About: Insights into DNA substrate selection by APOBEC3G from structural, biochemical, and functional studies

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About: Insights into DNA substrate selection by APOBEC3G from structural, biochemical, and functional studies Goto Sponge NotDistinct Permalink

An Entity of Type : schema:ScholarlyArticle, within Data Space : wasabi.inria.fr associated with source document(s)

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type	Academic Article research paper schema:ScholarlyArticle
isDefinedBy	Covid-on-the-Web dataset
has title	Insights into DNA substrate selection by APOBEC3G from structural, biochemical, and functional studies
Creator	Xiong, Yong Zhao, Qi Liu, Chang Buzovetsky, Olga Landau, Mark Sasaki, Tomoaki Anderson, Karen Burdick, Ryan Desimmie, Belete Pathak, Vinay Ziegler, Samantha
Source	Medline; PMC
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.
has issue date	2018-03-29(xsd:dateTime)
bibo:doi	10.1371/journal.pone.0195048
bibo:pmid	29596531
has license	cc0
sha1sum (hex)	6e0d5cb338ea8a2916c74b3b06789d3b21ac36a4
schema:url	https://doi.org/10.1371/journal.pone.0195048
resource representing a document's title	Insights into DNA substrate selection by APOBEC3G from structural, biochemical, and functional studies
has PubMed Central identifier	PMC5875850
has PubMed identifier	29596531
schema:publication	PLoS One
resource representing a document's body	covid:6e0d5cb338ea8a2916c74b3b06789d3b21ac36a4#body_text
is schema:about of	named entity 'ssDNA' named entity 'deoxycytidine' named entity 'pocket' named entity 'ssDNA' named entity 'loops' named entity 'deoxyuridine' named entity 'activity' named entity 'apolipoprotein' named entity 'Human' named entity 'protein' named entity 'catalytic site' named entity 'cytidine' named entity 'protein' named entity 'STUDIES' named entity 'BIOCHEMICAL' covid:arg/6e0d5cb338ea8a2916c74b3b06789d3b21ac36a4 named entity 'FUSION' named entity 'STRUCTURE' named entity 'HUMAN' named entity 'SPECIFIC' named entity 'DNA SEQUENCES' named entity 'DUE TO' named entity 'DNA' named entity 'CATALYTIC SITE' named entity 'SELECTING' named entity 'FAMILY' named entity 'DEOXYCYTIDINE' named entity 'PROTEINS' named entity 'LIGHT' named entity 'CATALYTIC' named entity 'CONVERSION' named entity 'FAMILY MEMBERS' named entity 'VIRAL' named entity 'TAILORED' named entity 'USING' named entity 'CCCA' named entity 'DIFFICULT' named entity 'CRYSTALLIZED' named entity 'SEQUENCE' named entity 'INHIBITOR' named entity 'PROVIDE' named entity 'OUR' named entity 'NOVEL' named entity 'PROTEIN ' named entity 'SEQUENCE MOTIF' named entity 'HELP' named entity 'HOW' named entity 'SCANS' named entity 'NUCLEOTIDE' named entity 'BIOCHEMISTRY' named entity 'TO CHARACTERIZE' named entity 'REVEALS' named entity 'EVIDENCE' named entity 'INNATE IMMUNE RESPONSE' named entity 'UNDERSTANDING' named entity 'HIV-1' named entity 'SELECTION' named entity 'RESULTS' named entity 'LIKE' named entity 'LOSS OF' named entity 'RECOGNIZE' named entity 'ACT' named entity 'SSDNA' named entity 'TRUNCATED' named entity 'CONFORMATION' named entity 'A3G' named entity 'PROTEIN' named entity 'PROTECTION OF TELOMERES PROTEIN 1' named entity 'EXAMPLE' named entity 'BINDING' named entity 'MRNA'

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