Structures of ATP-bound DNA ligase D in a closed domain conformation reveal a network of amino acid and metal contacts to the ATP phosphates
Abstract
DNA ligases are the sine qua non of genome integrity and essential for DNA replication and repair in all organisms. DNA ligases join 3'-OH and 5'-PO4 ends via a series of three nucleotidyl transfer steps. In step 1, ligase reacts with ATP or NAD+ to form a covalent ligase-(lysyl-N$$ζ$$)–AMP intermediate and release pyrophosphate (PPi) or nicotinamide mononucleotide. In step 2, AMP is transferred from ligase-adenylate to the 5'-PO4 DNA end to form a DNA-adenylate intermediate (AppDNA). In step 3, ligase catalyzes attack by a DNA 3'-OH on the DNA-adenylate to seal the two ends via a phosphodiester bond and release AMP. Eukaryal, archaeal, and many bacterial and viral DNA ligases are ATP-dependent. The catalytic core of ATP-dependent DNA ligases consists of an N-terminal nucleotidyltransferase domain fused to a C-terminal OB domain. Here we report crystal structures at 1.4–1.8 Å resolution of Mycobacterium tuberculosis LigD, an ATP-dependent DNA ligase dedicated to nonhomologous end joining, in complexes with ATP that highlight large movements of the OB domain (~50 Å), from a closed conformation in the ATP complex to an open conformation in the covalent ligase-AMP intermediate. The LigD·ATP structures revealed a network of amino acid contacts to the ATP phosphates that stabilize the transition state and orient the PPi leaving group. A complex with ATP and magnesium suggested a two-metal mechanism of lysine adenylylation driven by a catalytic Mg2+ that engages the ATP $$α$$ phosphate and a second metal that bridges the ATP $$β$$ and $$γ$$ phosphates.
- Authors:
-
- Sloan Kettering Inst., New York, NY (United States)
- Publication Date:
- Research Org.:
- Argonne National Lab. (ANL), Argonne, IL (United States). Advanced Photon Source (APS)
- Sponsoring Org.:
- National Institute of General Medical Sciences (NIGMS); National Institutes of Health (NIH); USDOE; National Cancer Institute (NCI)
- OSTI Identifier:
- 1513025
- Grant/Contract Number:
- P41GM103403; P41GM103473; P41GM111244; HEI S10RR029205; AC02-06CH11357; AC02-98CH10886; SC0012704; GM126945; AI64693; P30-CA008748
- Resource Type:
- Accepted Manuscript
- Journal Name:
- Journal of Biological Chemistry
- Additional Journal Information:
- Journal Volume: 294; Journal Issue: 13; Journal ID: ISSN 0021-9258
- Publisher:
- American Society for Biochemistry and Molecular Biology
- Country of Publication:
- United States
- Language:
- ENGLISH
- Subject:
- 59 BASIC BIOLOGICAL SCIENCES; DNA repair; enzyme structure; ATP; metal ion-protein interaction; catalysis; Mycobacterium tuberculosis; covalent nucleotidyltransferase; DNA ligase; lysyl–AMP; two metal mechanism
Citation Formats
Unciuleac, Mihaela-Carmen, Goldgur, Yehuda, and Shuman, Stewart. Structures of ATP-bound DNA ligase D in a closed domain conformation reveal a network of amino acid and metal contacts to the ATP phosphates. United States: N. p., 2019.
Web. doi:10.1074/jbc.RA119.007445.
Unciuleac, Mihaela-Carmen, Goldgur, Yehuda, & Shuman, Stewart. Structures of ATP-bound DNA ligase D in a closed domain conformation reveal a network of amino acid and metal contacts to the ATP phosphates. United States. https://doi.org/10.1074/jbc.RA119.007445
Unciuleac, Mihaela-Carmen, Goldgur, Yehuda, and Shuman, Stewart. Mon .
"Structures of ATP-bound DNA ligase D in a closed domain conformation reveal a network of amino acid and metal contacts to the ATP phosphates". United States. https://doi.org/10.1074/jbc.RA119.007445. https://www.osti.gov/servlets/purl/1513025.
