3GNA

Crystal structure of the RAG1 nonamer-binding domain with DNA

Summary for 3GNA

• Entry DOI: 10.2210/pdb3gna/pdb
• Related: 3GNB
• Descriptor: V(D)J recombination-activating protein 1, 5'-D(*AP*CP*TP*TP*AP*AP*CP*AP*AP*AP*AP*AP*CP*C)-3', 5'-D(*TP*GP*GP*TP*TP*TP*TP*TP*GP*TP*TP*AP*AP*G)-3', ... (4 entities in total)
• Functional Keywords: vdj recombination, dna recombination, dna-binding, endonuclease, hydrolase, metal-binding, nuclease, nucleus, zinc-finger, amino-acid biosynthesis, isomerase, lysine biosynthesis, recombination
• Biological source: Mus musculus (Mouse); More
• Cellular location: Nucleus: P15919
• Total number of polymer chains: 3
• Total formula weight: 19363.01

Authors

Yin, F.F.,Bailey, S.,Innis, C.A.,Steitz, T.A.,Schatz, D.G. (deposition date: 2009-03-16, release date: 2009-04-28, Last modification date: 2024-02-21)

Primary citation

Yin, F.F.,Bailey, S.,Innis, C.A.,Ciubotaru, M.,Kamtekar, S.,Steitz, T.A.,Schatz, D.G.
Structure of the RAG1 nonamer binding domain with DNA reveals a dimer that mediates DNA synapsis.
Nat.Struct.Mol.Biol., 16:499-508, 2009

PubMed Abstract: The products of recombination-activating genes RAG1 and RAG2 mediate the assembly of antigen receptor genes during lymphocyte development in a process known as V(D)J recombination. Lack of structural information for the RAG proteins has hindered mechanistic studies of this reaction. We report here the crystal structure of an essential DNA binding domain of the RAG1 catalytic core bound to its nonamer DNA recognition motif. The RAG1 nonamer binding domain (NBD) forms a tightly interwoven dimer that binds and synapses two nonamer elements, with each NBD making contact with both DNA molecules. Biochemical and biophysical experiments confirm that the two nonamers are in close proximity in the RAG1/2-DNA synaptic complex and demonstrate the functional importance of the protein-DNA contacts revealed in the structure. These findings reveal a previously unsuspected function for the NBD in DNA synapsis and have implications for the regulation of DNA binding and cleavage by RAG1 and RAG2.

PubMed: 19396172
DOI: 10.1038/nsmb.1593

Experimental method

X-RAY DIFFRACTION (2.4 Å)