Sandbox GGC9

Structure of RAG1/2-DNA Strand Transfer Complex (paired conformation)

spinqualitylabelsall models Structure of RAG1/2-DNA Strand Transfer Complex (Paired Conformation) Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image   Print3D RAG1 is the catalytic component of the RAG Complex. Together with RAG2, the RAG Complex functions to create antibodies for virtually any antigen. Function RAG1 and RAG2 together form the RAG Complex (RAG Recombinases), which is responsible for regulating the DNA cleavage phase during V(D)J recombination. V(D)J recombination functions to produce a plethora of immune molecules in developing B and T cells. The B and T immune cells contain proteins on their surfaces which allow for the recognition of different pathogens and elicits proper immune responses. The RAG genes, which are responsible for making these proteins, have different segments which are known as V, variable, D, diversity and J, joining. These segments can be combined and rearranged to create the diversity required for the proteins for the B and T cells. RAG1 functions as the catalytic portion while RAG2, although not catalytic, is required for RAG1 to function.[1] RAG1 controls the ability of the DNA to bind to the RSS or recombination signal sequences. RAG1 is able to to create a double-stranded break between the (RSS) and the adjacent coding sequence. This rearrangement is carried out in the following way: introduction of a nick in the DNA backbone through hairpin formation and then creating a hydroxyl group at the 3' end which attacks the phosphodiester bond on the opposite strand.[1] This mechanism is a direct transesterification reaction which results in four differentiated DNA ends. Studies of this recombination suggest that the RAG1/2 recombinase complex acts as a transposon, with similar mechanisms.[2] Histones also assist in the nicking and hairpinning of the strands. The result is the recombination of variable genes joining to produce proteins in a response to different pathogens.[1] Additionally to the role played in V(D)J recombination, RAG also assists B cell allelic exclusion which means that it is able to silence one allele of the B cell but can express the other allele. RAG1 also possess ubiquitin properties. Disease Mutations of the RAG recombinases are often occurring in patients being displaying immunodeficiency and Omenn syndrome. [3] Omenn's syndrome is a severe combined immunodeficiency. [4] Some characteristics include redness of skin, peeling skin, hair loss, chronic diarrhea, enlarged lymph nodes, swelling of liver and spleen, and increased levels of of serum IgE. [4] (Hsu et al 2011) Relevance Early intervention of people with Omenn's syndrome is important, because if left untreated it will be fatal. [4] Treatment of Omenn's syndrome includes bone marrow or cord blood stem cell transplantation. [4] Structural highlights The subunit structure is defined as a homodimer. The zinc site plays an important role in DNA cleavage; without the zinc site the DNA would not be able to be cleaved and would not form the essential hairpin structure.[5]Zinc Ligands Ring Zinc Finger of dimerization domain. Initial studies identified aspartic acid residues at positions 600 and 708 function to initiate catalysis.[7]Catalytic Residues In addition to the catalytic function of aspartic acid residues at 600 and 708. Researchers have discovered a trio of residues that are necessary for the DNA cleavage during V(D)J recombination. This trio includes the two catalytic residues as well as a Glutamic acid residue at position 962.[8]Residues responsible for DNA cleavage Residues 265-383 on RAG 1 contain ubiquitin ligase activity. Ubiquitin activity

References

[1] Grazini U, Zanardi F, Citterio E, Casola S, Goding CR, McBlane F. The RING domain of RAG1 ubiquitylates histone H3: a novel activity in chromatin-mediated regulation of V(D)J joining. Mol Cell. 2010 Jan 29;37(2):282-93. doi: 10.1016/j.molcel.2009.12.035. PMID: 20122409.

[2] Zhang Y, Corbett E, Wu S, Schatz DG. Structural basis for the activation and suppression of transposition during evolution of the RAG recombinase. EMBO J. 2020 Nov 2;39(21):e105857. doi: 10.15252/embj.2020105857. Epub 2020 Sep 18. PMID: 32945578; PMCID: PMC7604617.

[3] Chen, Karin et al. “Autoimmunity due to RAG deficiency and estimated disease incidence in RAG1/2 mutations.” The Journal of allergy and clinical immunology vol. 133,3 (2014): 880-2.e10. doi:10.1016/j.jaci.2013.11.038

[4] Omenn syndrome | Genetic and Rare Diseases Information Center (GARD) – an NCATS Program. Rarediseases.info.nih.gov. (2021). Retrieved 7 April 2021, from https://rarediseases.info.nih.gov/diseases/8198/omenn-syndrome.

[5] Gwyn, Lori M et al. “A zinc site in the C-terminal domain of RAG1 is essential for DNA cleavage activity.” Journal of molecular biology vol. 390,5 (2009): 863-78. doi:10.1016/j.jmb.2009.05.076

[6] Hsu, C., Yu-Yun Lee, J., & Chao, S. (2011). Omenn syndrome: a case report and review of literature. Dermatologica Sinica, 29(2). https://doi.org/doi.org/10.1016/j.dsi.2011.05.002

[7] Fugmann, S., Villey, I., Ptaszek, L., & Schatz, D. (2000). Identification of Two Catalytic Residues in RAG1 that Define a Single Active Site within the RAG1/RAG2 Protein Complex. Molecular Cell, 5(1), 97-107. https://doi.org/10.1016/s1097-2765(00)80406-2

[8] Swanson P. C. (2001). The DDE motif in RAG-1 is contributed in trans to a single active site that catalyzes the nicking and transesterification steps of V(D)J recombination. Molecular and cellular biology, 21(2), 449–458. https://doi.org/10.1128/MCB.21.2.449-458.2001