@article{osti_1513025,
title = {Structures of ATP-bound DNA ligase D in a closed domain conformation reveal a network of amino acid and metal contacts to the ATP phosphates},
author = {Unciuleac, Mihaela-Carmen and Goldgur, Yehuda and Shuman, Stewart},
abstractNote = {DNA ligases are the sine qua non of genome integrity and essential for DNA replication and repair in all organisms. DNA ligases join 3'-OH and 5'-PO4 ends via a series of three nucleotidyl transfer steps. In step 1, ligase reacts with ATP or NAD+ to form a covalent ligase-(lysyl-N$ζ$)–AMP intermediate and release pyrophosphate (PPi) or nicotinamide mononucleotide. In step 2, AMP is transferred from ligase-adenylate to the 5'-PO4 DNA end to form a DNA-adenylate intermediate (AppDNA). In step 3, ligase catalyzes attack by a DNA 3'-OH on the DNA-adenylate to seal the two ends via a phosphodiester bond and release AMP. Eukaryal, archaeal, and many bacterial and viral DNA ligases are ATP-dependent. The catalytic core of ATP-dependent DNA ligases consists of an N-terminal nucleotidyltransferase domain fused to a C-terminal OB domain. Here we report crystal structures at 1.4–1.8 Å resolution of Mycobacterium tuberculosis LigD, an ATP-dependent DNA ligase dedicated to nonhomologous end joining, in complexes with ATP that highlight large movements of the OB domain (~50 Å), from a closed conformation in the ATP complex to an open conformation in the covalent ligase-AMP intermediate. The LigD·ATP structures revealed a network of amino acid contacts to the ATP phosphates that stabilize the transition state and orient the PPi leaving group. A complex with ATP and magnesium suggested a two-metal mechanism of lysine adenylylation driven by a catalytic Mg2+ that engages the ATP $α$ phosphate and a second metal that bridges the ATP $β$ and $γ$ phosphates.},
doi = {10.1074/jbc.RA119.007445},
journal = {Journal of Biological Chemistry},
number = 13,
volume = 294,
place = {United States},
year = {Mon Feb 04 00:00:00 EST 2019},
month = {Mon Feb 04 00:00:00 EST 2019}
}
Web of Science
Works referenced in this record:
Bacterial Nonhomologous End Joining Ligases Preferentially Seal Breaks with a 3′-OH Monoribonucleotide
journal, January 2008
- Zhu, Hui; Shuman, Stewart
- Journal of Biological Chemistry, Vol. 283, Issue 13
Bacterial DNA repair by non-homologous end joining
journal, November 2007
- Shuman, Stewart; Glickman, Michael S.
- Nature Reviews Microbiology, Vol. 5, Issue 11
Structural and mutational analysis of archaeal ATP-dependent RNA ligase identifies amino acids required for RNA binding and catalysis
journal, February 2016
- Gu, Huiqiong; Yoshinari, Shigeo; Ghosh, Raka
- Nucleic Acids Research, Vol. 44, Issue 5
Structure of the Catalytic Region of DNA Ligase IV in Complex with an Artemis Fragment Sheds Light on Double-Strand Break Repair
journal, April 2013
- Ochi, Takashi; Gu, Xiaolong; Blundell, Tom L.
- Structure, Vol. 21, Issue 4
Atomic structure and nonhomologous end-joining function of the polymerase component of bacterial DNA ligase D
journal, January 2006
- Zhu, H.; Nandakumar, J.; Aniukwu, J.
- Proceedings of the National Academy of Sciences, Vol. 103, Issue 6
ATP-dependent DNA ligase from Thermococcus sp. 1519 displays a new arrangement of the OB-fold domain
journal, November 2012
- Petrova, T.; Bezsudnova, E. Y.; Boyko, K. M.
- Acta Crystallographica Section F Structural Biology and Crystallization Communications, Vol. 68, Issue 12
T4 DNA ligase structure reveals a prototypical ATP-dependent ligase with a unique mode of sliding clamp interaction
journal, August 2018
- Shi, Ke; Bohl, Thomas E.; Park, Jeonghyun
- Nucleic Acids Research, Vol. 46, Issue 19
Enzyme–adenylate structure of a bacterial ATP-dependent DNA ligase with a minimized DNA-binding surface
journal, October 2014
- Williamson, Adele; Rothweiler, Ulli; Leiros, Hanna-Kirsti Schrøder
- Acta Crystallographica Section D Biological Crystallography, Vol. 70, Issue 11
Structure of bacterial LigD 3'-phosphoesterase unveils a DNA repair superfamily
journal, June 2010
- Nair, P. A.; Smith, P.; Shuman, S.
