Structural analysis of the activation-induced deoxycytidine deaminase required in immunoglobulin diversification.
Activation-induced deoxycytidine deaminase (AID) initiates somatic hypermutation (SHM) and class-switch recombination (CSR) by deaminating C→U during transcription of Ig-variable (V) and Ig-switch (S) region DNA, which is essential to produce high-affinity antibodies. Here we report the crystal structure of a soluble human AID variant at 2.8Å resolution that favors targeting WRC motifs (W=A/T, R=A/G) in vitro, and executes Ig V SHM in Ramos B-cells. A specificity loop extending away from the active site to accommodate two purine bases next to C, differs significantly in sequence, length, and conformation from APOBEC proteins Apo3A and Apo3G, which strongly favor pyrimidines at -1 and -2 positions. Individual amino acid contributions to specificity and processivity were measured in relation to a proposed ssDNA binding cleft. This study provides a structural basis for residue contributions to DNA scanning properties unique to AID, and for disease mutations in human HIGM-2 syndrome.
Department of Biological Sciences, University of Southern California, Los Angeles, CA, 90089, United States.
Phuong
P
Pham
Department of Biological Sciences, University of Southern California, Los Angeles, CA, 90089, United States.
Samir A
SA
Afif
Department of Immunology, Graduate School of Medical Sciences, Kumamoto University, 1-1-1 Honjo, Chuo-ku, Kumamoto, 860-8556, Japan; Laboratory of Host Defence, Research Institute for Microbial Diseases, Osaka University, 3-1 Yamada-oka, Suita, 565-0871, Japan; World Premier International Research Center Initiative, Immunology Frontier Research Center, Osaka University, 3-1 Yamada-oka, Suita, 565-0871, Japan.
Mayuko
M
Shimoda
Laboratory of Host Defence, Research Institute for Microbial Diseases, Osaka University, 3-1 Yamada-oka, Suita, 565-0871, Japan; World Premier International Research Center Initiative, Immunology Frontier Research Center, Osaka University, 3-1 Yamada-oka, Suita, 565-0871, Japan.
Kazuhiko
K
Maeda
World Premier International Research Center Initiative, Immunology Frontier Research Center, Osaka University, 3-1 Yamada-oka, Suita, 565-0871, Japan; Tokyo Metropolitan Institute of Medical Science, 2-1-6, Kamikitazawa, Setagaya-ku, Tokyo, 156-8506, Japan.
Nobuo
N
Sakaguchi
Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, NC, 27709, United States.
Lars C
LC
Pedersen
Department of Biological Sciences, University of Southern California, Los Angeles, CA, 90089, United States; Department of Chemistry, University of Southern California, Los Angeles, CA 90089, United States. Electronic address: mgoodman@usc.edu.
Myron F
MF
Goodman
D000595:Amino Acid Sequence; D000818:Animals; D001402:B-Lymphocytes / Q000737:chemistry / Q000166:cytology / Q000276:immunology; D016367:Baculoviridae / Q000235:genetics / Q000378:metabolism; D020134:Catalytic Domain; D003001:Cloning, Molecular; D018360:Crystallography, X-Ray; D003564:Cytidine Deaminase / Q000737:chemistry* / Q000235:genetics / Q000276:immunology; D015870:Gene Expression; D006801:Humans; D053306:Hyper-IgM Immunodeficiency Syndrome / Q000276:immunology; D017578:Immunoglobulin Class Switching; D007136:Immunoglobulins / Q000737:chemistry* / Q000235:genetics; D008958:Models, Molecular; D009154:Mutation; D000072417:Protein Domains; D017433:Protein Structure, Secondary; D011994:Recombinant Proteins / Q000737:chemistry* / Q000235:genetics / Q000276:immunology; D061987:Sf9 Cells; D027041:Somatic Hypermutation, Immunoglobulin / Q000235:genetics*; D018411:Spodoptera; D000098830:AICDA (Activation-Induced Cytidine Deaminase)
D007136:Immunoglobulins; D011994:Recombinant Proteins; D000098830:AICDA (Activation-Induced Cytidine Deaminase); D003564:Cytidine Deaminase
AID X-ray crystal structure; Antibody diversity; Human HIGM-2 syndrome; IgV somatic hypermutation; Scanning processivity