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

Unciuleac, Mihaela-Carmen; Goldgur, Yehuda; Shuman, Stewart

doi:10.1074/jbc.RA119.007445

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

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 (PP_i) 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 PP_i 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:

Unciuleac, Mihaela-Carmen ^[1]; Goldgur, Yehuda ^[1]; Shuman, Stewart ^[1]

Sloan Kettering Inst., New York, NY (United States)

Publication Date:: Mon Feb 04 00:00:00 EST 2019

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.

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                    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

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                    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.

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@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}

}

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https://doi.org/10.1074/jbc.RA119.007445

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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
DOI: 10.1074/jbc.M705476200

Bacterial DNA repair by non-homologous end joining
journal, November 2007

Shuman, Stewart; Glickman, Michael S.
Nature Reviews Microbiology, Vol. 5, Issue 11
DOI: 10.1038/nrmicro1768

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
DOI: 10.1093/nar/gkw094

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
DOI: 10.1016/j.str.2013.02.014

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
DOI: 10.1073/pnas.0509083103

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
DOI: 10.1107/S1744309112043394

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
DOI: 10.1093/nar/gky776

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
DOI: 10.1107/S1399004714021099

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
DOI: 10.1073/pnas.1005830107

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
DOI: 10.1016/j.jmb.2006.05.062

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
DOI: 10.1107/S1744309109017485

Characterization of Agrobacterium tumefaciens DNA ligases C and D
journal, May 2007

Zhu, Hui; Shuman, Stewart
Nucleic Acids Research, Vol. 35, Issue 11
DOI: 10.1093/nar/gkm145

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
DOI: 10.1073/pnas.1516536112

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
DOI: 10.1073/pnas.1116827109

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
DOI: 10.1038/nsmb915

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
DOI: 10.1074/jbc.M401841200

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
DOI: 10.1016/S0092-8674(00)81260-X

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
DOI: 10.1016/S0092-8674(00)80236-6

Mutational Analysis of the Guanylyltransferase Component of Mammalian mRNA Capping Enzyme ^†
journal, July 2003

Sawaya, Rana; Shuman, Stewart
Biochemistry, Vol. 42, Issue 27
DOI: 10.1021/bi034396d

DNA and RNA ligases: structural variations and shared mechanisms
journal, February 2008

Pascal, John M.
Current Opinion in Structural Biology, Vol. 18, Issue 1
DOI: 10.1016/j.sbi.2007.12.008

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

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
DOI: 10.1016/S1097-2765(00)00115-5

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
DOI: 10.1038/s41467-018-05024-8

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
DOI: 10.1107/S0108767390010224

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
DOI: 10.1016/j.molcel.2007.02.026

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
DOI: 10.1093/nar/gky622

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
DOI: 10.1007/BF00197809

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
DOI: 10.1074/jbc.M513550200

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
DOI: 10.1016/j.jmb.2009.11.007

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
DOI: 10.1073/pnas.1209805109

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
DOI: 10.1074/jbc.M509658200

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
DOI: 10.1038/nsmb1266

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
DOI: 10.1016/j.cell.2006.08.038

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
DOI: 10.1107/S0021889897006766

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
DOI: 10.1074/jbc.M110.196766

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
DOI: 10.1073/pnas.1619220114

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
DOI: 10.1093/nar/gky1275

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
DOI: 10.1038/nature03082

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
DOI: 10.1016/j.molcel.2006.08.015

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
DOI: 10.1021/bi100503w

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
DOI: 10.1101/gad.1631908

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
DOI: 10.1016/j.sbi.2004.10.006

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
DOI: 10.1016/j.jmb.2006.10.046

[20] Processing of X-ray diffraction data collected in oscillation mode
book, January 1997

Otwinowski, Zbyszek; Minor, Wladek
Macromolecular Crystallography Part A, 307-326
DOI: 10.1016/S0076-6879(97)76066-X

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
DOI: 10.1038/s41467-021-21035-4

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
DOI: 10.1038/s41598-021-81903-3

