SNAP annotations: PDB entry 6v0v

PDB-id

6v0v; DSSR-derived features in text and JSON formats; DNAproDB

Class

recombination-DNA

Method

cryo-EM (3.61 Å)

Summary

cryo-EM structure of mouse wt rag1-2 nfc complex (dna0)

Reference

Chen X, Cui Y, Best RB, Wang H, Zhou ZH, Yang W, Gellert M (2020): "Cutting antiparallel DNA strands in a single active site." Nat.Struct.Mol.Biol., 27, 119-126. doi: 10.1038/s41594-019-0363-2.

Abstract

A single enzyme active site that catalyzes multiple reactions is a well-established biochemical theme, but how one nuclease site cleaves both DNA strands of a double helix has not been well understood. In analyzing site-specific DNA cleavage by the mammalian RAG1-RAG2 recombinase, which initiates V(D)J recombination, we find that the active site is reconfigured for the two consecutive reactions and the DNA double helix adopts drastically different structures. For initial nicking of the DNA, a locally unwound and unpaired DNA duplex forms a zipper via alternating interstrand base stacking, rather than melting as generally thought. The second strand cleavage and formation of a hairpin-DNA product requires a global scissor-like movement of protein and DNA, delivering the scissile phosphate into the rearranged active site.