6BWY

DNA substrate selection by APOBEC3G

6BWY の概要

• エントリーDOI: 10.2210/pdb6bwy/pdb
• 分子名称: DNA (30-MER), Protection of telomeres protein 1, DNA dC->dU-editing enzyme APOBEC-3G fusion, PHOSPHATE ION, ... (5 entities in total)
• 機能のキーワード: deaminase, dna binding, complex, hydrolase
• 由来する生物種: Schizosaccharomyces pombe (strain 972 / ATCC 24843) (Fission yeast); 詳細
• 細胞内の位置: Cytoplasm: Q9HC16
• タンパク質・核酸の鎖数: 8
• 化学式量合計: 206979.98

構造登録者

Ziegler, S.J.,Buzovetsky, O. (登録日: 2017-12-15, 公開日: 2018-04-18, 最終更新日: 2023-10-04)

主引用文献

Ziegler, S.J.,Liu, C.,Landau, M.,Buzovetsky, O.,Desimmie, B.A.,Zhao, Q.,Sasaki, T.,Burdick, R.C.,Pathak, V.K.,Anderson, K.S.,Xiong, Y.
Insights into DNA substrate selection by APOBEC3G from structural, biochemical, and functional studies.
PLoS ONE, 13:e0195048-e0195048, 2018

PubMed Abstract: Human apolipoprotein B mRNA-editing enzyme-catalytic polypeptide-like 3 (A3) proteins are a family of cytidine deaminases that catalyze the conversion of deoxycytidine (dC) to deoxyuridine (dU) in single-stranded DNA (ssDNA). A3 proteins act in the innate immune response to viral infection by mutating the viral ssDNA. One of the most well-studied human A3 family members is A3G, which is a potent inhibitor of HIV-1. Each A3 protein prefers a specific substrate sequence for catalysis-for example, A3G deaminates the third dC in the CCCA sequence motif. However, the interaction between A3G and ssDNA is difficult to characterize due to poor solution behavior of the full-length protein and loss of DNA affinity of the truncated protein. Here, we present a novel DNA-anchoring fusion strategy using the protection of telomeres protein 1 (Pot1) which has nanomolar affinity for ssDNA, with which we captured an A3G-ssDNA interaction. We crystallized a non-preferred adenine in the -1 nucleotide-binding pocket of A3G. The structure reveals a unique conformation of the catalytic site loops that sheds light onto how the enzyme scans substrate in the -1 pocket. Furthermore, our biochemistry and virology studies provide evidence that the nucleotide-binding pockets on A3G influence each other in selecting the preferred DNA substrate. Together, the results provide insights into the mechanism by which A3G selects and deaminates its preferred substrates and help define how A3 proteins are tailored to recognize specific DNA sequences. This knowledge contributes to a better understanding of the mechanism of DNA substrate selection by A3G, as well as A3G antiviral activity against HIV-1.

PubMed: 29596531
DOI: 10.1371/journal.pone.0195048

実験手法

X-RAY DIFFRACTION (2.9 Å)