.273.25.15458

Crystal Structure of the 2′-5′ RNA Ligase from Thermus thermophilus HB8
journal, June 2003


Usb1 controls U6 snRNP assembly through evolutionarily divergent cyclic phosphodiesterase activities
journal, September 2017

  • Didychuk, Allison L.; Montemayor, Eric J.; Carrocci, Tucker J.
  • Nature Communications, Vol. 8, Issue 1
  • DOI: 10.1038/s41467-017-00484-w

The 2′-5′ RNA Ligase of Escherichia coli: PURIFICATION, CLONING, AND GENOMIC DISRUPTION
journal, December 1996


XDS
journal, January 2010

  • Kabsch, Wolfgang
  • Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 2
  • DOI: 10.1107/S0907444909047337

Global landscape of protein complexes in the yeast Saccharomyces cerevisiae
journal, March 2006

  • Krogan, Nevan J.; Cagney, Gerard; Yu, Haiyuan
  • Nature, Vol. 440, Issue 7084
  • DOI: 10.1038/nature04670

U6 small nuclear RNA is transcribed by RNA polymerase III.
journal, November 1986

  • Kunkel, G. R.; Maser, R. L.; Calvet, J. P.
  • Proceedings of the National Academy of Sciences, Vol. 83, Issue 22
  • DOI: 10.1073/pnas.83.22.8575

Assigning Function to Yeast Proteins by Integration of Technologies
journal, December 2003


Crystal Structures of the Semireduced and Inhibitor-bound Forms of Cyclic Nucleotide Phosphodiesterase from Arabidopsis thaliana
journal, November 2001

  • Hofmann, Andreas; Grella, Melissa; Botos, Istvan
  • Journal of Biological Chemistry, Vol. 277, Issue 2
  • DOI: 10.1074/jbc.M107889200

Structural aspects of nucleotide ligand binding by a bacterial 2H phosphoesterase
journal, January 2017


Targeted Next-Generation Sequencing Appoints C16orf57 as Clericuzio-Type Poikiloderma with Neutropenia Gene
journal, January 2010

  • Volpi, Ludovica; Roversi, Gaia; Colombo, Elisa Adele
  • The American Journal of Human Genetics, Vol. 86, Issue 1
  • DOI: 10.1016/j.ajhg.2009.11.014

Myelin 2′,3′-Cyclic Nucleotide 3′-Phosphodiesterase: Active-Site Ligand Binding and Molecular Conformation
text, January 2012

  • Myllykoski, Matti; Raasakka, Arne; Han, Huijong
  • Deutsches Elektronen-Synchrotron, DESY, Hamburg
  • DOI: 10.3204/pubdb-2017-05054