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dc.contributor.authorMaiti, Atanu
dc.contributor.authorMyint, Wazo
dc.contributor.authorDelviks-Frankenberry, Krista A.
dc.contributor.authorHou, Shurong
dc.contributor.authorKanai, Tapan
dc.contributor.authorBalachandran, Vanivilasini
dc.contributor.authorSierra Rodriguez, Christina
dc.contributor.authorTripathi, Rashmi
dc.contributor.authorYilmaz, Nese Kurt
dc.contributor.authorPathak, Vinay K.
dc.contributor.authorSchiffer, Celia A.
dc.contributor.authorMatsuo, Hiroshi
dc.date2022-08-11T08:10:52.000
dc.date.accessioned2022-08-23T17:23:11Z
dc.date.available2022-08-23T17:23:11Z
dc.date.issued2020-11-20
dc.date.submitted2021-01-06
dc.identifier.citation<p>Maiti A, Myint W, Delviks-Frankenberry KA, Hou S, Kanai T, Balachandran V, Sierra Rodriguez C, Tripathi R, Kurt Yilmaz N, Pathak VK, Schiffer CA, Matsuo H. Crystal Structure of a Soluble APOBEC3G Variant Suggests ssDNA to Bind in a Channel that Extends between the Two Domains. J Mol Biol. 2020 Nov 20;432(23):6042-6060. doi: 10.1016/j.jmb.2020.10.020. Epub 2020 Oct 22. PMID: 33098858; PMCID: PMC7771068. <a href="https://doi.org/10.1016/j.jmb.2020.10.020">Link to article on publisher's site</a></p>
dc.identifier.issn0022-2836 (Linking)
dc.identifier.doi10.1016/j.jmb.2020.10.020
dc.identifier.pmid33098858
dc.identifier.urihttp://hdl.handle.net/20.500.14038/48900
dc.description.abstractAPOBEC3G (A3G) is a single-stranded DNA (ssDNA) cytosine deaminase that can restrict HIV-1 infection by mutating the viral genome. A3G consists of a non-catalytic N-terminal domain (NTD) and a catalytic C-terminal domain (CTD) connected by a short linker. While the CTD catalyzes cytosine deamination, the NTD is believed to provide additional affinity for ssDNA. Structures of both A3G domains have been solved individually; however, a full-length A3G structure has been challenging. Recently, crystal structures of full-length rhesus macaque A3G variants were solved which suggested dimerization mechanisms and RNA binding surfaces, whereas the dimerization appeared to compromise catalytic activity. We determined the crystal structure of a soluble variant of human A3G (sA3G) at 2.5 A and from these data generated a model structure of wild-type A3G. This model demonstrated that the NTD was rotated 90 degrees relative to the CTD along the major axis of the molecule, an orientation that forms a positively charged channel connected to the CTD catalytic site, consisting of NTD loop-1 and CTD loop-3. Structure-based mutations, in vitro deamination and DNA binding assays, and HIV-1 restriction assays identify R24, located in the NTD loop-1, as essential to a critical interaction with ssDNA. Furthermore, sA3G was shown to bind a deoxy-cytidine dinucleotide near the catalytic Zn(2+), yet not in the catalytic position, where the interactions between deoxy-cytidines and CTD loop-1 and loop-7 residues were different from those formed with substrate. These new interactions suggest a mechanism explaining why A3G exhibits a 3' to 5' directional preference in processive deamination.
dc.language.isoen_US
dc.relation<p><a href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Retrieve&list_uids=33098858&dopt=Abstract">Link to Article in PubMed</a></p>
dc.relation.urlhttps://doi.org/10.1016/j.jmb.2020.10.020
dc.subjectAPOBEC3G
dc.subjectHIV-1 restriction
dc.subjectco-crystal structure
dc.subjectcytosine deaminase
dc.subjectssDNA binding
dc.subjectBiochemistry
dc.subjectEnzymes and Coenzymes
dc.subjectMedicinal Chemistry and Pharmaceutics
dc.subjectMedicinal-Pharmaceutical Chemistry
dc.subjectMolecular Biology
dc.subjectStructural Biology
dc.subjectVirology
dc.subjectViruses
dc.titleCrystal Structure of a Soluble APOBEC3G Variant Suggests ssDNA to Bind in a Channel that Extends between the Two Domains
dc.typeJournal Article
dc.source.journaltitleJournal of molecular biology
dc.source.volume432
dc.source.issue23
dc.identifier.legacycoverpagehttps://escholarship.umassmed.edu/schiffer/44
dc.identifier.contextkey20950696
html.description.abstract<p>APOBEC3G (A3G) is a single-stranded DNA (ssDNA) cytosine deaminase that can restrict HIV-1 infection by mutating the viral genome. A3G consists of a non-catalytic N-terminal domain (NTD) and a catalytic C-terminal domain (CTD) connected by a short linker. While the CTD catalyzes cytosine deamination, the NTD is believed to provide additional affinity for ssDNA. Structures of both A3G domains have been solved individually; however, a full-length A3G structure has been challenging. Recently, crystal structures of full-length rhesus macaque A3G variants were solved which suggested dimerization mechanisms and RNA binding surfaces, whereas the dimerization appeared to compromise catalytic activity. We determined the crystal structure of a soluble variant of human A3G (sA3G) at 2.5 A and from these data generated a model structure of wild-type A3G. This model demonstrated that the NTD was rotated 90 degrees relative to the CTD along the major axis of the molecule, an orientation that forms a positively charged channel connected to the CTD catalytic site, consisting of NTD loop-1 and CTD loop-3. Structure-based mutations, in vitro deamination and DNA binding assays, and HIV-1 restriction assays identify R24, located in the NTD loop-1, as essential to a critical interaction with ssDNA. Furthermore, sA3G was shown to bind a deoxy-cytidine dinucleotide near the catalytic Zn(2+), yet not in the catalytic position, where the interactions between deoxy-cytidines and CTD loop-1 and loop-7 residues were different from those formed with substrate. These new interactions suggest a mechanism explaining why A3G exhibits a 3' to 5' directional preference in processive deamination.</p>
dc.identifier.submissionpathschiffer/44
dc.contributor.departmentSchiffer Lab
dc.contributor.departmentDepartment of Biochemistry and Molecular Pharmacology
dc.source.pages6042-6060


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