Cryo-EM structure of the EBV ribonucleotide reductase BORF2 and mechanism of APOBEC3B inhibition

Nadine M. Shaban, Rui Yan, Ke Shi, Sofia N. Moraes, Adam Z. Cheng, Michael A. Carpenter, Jason S. McLellan, Zhiheng Yu, Reuben S. Harris

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11 Scopus citations

Abstract

Viruses use a plethora of mechanisms to evade immune responses. A recent example is neutralization of the nuclear DNA cytosine deaminase APOBEC3B by the Epstein-Barr virus (EBV) ribonucleotide reductase subunit BORF2. Cryo-EM studies of APOBEC3B-BORF2 complexes reveal a large >1000-Å2 binding surface composed of multiple structural elements from each protein, which effectively blocks the APOBEC3B active site from accessing single-stranded DNA substrates. Evolutionary optimization is suggested by unique insertions in BORF2 absent from other ribonucleotide reductases and preferential binding to APOBEC3B relative to the highly related APOBEC3A and APOBEC3G enzymes. A molecular understanding of this pathogen-host interaction has potential to inform the development of drugs that block the interaction and liberate the natural antiviral activity of APOBEC3B. In addition, given a role for APOBEC3B in cancer mutagenesis, it may also be possible for information from the interaction to be used to develop DNA deaminase inhibitors.

Original languageEnglish (US)
Article numbereabm2827
JournalScience Advances
Volume8
Issue number17
DOIs
StatePublished - Apr 2022

Bibliographical note

Funding Information:
We would like to thank H. Aihara for providing constructs, W. Zhang and M. Shiozaki for grid preparation and screening assistance, X. Zhao for help with initial dataset collection, M. Brown for technical assistance in the early stages of the project, W. Brown for providing expertise with BLI experiments, and M. Jarvis for computational assistance. Funding: This work was supported, in part, by NCI P01-CA234228 (to R.S.H.); NIAID R56-AI150402 (to N.M.S.); and the University of Minnesota Masonic Cancer Center, Academic Health Center, and College of Biological Sciences. Contributions of J.S.M. were supported by Welch Foundation grant number F-0003-19620604. Salary support for S.N.M. was provided by NIAID T32-AI083196 and, subsequently, NIAID F31-AI161910. R.S.H. is the Margaret Harvey Schering Land Grant Chair for Cancer Research, a Distinguished University McKnight Professor, and an Investigator of the Howard Hughes Medical Institute. Author contributions: N.M.S. and R.S.H. initiated the project and lead the studies. N.M.S. conceptualized and designed the studies with input from authors. N.M.S. purified proteins and performed biochemical and BLI assays. N.M.S. and S.N.M. generated constructs. N.M.S. and R.Y. prepared and screened grids. R.Y. collected cryo-EM data. Z.Y. supervised cryo-EM data collection. J.S.M., R.Y., N.M.S., and Z.Y. processed cryo-EM datasets. J.S.M. processed the final cryo-EM data and calculated the deposited maps. N.M.S. and K.S. built and refined the structural model with input from J.S.M. S.N.M., A.Z.C., and N.M.S. performed immunoprecipitation assays. S.N.M. generated cell lines and performed and developed methods to quantify localization experiments. M.A.C. provided cell culture and technical expertise. N.M.S. and R.S.H. wrote the manuscript with contributions from all authors. Competing interests: The authors declare that they have no competing interests. Data and materials availability: Cryo-EM maps and a structural model have been deposited in the EMDB and PDB with accession codes EMD-24716, EMD-24715, EMD-24709, and PDB:7wr6, respectively. All other data needed to evaluate the conclusions of the paper are present in the paper and/or the Supplementary Materials.

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