The full-length structure of Thermus scotoductus OLD defines the ATP hydrolysis properties and catalytic mechanism of Class 1 OLD family nucleases
Abstract
Abstract OLD family nucleases contain an N-terminal ATPase domain and a C-terminal Toprim domain. Homologs segregate into two classes based on primary sequence length and the presence/absence of a unique UvrD/PcrA/Rep-like helicase gene immediately downstream in the genome. Although we previously defined the catalytic machinery controlling Class 2 nuclease cleavage, degenerate conservation of the C-termini between classes precludes pinpointing the analogous residues in Class 1 enzymes by sequence alignment alone. Our Class 2 structures also provide no information on ATPase domain architecture and ATP hydrolysis. Here we present the full-length structure of the Class 1 OLD nuclease from Thermus scotoductus (Ts) at 2.20 Å resolution, which reveals a dimerization domain inserted into an N-terminal ABC ATPase fold and a C-terminal Toprim domain. Structural homology with genome maintenance proteins identifies conserved residues responsible for Ts OLD ATPase activity. Ts OLD lacks the C-terminal helical domain present in Class 2 OLD homologs yet preserves the spatial organization of the nuclease active site, arguing that OLD proteins use a conserved catalytic mechanism for DNA cleavage. We also demonstrate that mutants perturbing ATP hydrolysis or DNA cleavage in vitro impair P2 OLD-mediated killing of recBC−Escherichia coli hosts, indicating that both the ATPase and nucleasemore »
- Authors:
-
- Department of Molecular Medicine, Cornell University, Ithaca, NY 14853, USA
- Publication Date:
- Research Org.:
- Argonne National Lab. (ANL), Argonne, IL (United States)
- Sponsoring Org.:
- USDOE; National Institutes of Health (NIH)
- OSTI Identifier:
- 1596875
- Alternate Identifier(s):
- OSTI ID: 1604201
- Grant/Contract Number:
- AC02-06CH11357
- Resource Type:
- Published Article
- Journal Name:
- Nucleic Acids Research
- Additional Journal Information:
- Journal Name: Nucleic Acids Research Journal Volume: 48 Journal Issue: 5; Journal ID: ISSN 0305-1048
- Publisher:
- Oxford University Press
- Country of Publication:
- United Kingdom
- Language:
- English
- Subject:
- 59 BASIC BIOLOGICAL SCIENCES
Citation Formats
Schiltz, Carl J., Adams, Myfanwy C., and Chappie, Joshua S. The full-length structure of Thermus scotoductus OLD defines the ATP hydrolysis properties and catalytic mechanism of Class 1 OLD family nucleases. United Kingdom: N. p., 2020.
Web. doi:10.1093/nar/gkaa059.
Schiltz, Carl J., Adams, Myfanwy C., & Chappie, Joshua S. The full-length structure of Thermus scotoductus OLD defines the ATP hydrolysis properties and catalytic mechanism of Class 1 OLD family nucleases. United Kingdom. https://doi.org/10.1093/nar/gkaa059
Schiltz, Carl J., Adams, Myfanwy C., and Chappie, Joshua S. Mon .
"The full-length structure of Thermus scotoductus OLD defines the ATP hydrolysis properties and catalytic mechanism of Class 1 OLD family nucleases". United Kingdom. https://doi.org/10.1093/nar/gkaa059.
@article{osti_1596875,
title = {The full-length structure of Thermus scotoductus OLD defines the ATP hydrolysis properties and catalytic mechanism of Class 1 OLD family nucleases},
author = {Schiltz, Carl J. and Adams, Myfanwy C. and Chappie, Joshua S.},
abstractNote = {Abstract OLD family nucleases contain an N-terminal ATPase domain and a C-terminal Toprim domain. Homologs segregate into two classes based on primary sequence length and the presence/absence of a unique UvrD/PcrA/Rep-like helicase gene immediately downstream in the genome. Although we previously defined the catalytic machinery controlling Class 2 nuclease cleavage, degenerate conservation of the C-termini between classes precludes pinpointing the analogous residues in Class 1 enzymes by sequence alignment alone. Our Class 2 structures also provide no information on ATPase domain architecture and ATP hydrolysis. Here we present the full-length structure of the Class 1 OLD nuclease from Thermus scotoductus (Ts) at 2.20 Å resolution, which reveals a dimerization domain inserted into an N-terminal ABC ATPase fold and a C-terminal Toprim domain. Structural homology with genome maintenance proteins identifies conserved residues responsible for Ts OLD ATPase activity. Ts OLD lacks the C-terminal helical domain present in Class 2 OLD homologs yet preserves the spatial organization of the nuclease active site, arguing that OLD proteins use a conserved catalytic mechanism for DNA cleavage. We also demonstrate that mutants perturbing ATP hydrolysis or DNA cleavage in vitro impair P2 OLD-mediated killing of recBC−Escherichia coli hosts, indicating that both the ATPase and nuclease activities are required for OLD function in vivo.},
doi = {10.1093/nar/gkaa059},
journal = {Nucleic Acids Research},
number = 5,
volume = 48,
place = {United Kingdom},
year = {2020},
month = {2}
}
https://doi.org/10.1093/nar/gkaa059
Works referenced in this record:
Role of the D-Loops in Allosteric Control of ATP Hydrolysis in an ABC Transporter
journal, December 2011
- Jones, Peter M.; George, Anthony M.