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
DOI: 10.17863/cam.45787

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
DOI: 10.17863/cam.65854

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DOI: 10.1093/nar/gkz596

Strategies for Developing CRISPR‐Based Gene Editing Methods in Bacteria
journal, November 2019

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DOI: 10.1002/smtd.201900560

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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

Abstract

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Solution NMR Studies of Chlorella Virus DNA Ligase-adenylate journal, January 2010

Molecular basis of bacterial protein Hen1 activating the ligase activity of bacterial protein Pnkp for RNA repair journal, July 2012

Molecular Architecture and Ligand Recognition Determinants for T4 RNA Ligase journal, November 2005

Structural basis for nick recognition by a minimal pluripotent DNA ligase journal, July 2007

RNA Ligase Structures Reveal the Basis for RNA Specificity and Conformational Changes that Drive Ligation Forward journal, October 2006

MOLREP an Automated Program for Molecular Replacement journal, December 1997

RNA 3′-Phosphate Cyclase (RtcA) Catalyzes Ligase-like Adenylylation of DNA and RNA 5′-Monophosphate Ends journal, November 2010

Two-metal versus one-metal mechanisms of lysine adenylylation by ATP-dependent and NAD + -dependent polynucleotide ligases journal, February 2017

Structure and two-metal mechanism of fungal tRNA ligase journal, December 2018

Human DNA ligase I completely encircles and partially unwinds nicked DNA journal, November 2004

A Flexible Interface between DNA Ligase and PCNA Supports Conformational Switching and Efficient Ligation of DNA journal, October 2006

Human DNA Ligase III Recognizes DNA Ends by Dynamic Switching between Two DNA-Bound States journal, July 2010

The pathways and outcomes of mycobacterial NHEJ depend on the structure of the broken DNA ends journal, February 2008

The polynucleotide ligase and RNA capping enzyme superfamily of covalent nucleotidyltransferases journal, December 2004

Structure and Function of a Mycobacterial NHEJ DNA Repair Polymerase journal, February 2007

[20] Processing of X-ray diffraction data collected in oscillation mode book, January 1997

Cavin1 intrinsically disordered domains are essential for fuzzy electrostatic interactions and caveola formation journal, February 2021

Multi-functionality of a tryptophan residue conserved in substrate-binding groove of GH19 chitinases journal, January 2021

PHENIX: a comprehensive Python-based system for macromolecular structure solution. text, January 2010

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

Structural intermediates of a DNA–ligase complex illuminate the role of the catalytic metal ion and mechanism of phosphodiester bond formation journal, July 2019

Strategies for Developing CRISPR‐Based Gene Editing Methods in Bacteria journal, November 2019

Bacterial Nonhomologous End Joining Ligases Preferentially Seal Breaks with a 3′-OH Monoribonucleotide
journal, January 2008

Bacterial DNA repair by non-homologous end joining
journal, November 2007

Structural and mutational analysis of archaeal ATP-dependent RNA ligase identifies amino acids required for RNA binding and catalysis
journal, February 2016

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

Atomic structure and nonhomologous end-joining function of the polymerase component of bacterial DNA ligase D
journal, January 2006

ATP-dependent DNA ligase from Thermococcus sp. 1519 displays a new arrangement of the OB-fold domain
journal, November 2012

T4 DNA ligase structure reveals a prototypical ATP-dependent ligase with a unique mode of sliding clamp interaction
journal, August 2018

Enzyme–adenylate structure of a bacterial ATP-dependent DNA ligase with a minimized DNA-binding surface
journal, October 2014

Structure of bacterial LigD 3'-phosphoesterase unveils a DNA repair superfamily
journal, June 2010

The Closed Structure of an Archaeal DNA Ligase from Pyrococcus furiosus
journal, July 2006

ATP-dependent DNA ligase from Archaeoglobus fulgidus displays a tightly closed conformation
journal, May 2009

Characterization of Agrobacterium tumefaciens DNA ligases C and D
journal, May 2007

Structure and two-metal mechanism of a eukaryal nick-sealing RNA ligase
journal, October 2015

The adenylyltransferase domain of bacterial Pnkp defines a unique RNA ligase family
journal, January 2012