- Proceedings of the National Academy of Sciences, Vol. 107, Issue 29
The Closed Structure of an Archaeal DNA Ligase from Pyrococcus furiosus
journal, July 2006
- Nishida, Hirokazu; Kiyonari, Shinichi; Ishino, Yoshizumi
- Journal of Molecular Biology, Vol. 360, Issue 5
ATP-dependent DNA ligase from Archaeoglobus fulgidus displays a tightly closed conformation
journal, May 2009
- Kim, Do Jin; Kim, Olesya; Kim, Hyeon-Woo
- Acta Crystallographica Section F Structural Biology and Crystallization Communications, Vol. 65, Issue 6
Characterization of Agrobacterium tumefaciens DNA ligases C and D
journal, May 2007
- Zhu, Hui; Shuman, Stewart
- Nucleic Acids Research, Vol. 35, Issue 11
Structure and two-metal mechanism of a eukaryal nick-sealing RNA ligase
journal, October 2015
- Unciuleac, Mihaela-Carmen; Goldgur, Yehuda; Shuman, Stewart
- Proceedings of the National Academy of Sciences, Vol. 112, Issue 45
The adenylyltransferase domain of bacterial Pnkp defines a unique RNA ligase family
journal, January 2012
- Smith, P.; Wang, L. K.; Nair, P. A.
- Proceedings of the National Academy of Sciences, Vol. 109, Issue 7
Mechanism of nonhomologous end-joining in mycobacteria: a low-fidelity repair system driven by Ku, ligase D and ligase C
journal, March 2005
- Gong, Chunling; Bongiorno, Paola; Martins, Alexandra
- Nature Structural & Molecular Biology, Vol. 12, Issue 4
Biochemical and Genetic Analysis of the Four DNA Ligases of Mycobacteria
journal, February 2004
- Gong, Chunling; Martins, Alexandra; Bongiorno, Paola
- Journal of Biological Chemistry, Vol. 279, Issue 20
Crystal Structure of an ATP-Dependent DNA Ligase from Bacteriophage T7
journal, May 1996
- Subramanya, Hosahalli S.; Doherty, Aidan J.; Ashford, Stephen R.
- Cell, Vol. 85, Issue 4
X-Ray Crystallography Reveals a Large Conformational Change during Guanyl Transfer by mRNA Capping Enzymes
journal, May 1997
- Håkansson, Kjell; Doherty, Aidan J.; Shuman, Stewart
- Cell, Vol. 89, Issue 4
Mutational Analysis of the Guanylyltransferase Component of Mammalian mRNA Capping Enzyme †
journal, July 2003
- Sawaya, Rana; Shuman, Stewart
- Biochemistry, Vol. 42, Issue 27
DNA and RNA ligases: structural variations and shared mechanisms
journal, February 2008
- Pascal, John M.
- Current Opinion in Structural Biology, Vol. 18, Issue 1
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
Crystal Structure of Eukaryotic DNA Ligase–Adenylate Illuminates the Mechanism of Nick Sensing and Strand Joining
journal, November 2000
- Odell, Mark; Sriskanda, Verl; Shuman, Stewart
- Molecular Cell, Vol. 6, Issue 5
Structures of DNA-bound human ligase IV catalytic core reveal insights into substrate binding and catalysis
journal, July 2018
- Kaminski, Andrea M.; Tumbale, Percy P.; Schellenberg, Matthew J.
- Nature Communications, Vol. 9, Issue 1
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
Last Stop on the Road to Repair: Structure of E. coli DNA Ligase Bound to Nicked DNA-Adenylate
journal, April 2007
- Nandakumar, Jayakrishnan; Nair, Pravin A.; Shuman, Stewart
- Molecular Cell, Vol. 26, Issue 2
DNA binding with a minimal scaffold: structure–function analysis of Lig E DNA ligases
journal, July 2018
- Williamson, Adele; Grgic, Miriam; Leiros, Hanna-Kirsti S.
- Nucleic Acids Research, Vol. 46, Issue 16
NMRPipe: A multidimensional spectral processing system based on UNIX pipes
journal, November 1995
- Delaglio, Frank; Grzesiek, Stephan; Vuister, GeertenW.
- Journal of Biomolecular NMR, Vol. 6, Issue 3
Crystal Structure and Nonhomologous End-joining Function of the Ligase Component of Mycobacterium DNA Ligase D
journal, February 2006
- Akey, David; Martins, Alexandra; Aniukwu, Jideofor
- Journal of Biological Chemistry, Vol. 281, Issue 19
Solution NMR Studies of Chlorella Virus DNA Ligase-adenylate
journal, January 2010
- Piserchio, Andrea; Nair, Pravin A.; Shuman, Stewart
- Journal of Molecular Biology, Vol. 395, Issue 2
Molecular basis of bacterial protein Hen1 activating the ligase activity of bacterial protein Pnkp for RNA repair
journal, July 2012
- Wang, P.; Chan, C. M.; Christensen, D.
- Proceedings of the National Academy of Sciences, Vol. 109, Issue 33
Molecular Architecture and Ligand Recognition Determinants for T4 RNA Ligase
journal, November 2005
- Omari, Kamel El; Ren, Jingshan; Bird, Louise E.
