8TX4

Crystal Structure of rA3G-ssDNA-GA

Summary for 8TX4

• Entry DOI: 10.2210/pdb8tx4/pdb
• Descriptor: DNA dC->dU-editing enzyme APOBEC-3G, DNA 22-mer with (5'-D(P*TP*GP*AP*TP*TP)-3'), ZINC ION, ... (5 entities in total)
• Functional Keywords: deaminase, apobec, hydrolase, hydrolase-dna complex, hydrolase/dna
• Biological source: Macaca mulatta (Rhesus monkey); More
• Total number of polymer chains: 2
• Total formula weight: 52061.70

Authors

Yang, H.,Pacheco, J.I.,Chen, X.S. (deposition date: 2023-08-22, release date: 2024-11-06)

Primary citation

Yang, H.,Pacheco, J.,Kim, K.,Bokani, A.,Ito, F.,Ebrahimi, D.,Chen, X.S.
Molecular mechanism for regulating APOBEC3G DNA editing function by the non-catalytic domain.
Nat Commun, 15:8773-8773, 2024

PubMed Abstract: APOBEC3G, part of the AID/APOBEC cytidine deaminase family, is crucial for antiviral immunity. It has two zinc-coordinated cytidine-deaminase domains. The non-catalytic N-terminal domain strongly binds to nucleic acids, whereas the C-terminal domain catalyzes C-to-U editing in single-stranded DNA. The interplay between the two domains is not fully understood. Here, we show that DNA editing function of rhesus macaque APOBEC3G on linear and hairpin loop DNA is enhanced by AA or GA dinucleotide motifs present downstream in the 3'-direction of the target-C editing sites. The effective distance between AA/GA and the target-C sites is contingent on the local DNA secondary structure. We present two co-crystal structures of rhesus macaque APOBEC3G bound to ssDNA containing AA and GA, revealing the contribution of the non-catalytic domain in capturing AA/GA DNA. Our findings elucidate the molecular mechanism of APOBEC3G's cooperative function, which is critical for its antiviral role and its contribution to mutations in cancer genomes.

PubMed: 39389938
DOI: 10.1038/s41467-024-52671-1

Experimental method

X-RAY DIFFRACTION (1.9 Å)