Atomic structures of the RNA end-healing 5′-OH kinase and 2′,3′-cyclic phosphodiesterase domains of fungal tRNA ligase: conformational switches in the kinase upon binding of the GTP phosphate donor
Abstract
Fungal tRNA ligase (Trl1) rectifies RNA breaks with 2',3'-cyclic-PO4 and 5'-OH termini. Trl1 consists of three catalytic modules: an N-terminal ligase (LIG) domain; a central polynucleotide kinase (KIN) domain; and a C-terminal cyclic phosphodiesterase (CPD) domain. Trl1 enzymes found in all human fungal pathogens are untapped targets for antifungal drug discovery. Here we report a 1.9 Å crystal structure of Trl1 KIN-CPD from the pathogenic fungus Candida albicans, which adopts an extended conformation in which separate KIN and CPD domains are connected by an unstructured linker. CPD belongs to the 2H phosphotransferase superfamily by dint of its conserved central concave β sheet and interactions of its dual HxT motif histidines and threonines with phosphate in the active site. Additional active site motifs conserved among the fungal CPD clade of 2H enzymes are identified. We present structures of the Candida Trl1 KIN domain at 1.5 to 2.0 Å resolution—as apoenzyme and in complexes with GTP•Mg2+, IDP•PO4, and dGDP•PO4—that highlight conformational switches in the G-loop (which recognizes the guanine base) and lid-loop (poised over the nucleotide phosphates) that accompany nucleotide binding.
- Authors:
-
- Molecular Biology Program, Sloan-Kettering Institute, New York, NY 10065, USA
- Structural Biology Program, Sloan-Kettering Institute, New York, NY 10065, USA
- Microbiology and Immunology Department, Weill Cornell Medical College, New York, NY 10065, USA
- Publication Date:
- Research Org.:
- Argonne National Laboratory (ANL), Argonne, IL (United States). Advanced Photon Source (APS)
- Sponsoring Org.:
- USDOE; National Institutes of Health (NIH); National Cancer Institute (NCI); German Research Foundation (DFG)
- OSTI Identifier:
- 1607550
- Alternate Identifier(s):
- OSTI ID: 1578227
- Grant/Contract Number:
- AC02-06CH11357; R35-GM126945; 394320208; P30-CA008748; P41GM103403; HEI-S10RR029205
- Resource Type:
- Published Article
- Journal Name:
- Nucleic Acids Research
- Additional Journal Information:
- Journal Name: Nucleic Acids Research; Journal ID: ISSN 0305-1048
- Publisher:
- Oxford University Press
- Country of Publication:
- United Kingdom
- Language:
- English
- Subject:
- 59 BASIC BIOLOGICAL SCIENCES
Citation Formats
Banerjee, Ankan, Goldgur, Yehuda, Schwer, Beate, and Shuman, Stewart. Atomic structures of the RNA end-healing 5′-OH kinase and 2′,3′-cyclic phosphodiesterase domains of fungal tRNA ligase: conformational switches in the kinase upon binding of the GTP phosphate donor. United Kingdom: N. p., 2019.
Web. doi:10.1093/nar/gkz1049.
Banerjee, Ankan, Goldgur, Yehuda, Schwer, Beate, & Shuman, Stewart. Atomic structures of the RNA end-healing 5′-OH kinase and 2′,3′-cyclic phosphodiesterase domains of fungal tRNA ligase: conformational switches in the kinase upon binding of the GTP phosphate donor. United Kingdom. https://doi.org/10.1093/nar/gkz1049
Banerjee, Ankan, Goldgur, Yehuda, Schwer, Beate, and Shuman, Stewart. Wed .
"Atomic structures of the RNA end-healing 5′-OH kinase and 2′,3′-cyclic phosphodiesterase domains of fungal tRNA ligase: conformational switches in the kinase upon binding of the GTP phosphate donor". United Kingdom. https://doi.org/10.1093/nar/gkz1049.
