6NJU

Mouse endonuclease G mutant H97A bound to A-DNA

Summary for 6NJU

• Entry DOI: 10.2210/pdb6nju/pdb
• Descriptor: Endonuclease G, mitochondrial, DNA (5'-D(CCGGCGCCGG)-3'), MAGNESIUM ION, ... (6 entities in total)
• Functional Keywords: complex, endonuclease, recombination
• Biological source: Mus musculus (Mouse); More
• Total number of polymer chains: 5
• Total formula weight: 114973.79

Authors

Vander Zanden, C.M.,Ho, E.N.,Czarny, R.S.,Robertson, A.B.,Ho, P.S. (deposition date: 2019-01-04, release date: 2020-01-08, Last modification date: 2024-10-09)

Primary citation

Vander Zanden, C.M.,Czarny, R.S.,Ho, E.N.,Robertson, A.B.,Ho, P.S.
Structural adaptation of vertebrate endonuclease G for 5-hydroxymethylcytosine recognition and function.
Nucleic Acids Res., 48:3962-3974, 2020

PubMed 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.

PubMed: 32095813
DOI: 10.1093/nar/gkaa117

Experimental method

X-RAY DIFFRACTION (2.35 Å)