DNA binding with a minimal scaffold: structure-function analysis of Lig E DNA ligases

Nucleic Acids Research
Adele WilliamsonHanna-Kirsti S Leiros

Abstract

DNA ligases join breaks in the phosphodiester backbone of DNA by catalysing the formation of bonds between opposing 5'P and 3'OH ends in an adenylation-dependent manner. Catalysis is accompanied by reorientation of two core domains to provide access to the active site for cofactor utilization and enable substrate binding and product release. The general paradigm is that DNA ligases engage their DNA substrate through complete encirclement of the duplex, completed by inter-domain kissing contacts via loops or additional domains. The recent structure of a minimal Lig E-type DNA ligase, however, implies it must use a different mechanism, as it lacks any domains or loops appending the catalytic core which could complete encirclement. In the present study, we have used a structure-guided mutagenesis approach to investigate the role of conserved regions in the Lig E proteins with respect to DNA binding. We report the structure of a Lig-E type DNA ligase bound to the nicked DNA-adenylate reaction intermediate, confirming that complete encirclement is unnecessary for substrate engagement. Biochemical and biophysical measurements of point mutants to residues implicated in binding highlight the importance of basic residues in the OB domai...Continue Reading

References

Feb 28, 1998·Nucleic Acids Research·V Sriskanda, S Shuman
Feb 9, 2006·Chemical Reviews·Alan E TomkinsonTom Ellenberger

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Citations

May 5, 2020·Nucleic Acids Research·Adele Williamson, Hanna-Kirsti S Leiros
Jul 25, 2019·Nucleic Acids Research·Michiel VanmeertEveline Lescrinier
Mar 4, 2019·Extremophiles : Life Under Extreme Conditions·Kristel BergAdele Williamson

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Methods Mentioned

BETA
X-ray

Software Mentioned

XSCALE
AIMLESS
PDBeFold
XDS
MST
Phaser
RING
COOT
Psy
Thermofisher GeneArt

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