@article{osti_1607550,
title = {Atomic structures of the RNA end-healing 5′-OH kinase and 2′,3′-cyclic phosphodiesterase domains of fungal tRNA ligase: conformational switches in the kinase upon binding of the GTP phosphate donor},
author = {Banerjee, Ankan and Goldgur, Yehuda and Schwer, Beate and Shuman, Stewart},
abstractNote = {Fungal tRNA ligase (Trl1) rectifies RNA breaks with 2',3'-cyclic-PO4 and 5'-OH termini. Trl1 consists of three catalytic modules: an N-terminal ligase (LIG) domain; a central polynucleotide kinase (KIN) domain; and a C-terminal cyclic phosphodiesterase (CPD) domain. Trl1 enzymes found in all human fungal pathogens are untapped targets for antifungal drug discovery. Here we report a 1.9 Å crystal structure of Trl1 KIN-CPD from the pathogenic fungus Candida albicans, which adopts an extended conformation in which separate KIN and CPD domains are connected by an unstructured linker. CPD belongs to the 2H phosphotransferase superfamily by dint of its conserved central concave β sheet and interactions of its dual HxT motif histidines and threonines with phosphate in the active site. Additional active site motifs conserved among the fungal CPD clade of 2H enzymes are identified. We present structures of the Candida Trl1 KIN domain at 1.5 to 2.0 Å resolution—as apoenzyme and in complexes with GTP•Mg2+, IDP•PO4, and dGDP•PO4—that highlight conformational switches in the G-loop (which recognizes the guanine base) and lid-loop (poised over the nucleotide phosphates) that accompany nucleotide binding.},
doi = {10.1093/nar/gkz1049},
journal = {Nucleic Acids Research},
number = ,
volume = ,
place = {United Kingdom},
year = {Wed Nov 13 00:00:00 EST 2019},
month = {Wed Nov 13 00:00:00 EST 2019}
}
Free Publicly Available Full Text
Publisher's Version of Record
https://doi.org/10.1093/nar/gkz1049
https://doi.org/10.1093/nar/gkz1049
Other availability
Search WorldCat to find libraries that may hold this journal
Cited by: 4 works
Citation information provided by
Web of Science
Web of Science
Save to My Library
You must Sign In or Create an Account in order to save documents to your library.
Works referenced in this record:
Transient ADP-ribosylation of a 2′-Phosphate Implicated in Its Removal from Ligated tRNA during Splicing in Yeast
journal, January 1999
- Spinelli, Sherry L.; Kierzek, Ryszard; Turner, Douglas H.
- Journal of Biological Chemistry, Vol. 274, Issue 5
Distinct Contributions of Enzymic Functional Groups to the 2′,3′-Cyclic Phosphodiesterase, 3′-Phosphate Guanylylation, and 3′-ppG/5′-OH Ligation Steps of the Escherichia coli RtcB Nucleic Acid Splicing Pathway
journal, February 2016
- Maughan, William P.; Shuman, Stewart
- Journal of Bacteriology, Vol. 198, Issue 8
Structural basis for the GTP specificity of the RNA kinase domain of fungal tRNA ligase
journal, November 2017
- Remus, Barbara S.; Goldgur, Yehuda; Shuman, Stewart
- Nucleic Acids Research, Vol. 45, Issue 22
RNA ligase RtcB splices 3'-phosphate and 5'-OH ends via covalent RtcB-(histidinyl)-GMP and polynucleotide-(3')pp(5')G intermediates
journal, April 2012
- Chakravarty, A. K.; Subbotin, R.; Chait, B. T.
- Proceedings of the National Academy of Sciences, Vol. 109, Issue 16
An intact unfolded protein response in Trpt1 knockout mice reveals phylogenic divergence in pathways for RNA ligation
journal, December 2007
- Harding, H. P.; Lackey, J. G.; Hsu, H. -C.
- RNA, Vol. 14, Issue 2
Structures of bacterial polynucleotide kinase in a Michaelis complex with GTP*Mg2+ and 5'-OH oligonucleotide and a product complex with GDP*Mg2+ and 5'-PO4 oligonucleotide reveal a mechanism of general acid-base catalysis and the determinants of phosphoacceptor recognition
journal, October 2013
- Das, U.; Wang, L. K.; Smith, P.
- Nucleic Acids Research, Vol. 42, Issue 2
Structure and mechanism of activity of the cyclic phosphodiesterase of Appr>p, a product of the tRNA splicing reaction
journal, November 2000
- Hofmann, A.
- The EMBO Journal, Vol. 19, Issue 22
Mammalian 2',3' cyclic nucleotide phosphodiesterase (CNP) can function as a tRNA splicing enzyme in vivo
journal, December 2007
- Schwer, B.; Aronova, A.; Ramirez, A.
- RNA, Vol. 14, Issue 2
A kinetic framework for tRNA ligase and enforcement of a 2'-phosphate requirement for ligation highlights the design logic of an RNA repair machine
journal, March 2013
- Remus, B. S.; Shuman, S.