- The Journal of Physical Chemistry A, Vol. 116, Issue 11
The crystal structure of DNA mismatch repair protein MutS binding to a G·T mismatch
journal, October 2000
- Lamers, Meindert H.; Perrakis, Anastassis; Enzlin, Jacqueline H.
- Nature, Vol. 407, Issue 6805
RecA-like motor ATPases—lessons from structures
journal, November 2004
- Ye, Jiqing; Osborne, Andrew R.; Groll, Michael
- Biochimica et Biophysica Acta (BBA) - Bioenergetics, Vol. 1659, Issue 1
ATP-dependent conformational change in ABC-ATPase RecF serves as a switch in DNA repair
journal, February 2018
- Tang, Qun; Liu, Yan-Ping; Shan, Hai-Huan
- Scientific Reports, Vol. 8, Issue 1
The membrane-bound proteins of periplasmic permeases form a complex. Identification of the histidine permease HisQMP complex
journal, May 1991
- Kerppola, R. E.; Shyamala, V. K.; Klebba, P.
- Journal of Biological Chemistry, Vol. 266, Issue 15
Bacteriophage Lambda; Abortive Infection of Bacteria Lysogenic for Phage P2
journal, July 1970
- Lindahl, G.; Sironi, G.; Bialy, H.
- Proceedings of the National Academy of Sciences, Vol. 66, Issue 3
Genome Scanning for Conditionally Essential Genes in Salmonella enterica Serotype Typhimurium
journal, February 2012
- Khatiwara, Anita; Jiang, Tieshan; Sung, Sam-Sun
- Applied and Environmental Microbiology, Vol. 78, Issue 9
Crystal structures of mismatch repair protein MutS and its complex with a substrate DNA
journal, October 2000
- Obmolova, Galina; Ban, Changill; Hsieh, Peggy
- Nature, Vol. 407, Issue 6805
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
Structural characterization of Class 2 OLD family nucleases supports a two-metal catalysis mechanism for cleavage
journal, August 2019
- Schiltz, Carl J.; Lee, April; Partlow, Edward A.
- Nucleic Acids Research, Vol. 47, Issue 17
Dali server: conservation mapping in 3D
journal, May 2010
- Holm, Liisa; Rosenstr�m, P�ivi
- Nucleic Acids Research, Vol. 38, Issue suppl_2
Distinct Structural and Functional Properties of the ATPase Sites in an Asymmetric ABC Transporter
journal, October 2006
- Procko, Erik; Ferrin-O'Connell, Ian; Ng, Sze-Ling
- Molecular Cell, Vol. 24, Issue 1
Anomalous diffraction in crystallographic phase evaluation
journal, February 2014
- Hendrickson, Wayne A.
- Quarterly Reviews of Biophysics, Vol. 47, Issue 1
The Q loops of the human multidrug resistance transporter ABCB1 are necessary to couple drug binding to the ATP catalytic cycle
journal, October 2014
- Zolnerciks, Joseph K.; Akkaya, Begum G.; Snippe, Marjolein
- The FASEB Journal, Vol. 28, Issue 10
Structure and mechanism of ABC transporter proteins
journal, August 2007
- Hollenstein, Kaspar; Dawson, Roger JP; Locher, Kaspar P.
- Current Opinion in Structural Biology, Vol. 17, Issue 4
In Vivo Studies of Temperature-Sensitive recB and recC Mutants
journal, January 1974
- Kushner, Sidney R.
- Journal of Bacteriology, Vol. 120, Issue 3
H662 is the linchpin of ATP hydrolysis in the nucleotide-binding domain of the ABC transporter HlyB
journal, May 2005
- Zaitseva, Jelena; Jenewein, Stefan; Jumpertz, Thorsten
- The EMBO Journal, Vol. 24, Issue 11
Nucleases: diversity of structure, function and mechanism
journal, September 2010
- Yang, Wei
- Quarterly Reviews of Biophysics, Vol. 44, Issue 1
Structure of Full-Length SMC and Rearrangements Required for Chromosome Organization
journal, July 2017
- Diebold-Durand, Marie-Laure; Lee, Hansol; Ruiz Avila, Laura B.
