Structural adaptation of vertebrate endonuclease G for 5-hydroxymethylcytosine recognition and function
Open Access
- 25 February 2020
- journal article
- research article
- Published by Oxford University Press (OUP) in Nucleic Acids Research
- Vol. 48 (7), 3962-3974
- https://doi.org/10.1093/nar/gkaa117
Abstract
Modified DNA bases functionally distinguish the taxonomic forms of life—5-methylcytosine separates prokaryotes from eukaryotes and 5-hydroxymethylcytosine (5hmC) invertebrates from vertebrates. We demonstrate here that mouse endonuclease G (mEndoG) shows specificity for both 5hmC and Holliday junctions. The enzyme has higher affinity (>50-fold) for junctions over duplex DNAs. A 5hmC-modification shifts the position of the cut site and increases the rate of DNA cleavage in modified versus unmodified junctions. The crystal structure of mEndoG shows that a cysteine (Cys69) is positioned to recognize 5hmC through a thiol-hydroxyl hydrogen bond. Although this Cys is conserved from worms to mammals, a two amino acid deletion in the vertebrate relative to the invertebrate sequence unwinds an α-helix, placing the thiol of Cys69 into the mEndoG active site. Mutations of Cys69 with alanine or serine show 5hmC-specificity that mirrors the hydrogen bonding potential of the side chain (C–H < S–H < O–H). A second orthogonal DNA binding site identified in the mEndoG structure accommodates a second arm of a junction. Thus, the specificity of mEndoG for 5hmC and junctions derives from structural adaptations that distinguish the vertebrate from the invertebrate enzyme, thereby thereby supporting a role for 5hmC in recombination processes.Funding Information
- National Science Foundation (MCB-1515521, CBET-1905328)
- National Institutes of Health (F31GM113580)
- Southern and Eastern Norway Regional Health Authority (2014017)
This publication has 62 references indexed in Scilit:
- Thymine DNA Glycosylase Can Rapidly Excise 5-Formylcytosine and 5-Carboxylcytosine: POTENTIAL IMPLICATIONS FOR ACTIVE DEMETHYLATION OF CpG SITESOnline Journal of Public Health Informatics, 2011
- Thymine DNA Glycosylase Is Essential for Active DNA Demethylation by Linked Deamination-Base Excision RepairCell, 2011
- Hydroxylation of 5-Methylcytosine by TET1 Promotes Active DNA Demethylation in the Adult BrainCell, 2011
- Tet1 and Tet2 Regulate 5-Hydroxymethylcytosine Production and Cell Lineage Specification in Mouse Embryonic Stem CellsCell Stem Cell, 2011
- Endonuclease G plays a role in immunoglobulin class switch DNA recombination by introducing double-strand breaks in switch regionsMolecular Immunology, 2011
- Selective chemical labeling reveals the genome-wide distribution of 5-hydroxymethylcytosineNature Biotechnology, 2011
- Structural Changes Common to Catalysis in the Tpx Peroxiredoxin SubfamilyJournal of Molecular Biology, 2009
- The Drosophila melanogaster Gene cg4930 Encodes a High Affinity Inhibitor for Endonuclease GOnline Journal of Public Health Informatics, 2009
- Phylogenomic analysis of the emergence of GC-rich transcription elementsProceedings of the National Academy of Sciences of the United States of America, 2007
- Endonuclease G: A role for the enzyme in recombination and cellular proliferationProceedings of the National Academy of Sciences of the United States of America, 2006