6GRC

eukaryotic junction-resolving enzyme GEN-1 binding with Sodium

Summary for 6GRC

• Entry DOI: 10.2210/pdb6grc/pdb
• Descriptor: Nuclease-like protein, DNA (5'-D(*TP*GP*AP*GP*CP*GP*GP*TP*GP*GP*TP*TP*GP*GP*T)-3'), DNA (5'-D(*TP*AP*CP*CP*CP*AP*CP*CP*AP*CP*CP*GP*CP*TP*CP*A)-3'), ... (5 entities in total)
• Functional Keywords: 4-way holiday junction, resolvase, dna recombination, gen1, h2th, potassium, dna
• Biological source: Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719); More
• Total number of polymer chains: 3
• Total formula weight: 68546.76

Authors

Lilley, D.M.J.,Liu, Y.,Freeman, D.J. (deposition date: 2018-06-11, release date: 2018-09-26, Last modification date: 2024-11-06)

Primary citation

Liu, Y.,Freeman, A.D.,Declais, A.C.,Lilley, D.M.J.
A monovalent ion in the DNA binding interface of the eukaryotic junction-resolving enzyme GEN1.
Nucleic Acids Res., 46:11089-11098, 2018

PubMed Abstract: GEN1 is a member of the FEN/EXO family of structure-selective nucleases that cleave 1 nt 3' to a variety of branchpoints. For each, the H2TH motif binds a monovalent ion and plays an important role in binding one helical arm of the substrates. We investigate here the importance of this metal ion on substrate specificity and GEN1 structure. In the presence of K+ ions the substrate specificity is wider than in Na+, yet four-way junctions remain the preferred substrate. In a combination of K+ and Mg2+ second strand cleavage is accelerated 17-fold, ensuring bilateral cleavage of the junction. We have solved crystal structures of Chaetomium thermophilum GEN1 with Cs+, K+ and Na+ bound. With bound Cs+ the loop of the H2TH motif extends toward the active site so that D199 coordinates a Mg2+, buttressed by an interaction of the adjacent Y200. With the lighter ions bound the H2TH loop changes conformation and retracts away from the active site. We hypothesize this conformational change might play a role in second strand cleavage acceleration.

PubMed: 30247722
DOI: 10.1093/nar/gky863

Experimental method

X-RAY DIFFRACTION (2.452 Å)