- Molecular Cell, Vol. 67, Issue 2
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
ATP ‐dependent DNA binding, unwinding, and resection by the Mre11/Rad50 complex
journal, December 2015
- Liu, Yaqi; Sung, Sihyun; Kim, Youngran
- The EMBO Journal, Vol. 35, Issue 7
Mechanism of formation of a toroid around DNA by the mismatch sensor protein
journal, November 2017
- Nirwal, Shivlee; Kulkarni, Dhananjaya S.; Sharma, Amit
- Nucleic Acids Research, Vol. 46, Issue 1
Rad50 ATPase activity is regulated by DNA ends and requires coordination of both active sites
journal, March 2017
- Deshpande, Rajashree A.; Lee, Ji-Hoon; Paull, Tanya T.
- Nucleic Acids Research, Vol. 45, Issue 9
Invited review: Architectures and mechanisms of ATP binding cassette proteins
journal, May 2016
- Hopfner, Karl‐Peter
- Biopolymers, Vol. 105, Issue 8
Snapshots of the maltose transporter during ATP hydrolysis
journal, August 2011
- Oldham, M. L.; Chen, J.
- Proceedings of the National Academy of Sciences, Vol. 108, Issue 37
Toprim--a conserved catalytic domain in type IA and II topoisomerases, DnaG-type primases, OLD family nucleases and RecR proteins
journal, September 1998
- Aravind, L.
- Nucleic Acids Research, Vol. 26, Issue 18
An Interaction between the Walker A and D-loop Motifs Is Critical to ATP Hydrolysis and Cooperativity in Bacteriophage T4 Rad50
journal, May 2011
- De la Rosa, Metzere Bierlein; Nelson, Scott W.
- Journal of Biological Chemistry, Vol. 286, Issue 29
Structure, Function, and Evolution of Bacterial ATP-Binding Cassette Systems
journal, June 2008
- Davidson, A. L.; Dassa, E.; Orelle, C.
- Microbiology and Molecular Biology Reviews, Vol. 72, Issue 2
Structure of a Pancreatic ATP-Sensitive Potassium Channel
journal, January 2017
- Li, Ningning; Wu, Jing-Xiang; Ding, Dian
- Cell, Vol. 168, Issue 1-2
A dynamic allosteric pathway underlies Rad50 ABC ATPase function in DNA repair
journal, January 2018
- Boswell, Zachary K.; Rahman, Samiur; Canny, Marella D.
- Scientific Reports, Vol. 8, Issue 1
The Rad50 Signature Motif: Essential to ATP Binding and Biological Function
journal, January 2004
- Moncalian, Gabriel; Lengsfeld, Bettina; Bhaskara, Venugopal
- Journal of Molecular Biology, Vol. 335, Issue 4
Scaling and assessment of data quality
journal, December 2005
- Evans, Philip
- Acta Crystallographica Section D Biological Crystallography, Vol. 62, Issue 1, p. 72-82
ConSurf 2016: an improved methodology to estimate and visualize evolutionary conservation in macromolecules
journal, May 2016
- Ashkenazy, Haim; Abadi, Shiran; Martz, Eric
- Nucleic Acids Research, Vol. 44, Issue W1
Single-molecule imaging of UvrA and UvrB recruitment to DNA lesions in living Escherichia coli
journal, August 2016
- Stracy, Mathew; Jaciuk, Marcin; Uphoff, Stephan
- Nature Communications, Vol. 7, Issue 1
UCSF Chimera?A visualization system for exploratory research and analysis
journal, January 2004
- Pettersen, Eric F.; Goddard, Thomas D.; Huang, Conrad C.
- Journal of Computational Chemistry, Vol. 25, Issue 13
Structure of the Human MutSα DNA Lesion Recognition Complex
journal, May 2007
- Warren, Joshua J.; Pohlhaus, Timothy J.; Changela, Anita
- Molecular Cell, Vol. 26, Issue 4
Structural conservation of RecF and Rad50: implications for DNA recognition and RecF function
journal, January 2007
- Koroleva, Olga; Makharashvili, Nodar; Courcelle, Charmain T.
- The EMBO Journal, Vol. 26, Issue 3
Mutants of Escherichia coli unable to be lysogenized by the temperate bacteriophage P2
journal, February 1969
- Sironi, G.
- Virology, Vol. 37, Issue 2
The old exonuclease of bacteriophage P2.
journal, February 1995
- Myung, H.; Calendar, R.
- Journal of Bacteriology, Vol. 177, Issue 3
CFTR structure and cystic fibrosis
journal, July 2014
- Cant, Natasha; Pollock, Naomi; Ford, Robert C.
- The International Journal of Biochemistry & Cell Biology, Vol. 52