- Journal of Biological Chemistry, Vol. 281, Issue 3
Structural basis for nick recognition by a minimal pluripotent DNA ligase
journal, July 2007
- Nair, Pravin A.; Nandakumar, Jayakrishnan; Smith, Paul
- Nature Structural & Molecular Biology, Vol. 14, Issue 8
RNA Ligase Structures Reveal the Basis for RNA Specificity and Conformational Changes that Drive Ligation Forward
journal, October 2006
- Nandakumar, Jayakrishnan; Shuman, Stewart; Lima, Christopher D.
- Cell, Vol. 127, Issue 1
MOLREP an Automated Program for Molecular Replacement
journal, December 1997
- Vagin, A.; Teplyakov, A.
- Journal of Applied Crystallography, Vol. 30, Issue 6, p. 1022-1025
RNA 3′-Phosphate Cyclase (RtcA) Catalyzes Ligase-like Adenylylation of DNA and RNA 5′-Monophosphate Ends
journal, November 2010
- Chakravarty, Anupam K.; Shuman, Stewart
- Journal of Biological Chemistry, Vol. 286, Issue 6
Two-metal versus one-metal mechanisms of lysine adenylylation by ATP-dependent and NAD + -dependent polynucleotide ligases
journal, February 2017
- Unciuleac, Mihaela-Carmen; Goldgur, Yehuda; Shuman, Stewart
- Proceedings of the National Academy of Sciences, Vol. 114, Issue 10
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
Human DNA ligase I completely encircles and partially unwinds nicked DNA
journal, November 2004
- Pascal, John M.; O'Brien, Patrick J.; Tomkinson, Alan E.
- Nature, Vol. 432, Issue 7016
A Flexible Interface between DNA Ligase and PCNA Supports Conformational Switching and Efficient Ligation of DNA
journal, October 2006
- Pascal, John M.; Tsodikov, Oleg V.; Hura, Greg L.
- Molecular Cell, Vol. 24, Issue 2
Human DNA Ligase III Recognizes DNA Ends by Dynamic Switching between Two DNA-Bound States
journal, July 2010
- Cotner-Gohara, Elizabeth; Kim, In-Kwon; Hammel, Michal
- Biochemistry, Vol. 49, Issue 29
The pathways and outcomes of mycobacterial NHEJ depend on the structure of the broken DNA ends
journal, February 2008
- Aniukwu, J.; Glickman, M. S.; Shuman, S.
- Genes & Development, Vol. 22, Issue 4
The polynucleotide ligase and RNA capping enzyme superfamily of covalent nucleotidyltransferases
journal, December 2004
- Shuman, Stewart; Lima, Christopher D.
- Current Opinion in Structural Biology, Vol. 14, Issue 6
Structure and Function of a Mycobacterial NHEJ DNA Repair Polymerase
journal, February 2007
- Pitcher, Robert S.; Brissett, Nigel C.; Picher, Angel J.
- Journal of Molecular Biology, Vol. 366, Issue 2
[20] Processing of X-ray diffraction data collected in oscillation mode
book, January 1997
- Otwinowski, Zbyszek; Minor, Wladek
- Macromolecular Crystallography Part A, 307-326
Cavin1 intrinsically disordered domains are essential for fuzzy electrostatic interactions and caveola formation
journal, February 2021
- Tillu, Vikas A.; Rae, James; Gao, Ya
- Nature Communications, Vol. 12, Issue 1
Multi-functionality of a tryptophan residue conserved in substrate-binding groove of GH19 chitinases
journal, January 2021
- Nagata, Takuya; Shinya, Shoko; Ohnuma, Takayuki
- Scientific Reports, Vol. 11, Issue 1
PHENIX: a comprehensive Python-based system for macromolecular structure solution.
text, January 2010
- Adams, Paul D.; Afonine, Pavel V.; Bunkóczi, Gábor
- Apollo - University of Cambridge Repository
Structure of the catalytic region of DNA ligase IV in complex with an Artemis fragment sheds light on double-strand break repair.
text, January 2013
- Ochi, Takashi; Gu, Xiaolong; Blundell, Tom
- Apollo - University of Cambridge Repository
Works referencing / citing this record:
Structural intermediates of a DNA–ligase complex illuminate the role of the catalytic metal ion and mechanism of phosphodiester bond formation
journal, July 2019
- Williamson, Adele; Leiros, Hanna-Kirsti S.
- Nucleic Acids Research, Vol. 47, Issue 14
Strategies for Developing CRISPR‐Based Gene Editing Methods in Bacteria
journal, November 2019
- Wu, Zhaowei; Wang, Yujue; Zhang, Yifei
- Small Methods, Vol. 4, Issue 2