PDBsum entry 6xnx

Recombination

PDB id: 6xnx

Contents

Protein chains

549 a.a.

342 a.a.

DNA/RNA

Metals

_ZN ×2

_MG ×4

PDB id:

6xnx

Name:

Recombination

Title:

Structure of rag1 (r848m/e649v)-rag2-DNA strand transfer complex (dynamic-form)

Structure:

V(d)j recombination-activating protein 1. Chain: a, c. Synonym: rag-1. Engineered: yes. Mutation: yes. V(d)j recombination-activating protein 2. Chain: b, d. Synonym: rag-2. Engineered: yes.

Source:

Mus musculus. Mouse. Organism_taxid: 10090. Gene: rag1. Expressed in: homo sapiens. Expression_system_taxid: 9606. Expression_system_cell_line: expi293f. Gene: rag2, rag-2. Synthetic: yes.

Authors:

Y.Zhang,E.Corbett,S.Wu,D.G.Schatz

Key ref:

Y.Zhang et al. (2020). Structural basis for the activation and suppression of transposition during evolution of the RAG recombinase. EMBO J, 39, e105857. PubMed id: 32945578 DOI: 10.15252/embj.2020105857

Date:

05-Jul-20 Release date: 26-Aug-20

Protein chains

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

Seq: 1040 a.a.

Struc: 549 a.a.*

Protein chains

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

Seq: 527 a.a.

Struc: 342 a.a.*

* PDB and UniProt seqs differ at 3 residue positions (black crosses)

DNA/RNA chains

G-C-C-T-A-C-T-A-C-C-A-C-T-G-T-G-C-G-G-T-A-G-C-C-C-T-A-T-C-C-T-G 32 bases

A-C-T-A-C-C-A-C-T-G-T-G-C-G-G-T-A-G-C-C-C-T-A-T-C-C-T-G 28 bases

C-A-G-G-A-T-A-G-G-G-C-T-A-C 14 bases

C-A-G-G-A-T-A-G-G-G-C-T-A-C 14 bases

C-A-C-A-G-T-G-G-T-A-G-T 12 bases

C-A-C-A-G-T-G-G-T-A-G-T-A-G-G-C 16 bases

Enzyme reactions

• Enzyme class 2: Chains A, C: 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: Chains A, C: E.C.3.1.-.-
• Enzyme class 4: Chains B, D: E.C.?

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: 10.15252/embj.2020105857

EMBO J 39:e105857 (2020)

PubMed id: 32945578

Structural basis for the activation and suppression of transposition during evolution of the RAG recombinase.

Y.Zhang, E.Corbett, S.Wu, D.G.Schatz.

ABSTRACT

Jawed vertebrate adaptive immunity relies on the RAG1/RAG2 (RAG) recombinase, a domesticated transposase, for assembly of antigen receptor genes. Using an integration-activated form of RAG1 with methionine at residue 848 and cryo-electron microscopy, we determined structures that capture RAG engaged with transposon ends and U-shaped target DNA prior to integration (the target capture complex) and two forms of the RAG strand transfer complex that differ based on whether target site DNA is annealed or dynamic. Target site DNA base unstacking, flipping, and melting by RAG1 methionine 848 explain how this residue activates transposition, how RAG can stabilize sharp bends in target DNA, and why replacement of residue 848 by arginine during RAG domestication led to suppression of transposition activity. RAG2 extends a jawed vertebrate-specific loop to interact with target site DNA, and functional assays demonstrate that this loop represents another evolutionary adaptation acquired during RAG domestication to inhibit transposition. Our findings identify mechanistic principles of the final step in cut-and-paste transposition and the molecular and structural logic underlying the transformation of RAG from transposase to recombinase.