- RNA, Vol. 19, Issue 5
A 2′-Phosphotransferase Implicated in tRNA Splicing Is Essential in Saccharomyces cerevisiae
journal, May 1997
- Culver, Gloria M.; McCraith, Stephen M.; Consaul, Sandra A.
- Journal of Biological Chemistry, Vol. 272, Issue 20
Analysis of 2'-phosphotransferase (Tpt1p) from Saccharomyces cerevisiae: Evidence for a conserved two-step reaction mechanism
journal, January 2005
- Steiger, M. A.
- RNA, Vol. 11, Issue 1
HSPC117 Is the Essential Subunit of a Human tRNA Splicing Ligase Complex
journal, February 2011
- Popow, J.; Englert, M.; Weitzer, S.
- Science, Vol. 331, Issue 6018
Substrate Recognition by a Yeast 2‘-Phosphotransferase Involved in tRNA Splicing and by Its Escherichia coli Homolog †
journal, November 2001
- Steiger, Michelle A.; Kierzek, Ryszard; Turner, Douglas H.
- Biochemistry, Vol. 40, Issue 46
Disruption of Cnp1 uncouples oligodendroglial functions in axonal support and myelination
journal, February 2003
- Lappe-Siefke, Corinna; Goebbels, Sandra; Gravel, Michel
- Nature Genetics, Vol. 33, Issue 3
Structure and mechanism of E. coli RNA 2′,3′-cyclic phosphodiesterase
journal, September 2014
- Remus, Barbara S.; Jacewicz, Agata; Shuman, Stewart
- RNA, Vol. 20, Issue 11
Candida auris : The Canary in the Mine of Antifungal Drug Resistance
journal, August 2019
- Montoya, Marhiah C.; Moye-Rowley, W. Scott; Krysan, Damian J.
- ACS Infectious Diseases, Vol. 5, Issue 9
Novel activity of a yeast ligase deletion polypeptide. Evidence for GTP-dependent tRNA splicing.
journal, February 1993
- Westaway, S. K.; Belford, H. G.; Apostol, B. L.
- Journal of Biological Chemistry, Vol. 268, Issue 4
The R tc B RNA ligase is an essential component of the metazoan unfolded protein response
journal, November 2014
- Kosmaczewski, Sara Guckian; Edwards, Tyson James; Han, Sung Min
- EMBO reports, Vol. 15, Issue 12
Structure of tRNA splicing enzyme Tpt1 illuminates the mechanism of RNA 2′-PO4 recognition and ADP-ribosylation
journal, January 2019
- Banerjee, Ankan; Munir, Annum; Abdullahu, Leonora
- Nature Communications, Vol. 10, Issue 1
tRNA Ligase Is Required for Regulated mRNA Splicing in the Unfolded Protein Response
journal, November 1996
- Sidrauski, Carmela; Cox, Jeffery S.; Walter, Peter
- Cell, Vol. 87, Issue 3
Improved methods for building protein models in electron density maps and the location of errors in these models
journal, March 1991
- Jones, T. A.; Zou, J. Y.; Cowan, S. W.
- Acta Crystallographica Section A Foundations of Crystallography, Vol. 47, Issue 2, p. 110-119
Detection of novel members, structure-function analysis and evolutionary classification of the 2H phosphoesterase superfamily
journal, December 2002
- Mazumder, R.
- Nucleic Acids Research, Vol. 30, Issue 23
Two-step mechanism and step-arrest mutants of Runella slithyformis NAD + -dependent tRNA 2′-phosphotransferase Tpt1
journal, June 2018
- Munir, Annum; Abdullahu, Leonora; Damha, Masad J.
- RNA, Vol. 24, Issue 9
Structural and mechanistic insights into guanylylation of RNA-splicing ligase RtcB joining RNA between 3'-terminal phosphate and 5'-OH
journal, September 2012
- Englert, M.; Xia, S.; Okada, C.
- Proceedings of the National Academy of Sciences, Vol. 109, Issue 38
Searching protein structure databases with DaliLite v.3
journal, September 2008
- Holm, L.; Kaariainen, S.; Rosenstrom, P.
