UMMS Affiliation
Department of Biochemistry and Molecular Pharmacology; Schiffer Lab
Publication Date
2018-05-14
Document Type
Article
Disciplines
Amino Acids, Peptides, and Proteins | Biochemistry | Enzymes and Coenzymes | Genetic Phenomena | Genetics and Genomics | Molecular Biology | Nucleic Acids, Nucleotides, and Nucleosides | Structural Biology
Abstract
The APOBEC3 (A3) family of human cytidine deaminases is renowned for providing a first line of defense against many exogenous and endogenous retroviruses. However, the ability of these proteins to deaminate deoxycytidines in ssDNA makes A3s a double-edged sword. When overexpressed, A3s can mutate endogenous genomic DNA resulting in a variety of cancers. Although the sequence context for mutating DNA varies among A3s, the mechanism for substrate sequence specificity is not well understood. To characterize substrate specificity of A3A, a systematic approach was used to quantify the affinity for substrate as a function of sequence context, length, secondary structure, and solution pH. We identified the A3A ssDNA binding motif as (T/C)TC(A/G), which correlated with enzymatic activity. We also validated that A3A binds RNA in a sequence specific manner. A3A bound tighter to substrate binding motif within a hairpin loop compared to linear oligonucleotide, suggesting A3A affinity is modulated by substrate structure. Based on these findings and previously published A3A-ssDNA co-crystal structures, we propose a new model with intra-DNA interactions for the molecular mechanism underlying A3A sequence preference. Overall, the sequence and structural preferences identified for A3A leads to a new paradigm for identifying A3A's involvement in mutation of endogenous or exogenous DNA.
Rights and Permissions
© The Author(s) 2018. Open Access: This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.
DOI of Published Version
10.1038/s41598-018-25881-z
Source
Sci Rep. 2018 May 14;8(1):7511. doi: 10.1038/s41598-018-25881-z. Link to article on publisher's site
Journal/Book/Conference Title
Scientific reports
Related Resources
PubMed ID
29760455
Repository Citation
Silvas TV, Hou S, Myint W, Nalivaika EA, Somasundaran M, Kelch BA, Matsuo H, Yilmaz NK, Schiffer CA. (2018). Substrate sequence selectivity of APOBEC3A implicates intra-DNA interactions. Open Access Articles. https://doi.org/10.1038/s41598-018-25881-z. Retrieved from https://escholarship.umassmed.edu/oapubs/3475
Creative Commons License
This work is licensed under a Creative Commons Attribution 4.0 License.
Included in
Amino Acids, Peptides, and Proteins Commons, Biochemistry Commons, Enzymes and Coenzymes Commons, Genetic Phenomena Commons, Genetics and Genomics Commons, Molecular Biology Commons, Nucleic Acids, Nucleotides, and Nucleosides Commons, Structural Biology Commons