PDBsum entry 6v0v

Recombination/DNA

PDB id: 6v0v

Contents

Protein chains

541 a.a.

346 a.a.

DNA/RNA

Metals

_ZN

_CA ×2

PDB id:

6v0v

Name:

Recombination/DNA

Title:

Cryo-em structure of mouse wt rag1/2 nfc complex (dna0)

Structure:

V(d)j recombination-activating protein 1. Chain: a. Synonym: rag-1. Engineered: yes. V(d)j recombination-activating protein 2. Chain: b. Synonym: rag-2. Engineered: yes. DNA (30-mer).

Source:

Mus musculus. Mouse. Organism_taxid: 10090. Gene: rag1. Expressed in: homo sapiens. Expression_system_taxid: 9606. Gene: rag2, rag-2. Synthetic: yes. Escherichia coli.

Authors:

X.Chen,W.Yang,M.Gellert

Key ref:

X.Chen et al. (2020). Cutting antiparallel DNA strands in a single active site. Nat Struct Mol Biol, 27, 119-126. PubMed id: 32015552 DOI: 10.1038/s41594-019-0363-2

Date:

19-Nov-19 Release date: 29-Jan-20

Protein chain

P15919  (RAG1_MOUSE) -  V(D)J recombination-activating protein 1 from Mus musculus

Seq: 1040 a.a.

Struc: 541 a.a.

Protein chain

P21784  (RAG2_MOUSE) -  V(D)J recombination-activating protein 2 from Mus musculus

Seq: 527 a.a.

Struc: 346 a.a.

DNA/RNA chains

G-C-T-G-T-A-T-C-A-C-T-G-T-G-T-A-A-G-A-C-A-G-G-C-C-A-G-A-T-C 30 bases

G-A-T-C-T-G-G-C-C-T-G-T-C-T-T-A-C-A-C-A-G-T-G-A-T-A-C-A-G-C 30 bases

Enzyme reactions

• Enzyme class 2: Chain A: E.C.2.3.2.27 - RING-type E3 ubiquitin transferase.
• Reaction: S-ubiquitinyl-[E2 ubiquitin-conjugating enzyme]-L-cysteine + [acceptor protein]-L-lysine = [E2 ubiquitin-conjugating enzyme]-L-cysteine + N₆- ubiquitinyl-[acceptor protein]-L-lysine
• Enzyme class 3: Chain A: E.C.3.1.-.-

Note, where more than one E.C. class is given (as above), each may correspond to a different protein domain or, in the case of polyprotein precursors, to a different mature protein.

DOI no: 10.1038/s41594-019-0363-2

Nat Struct Mol Biol 27:119-126 (2020)

PubMed id: 32015552

Cutting antiparallel DNA strands in a single active site.

X.Chen, Y.Cui, R.B.Best, H.Wang, Z.H.Zhou, W.Yang, M.Gellert.

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.