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

Ke Shi, Thomas E. Bohl, Jeonghyun Park, Andrew Zasada, Shray Malik, Surajit Banerjee, Vincent Tran, Na Li, Zhiqi Yin, Fredy Kurniawan, Kayo Orellana, Hideki Aihara

Research output: Contribution to journalArticlepeer-review

15 Scopus citations

Abstract

DNA ligases play essential roles in DNA replication and repair. Bacteriophage T4 DNA ligase is the first ATP-dependent ligase enzyme to be discovered and is widely used in molecular biology, but its structure remained unknown. Our crystal structure of T4 DNA ligase bound to DNA shows a compact -helical DNA-binding domain (DBD), nucleotidyl-transferase (NTase) domain, and OB-fold domain, which together fully encircle DNA. The DBD of T4 DNA ligase exhibits remarkable structural homology to the core DNA-binding helices of the larger DBDs from eukaryotic and archaeal DNA ligases, but it lacks additional structural components required for protein interactions. T4 DNA ligase instead has a flexible loop insertion within the NTase domain, which binds tightly to the T4 sliding clamp gp45 in a novel -helical PIP-box conformation. Thus, T4 DNA ligase represents a prototype of the larger eukaryotic and archaeal DNA ligases, with a uniquely evolved mode of protein interaction that may be important for efficient DNA replication.

Original languageEnglish (US)
Pages (from-to)10474-10488
Number of pages15
JournalNucleic acids research
Volume46
Issue number19
DOIs
StatePublished - Nov 2 2018

Bibliographical note

Funding Information:
We thank John M. Pascal and Brian A. Kelch for hLig1 and T4 gp44/62 expression plasmid, respectively, and Ming Li for help with gel analysis. The authors acknowledge the Minnesota Supercomputing Institute (MSI) at the University of Minnesota for providing resources that contributed to the research results reported within this paper. Northeastern Collaborative Access Team beamlines are funded by the US National Institutes of Health [NIGMS P41-GM103403]; The Pilatus 6M detector on 24-ID-C beamline is funded by a NIH-ORIP HEI grant [S10 RR029205]; Advanced Photon Source is a U.S. Department of Energy (DOE) Office of Science User Facility operated for the DOE Office of Science by Argonne National Laboratory under contract [DE-AC02-06CH11357]; UROP (Undergraduate Research Opportunities Program) from the University of Minnesota (to J.P. and V.T.); a fellowship from 3M corporation to TEB; NIH grant [R35 GM118047 to H.A.]. Funding for open access charge: National Institutes of Health.

Funding Information:
Northeastern Collaborative Access Team beamlines are funded by the US National Institutes of Health [NIGMS P41-GM103403]; The Pilatus 6M detector on 24-ID-C beamline is funded by a NIH-ORIP HEI grant [S10 RR029205]; Advanced Photon Source is a U.S. Department of Energy (DOE) Office of Science User Facility operated for the DOE Office of Science by Argonne National Laboratory under contract [DE-AC02-06CH11357]; UROP (Undergraduate Research Opportunities Program) from the University of Minnesota (to J.P. and V.T.); a fellowship from 3M corporation to TEB; NIH grant [R35 GM118047 to H.A.]. Funding for open access charge: National Institutes of Health. Conflict of interest statement. None declared.

Publisher Copyright:
© The Author(s) 2018.

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