H3K4me3 induces allosteric conformational changes in the DNA-binding and catalytic regions of the V(D)J recombinase.
V(D)J recombination is initiated by the recombination-activating gene (RAG) recombinase, consisting of RAG-1 and RAG-2 subunits. The susceptibility of gene segments to cleavage by RAG is associated with histone modifications characteristic of active chromatin, including trimethylation of histone H3 at lysine 4 (H3K4me3). Binding of H3K4me3 by a plant homeodomain (PHD) in RAG-2 stimulates substrate binding and catalysis, which are functions of RAG-1. This has suggested an allosteric mechanism in which information regarding occupancy of the RAG-2 PHD is transmitted to RAG-1. To determine whether the conformational distribution of RAG is altered by H3K4me3, we mapped changes in solvent accessibility of cysteine thiols by differential isotopic chemical footprinting. Binding of H3K4me3 to the RAG-2 PHD induces conformational changes in RAG-1 within a DNA-binding domain and in the ZnH2 domain, which acts as a scaffold for the catalytic center. Thus, engagement of H3K4me3 by the RAG-2 PHD is associated with dynamic conformational changes in RAG-1, consistent with allosteric control by active chromatin.
Department of Molecular Biology and Genetics, The Johns Hopkins University School of Medicine, Baltimore, MD 21205.|Institute for Cell Engineering, The Johns Hopkins University School of Medicine, Baltimore, MD 21205.
John
J
Bettridge
McKusick-Nathans Institute of Genetic Medicine, The Johns Hopkins University School of Medicine, Baltimore, MD 21205.|Department of Biological Chemistry, The Johns Hopkins University School of Medicine, Baltimore, MD 21205.
Chan Hyun
CH
Na
McKusick-Nathans Institute of Genetic Medicine, The Johns Hopkins University School of Medicine, Baltimore, MD 21205.|Department of Biological Chemistry, The Johns Hopkins University School of Medicine, Baltimore, MD 21205.
Akhilesh
0000-0001-9943-6127
A
Pandey
Department of Molecular Biology and Genetics, The Johns Hopkins University School of Medicine, Baltimore, MD 21205; sdesider@jhmi.edu.|Institute for Cell Engineering, The Johns Hopkins University School of Medicine, Baltimore, MD 21205.
Stephen
S
Desiderio
D000494:Allosteric Regulation; D001665:Binding Sites; D020134:Catalytic Domain; D002843:Chromatin / Q000378:metabolism*; D003545:Cysteine / Q000378:metabolism; D004247:DNA / Q000378:metabolism; D019175:DNA Methylation; D016654:Genes, RAG-1 / Q000502:physiology*; D006657:Histones / Q000378:metabolism*; D008239:Lysine / Q000378:metabolism; D018521:Plant Physiological Phenomena; D010940:Plant Proteins / Q000737:chemistry*; D011485:Protein Binding; D011487:Protein Conformation; D060152:V(D)J Recombination; D045567:VDJ Recombinases / Q000737:chemistry*
D002843:Chromatin; D006657:Histones; D010940:Plant Proteins; D004247:DNA; D045567:VDJ Recombinases; D008239:Lysine; D003545:Cysteine
DNA recombination; allosteric control; epigenetic modification; genomic plasticity; immune development