- Bioinformatics, Vol. 24, Issue 23
Myelin 2′,3′-Cyclic Nucleotide 3′-Phosphodiesterase: Active-Site Ligand Binding and Molecular Conformation
journal, February 2012
- Myllykoski, Matti; Raasakka, Arne; Han, Huijong
- PLoS ONE, Vol. 7, Issue 2
Structures of the Noncanonical RNA Ligase RtcB Reveal the Mechanism of Histidine Guanylylation
journal, April 2013
- Desai, Kevin K.; Bingman, Craig A.; Phillips, George N.
- Biochemistry, Vol. 52, Issue 15
tRNA Splicing
journal, May 1998
- Abelson, John; Trotta, Christopher R.; Li, Hong
- Journal of Biological Chemistry, Vol. 273, Issue 21
An NAD derivative produced during transfer RNA splicing: ADP-ribose 1"-2" cyclic phosphate
journal, July 1993
- Culver, G.; McCraith, S.; Zillmann, M.
- Science, Vol. 261, Issue 5118
Solution structure of the catalytic domain of RICH protein from goldfish: Solution structure of the RICH catalytic domain
journal, February 2007
- Kozlov, Guennadi; Denisov, Alexey Y.; Pomerantseva, Ekaterina
- FEBS Journal, Vol. 274, Issue 6
Crystal structure of the C-terminal 2′,5′-phosphodiesterase domain of group a rotavirus protein VP3: Structure of Vp3 2′,5′-Phosphodiesterase Domain
journal, March 2015
- Brandmann, Tobias; Jinek, Martin
- Proteins: Structure, Function, and Bioinformatics, Vol. 83, Issue 5
RtcB, a Novel RNA Ligase, Can Catalyze tRNA Splicing and HAC1 mRNA Splicing in Vivo
journal, July 2011
- Tanaka, Naoko; Meineke, Birthe; Shuman, Stewart
- Journal of Biological Chemistry, Vol. 286, Issue 35
Structure-function analysis of the kinase-CPD domain of yeast tRNA ligase (Trl1) and requirements for complementation of tRNA splicing by a plant Trl1 homolog
journal, January 2006
- Wang, L. K.
- Nucleic Acids Research, Vol. 34, Issue 2
Distinctive kinetics and substrate specificities of plant and fungal tRNA ligases
journal, February 2014
- Remus, B. S.; Shuman, S.
- RNA, Vol. 20, Issue 4
Characterization of the tRNA ligases of pathogenic fungi Aspergillus fumigatus and Coccidioides immitis
journal, August 2016
- Remus, Barbara S.; Schwer, Beate; Shuman, Stewart
- RNA, Vol. 22, Issue 10
Mechanism of action of a yeast RNA ligase in tRNA splicing
journal, February 1983
- Greer, Chris L.; Peebles, Craig L.; Gegenheimer, Peter
- Cell, Vol. 32, Issue 2
Structure and two-metal mechanism of fungal tRNA ligase
journal, December 2018
- Banerjee, Ankan; Ghosh, Shreya; Goldgur, Yehuda
- Nucleic Acids Research, Vol. 47, Issue 3
[20] Processing of X-ray diffraction data collected in oscillation mode
book, January 1997
- Otwinowski, Zbyszek; Minor, Wladek
- Macromolecular Crystallography Part A, 307-326
Gene Essentiality Analyzed by In Vivo Transposon Mutagenesis and Machine Learning in a Stable Haploid Isolate of Candida albicans
journal, October 2018
- Segal, Ella Shtifman; Gritsenko, Vladimir; Levitan, Anton
- mBio, Vol. 9, Issue 5
Genetic and Biochemical Analysis of the Functional Domains of Yeast tRNA Ligase
journal, August 2003
- Sawaya, Rana; Schwer, Beate; Shuman, Stewart
- Journal of Biological Chemistry, Vol. 278, Issue 45
Structural and Biochemical Analysis of the Phosphate Donor Specificity of the Polynucleotide Kinase Component of the Bacterial Pnkp•Hen1 RNA Repair System
journal, June 2013
- Das, Ushati; Wang, Li Kai; Smith, Paul
- Biochemistry, Vol. 52, Issue 27
Deletion analysis of a multifunctional yeast tRNA ligase polypeptide. Identification of essential and dispensable functional domains.
journal, April 1991
- Apostol, B. L.; Westaway, S. K.; Abelson, J.
- Journal of Biological Chemistry, Vol. 266, Issue 12
Structure-function analysis of yeast tRNA ligase
journal, June 2005
- Wang, L. K.
- RNA, Vol. 11, Issue 6