Small-Angle X-ray Scattering (SAXS) Measurements of APOBEC3G Provide Structural Basis for Binding of Single-Stranded DNA and Processivity

Simple item page
dc.citation.issue9
dc.citation.volume14
dc.contributor.authorBarzak FM
dc.contributor.authorRyan TM
dc.contributor.authorMohammadzadeh N
dc.contributor.authorHarjes S
dc.contributor.authorKvach MV
dc.contributor.authorKurup HM
dc.contributor.authorKrause KL
dc.contributor.authorChelico L
dc.contributor.authorFilichev VV
dc.contributor.authorHarjes E
dc.contributor.authorJameson GB
dc.contributor.editorDe la Torre JC
dc.contributor.editorAndrei G
dc.coverage.spatialSwitzerland
dc.date.accessioned2023-11-01T23:57:36Z
dc.date.accessioned2024-07-25T06:35:29Z
dc.date.available2022-09-06
dc.date.available2023-11-01T23:57:36Z
dc.date.available2024-07-25T06:35:29Z
dc.date.issued2022-09-06
dc.description.abstractAPOBEC3 enzymes are polynucleotide deaminases, converting cytosine to uracil on single-stranded DNA (ssDNA) and RNA as part of the innate immune response against viruses and retrotransposons. APOBEC3G is a two-domain protein that restricts HIV. Although X-ray single-crystal structures of individual catalytic domains of APOBEC3G with ssDNA as well as full-length APOBEC3G have been solved recently, there is little structural information available about ssDNA interaction with the full-length APOBEC3G or any other two-domain APOBEC3. Here, we investigated the solution-state structures of full-length APOBEC3G with and without a 40-mer modified ssDNA by small-angle X-ray scattering (SAXS), using size-exclusion chromatography (SEC) immediately prior to irradiation to effect partial separation of multi-component mixtures. To prevent cytosine deamination, the target 2'-deoxycytidine embedded in 40-mer ssDNA was replaced by 2'-deoxyzebularine, which is known to inhibit APOBEC3A, APOBEC3B and APOBEC3G when incorporated into short ssDNA oligomers. Full-length APOBEC3G without ssDNA comprised multiple multimeric species, of which tetramer was the most scattering species. The structure of the tetramer was elucidated. Dimeric interfaces significantly occlude the DNA-binding interface, whereas the tetrameric interface does not. This explains why dimers completely disappeared, and monomeric protein species became dominant, when ssDNA was added. Data analysis of the monomeric species revealed a full-length APOBEC3G-ssDNA complex that gives insight into the observed "jumping" behavior revealed in studies of enzyme processivity. This solution-state SAXS study provides the first structural model of ssDNA binding both domains of APOBEC3G and provides data to guide further structural and enzymatic work on APOBEC3-ssDNA complexes.
dc.description.confidentialfalse
dc.edition.editionSeptember 2022
dc.format.pagination1974-
dc.identifier.author-urlhttps://www.ncbi.nlm.nih.gov/pubmed/36146779
dc.identifier.citationBarzak FM, Ryan TM, Mohammadzadeh N, Harjes S, Kvach MV, Kurup HM, Krause KL, Chelico L, Filichev VV, Harjes E, Jameson GB. (2022). Small-Angle X-ray Scattering (SAXS) Measurements of APOBEC3G Provide Structural Basis for Binding of Single-Stranded DNA and Processivity.. Viruses. 14. 9. (pp. 1974-).
dc.identifier.doi10.3390/v14091974
dc.identifier.eissn1999-4915
dc.identifier.elements-typejournal-article
dc.identifier.issn1999-4915
dc.identifier.number1974
dc.identifier.piiv14091974
dc.identifier.urihttps://mro.massey.ac.nz/handle/10179/70499
dc.languageeng
dc.publisherMDPI (Basel, Switzerland)
dc.publisher.urihttps://www.mdpi.com/1999-4915/14/9/1974
dc.relation.isPartOfViruses
dc.rights(c) 2022 The Author/s
dc.rightsCC BY 4.0
dc.rights.urihttps://creativecommons.org/licenses/by/4.0/
dc.subjectAPOBEC3
dc.subjectAPOBEC3G
dc.subjectSAXS
dc.subjectprotein–DNA complex
dc.subjectAPOBEC-3G Deaminase
dc.subjectCytidine Deaminase
dc.subjectCytosine
dc.subjectDNA, Single-Stranded
dc.subjectDeoxycytidine
dc.subjectPolynucleotides
dc.subjectProtein Binding
dc.subjectProteins
dc.subjectRNA
dc.subjectRetroelements
dc.subjectScattering, Small Angle
dc.subjectUracil
dc.subjectX-Ray Diffraction
dc.subjectX-Rays
dc.titleSmall-Angle X-ray Scattering (SAXS) Measurements of APOBEC3G Provide Structural Basis for Binding of Single-Stranded DNA and Processivity
dc.typeJournal article
pubs.elements-id456932
pubs.organisational-groupOther
Files
Original bundle
Now showing 1 - 2 of 2
Thumbnail Image
Name:
Published version
Size:
2.98 MB
Format:
Adobe Portable Document Format
Description:
Download
Thumbnail Image
Name:
Evidence
Size:
329.93 KB
Format:
Adobe Portable Document Format
Description:
Download
Collections
Journal Articles