Mechanism of nonhomologous end-joining in mycobacteria: a low-fidelity repair system driven by Ku, ligase D and ligase C
journal, March 2005

Biochemical and Genetic Analysis of the Four DNA Ligases of Mycobacteria
journal, February 2004

Crystal Structure of an ATP-Dependent DNA Ligase from Bacteriophage T7
journal, May 1996

X-Ray Crystallography Reveals a Large Conformational Change during Guanyl Transfer by mRNA Capping Enzymes
journal, May 1997

Mutational Analysis of the Guanylyltransferase Component of Mammalian mRNA Capping Enzyme ^†
journal, July 2003

DNA and RNA ligases: structural variations and shared mechanisms
journal, February 2008

PHENIX: a comprehensive Python-based system for macromolecular structure solution
journal, January 2010

Crystal Structure of Eukaryotic DNA Ligase–Adenylate Illuminates the Mechanism of Nick Sensing and Strand Joining
journal, November 2000

Structures of DNA-bound human ligase IV catalytic core reveal insights into substrate binding and catalysis
journal, July 2018

Improved methods for building protein models in electron density maps and the location of errors in these models
journal, March 1991

Last Stop on the Road to Repair: Structure of E. coli DNA Ligase Bound to Nicked DNA-Adenylate
journal, April 2007

DNA binding with a minimal scaffold: structure–function analysis of Lig E DNA ligases
journal, July 2018

NMRPipe: A multidimensional spectral processing system based on UNIX pipes
journal, November 1995

Crystal Structure and Nonhomologous End-joining Function of the Ligase Component of Mycobacterium DNA Ligase D
journal, February 2006

Solution NMR Studies of Chlorella Virus DNA Ligase-adenylate
journal, January 2010

Molecular basis of bacterial protein Hen1 activating the ligase activity of bacterial protein Pnkp for RNA repair
journal, July 2012

Molecular Architecture and Ligand Recognition Determinants for T4 RNA Ligase
journal, November 2005

Structural basis for nick recognition by a minimal pluripotent DNA ligase
journal, July 2007

RNA Ligase Structures Reveal the Basis for RNA Specificity and Conformational Changes that Drive Ligation Forward
journal, October 2006

MOLREP an Automated Program for Molecular Replacement
journal, December 1997

RNA 3′-Phosphate Cyclase (RtcA) Catalyzes Ligase-like Adenylylation of DNA and RNA 5′-Monophosphate Ends
journal, November 2010

Two-metal versus one-metal mechanisms of lysine adenylylation by ATP-dependent and NAD ⁺ -dependent polynucleotide ligases
journal, February 2017

Structure and two-metal mechanism of fungal tRNA ligase
journal, December 2018

Human DNA ligase I completely encircles and partially unwinds nicked DNA
journal, November 2004

A Flexible Interface between DNA Ligase and PCNA Supports Conformational Switching and Efficient Ligation of DNA
journal, October 2006

Human DNA Ligase III Recognizes DNA Ends by Dynamic Switching between Two DNA-Bound States
journal, July 2010

The pathways and outcomes of mycobacterial NHEJ depend on the structure of the broken DNA ends
journal, February 2008

The polynucleotide ligase and RNA capping enzyme superfamily of covalent nucleotidyltransferases
journal, December 2004

Structure and Function of a Mycobacterial NHEJ DNA Repair Polymerase
journal, February 2007

[20] Processing of X-ray diffraction data collected in oscillation mode
book, January 1997

Cavin1 intrinsically disordered domains are essential for fuzzy electrostatic interactions and caveola formation
journal, February 2021

Multi-functionality of a tryptophan residue conserved in substrate-binding groove of GH19 chitinases
journal, January 2021

PHENIX: a comprehensive Python-based system for macromolecular structure solution.
text, January 2010

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

Structural intermediates of a DNA–ligase complex illuminate the role of the catalytic metal ion and mechanism of phosphodiester bond formation
journal, July 2019

Strategies for Developing CRISPR‐Based Gene Editing Methods in Bacteria
journal, November 2019