4ROV

The crystal structure of novel APOBEC3G CD2 head-to-tail dimer suggests the binding mode of full-length APOBEC3G to HIV-1 ssDNA

Summary for 4ROV

• Entry DOI: 10.2210/pdb4rov/pdb
• Related: 2JYW 4ROW
• Descriptor: DNA dC->dU-editing enzyme APOBEC-3G, ZINC ION (3 entities in total)
• Functional Keywords: zinc finger, dna deamination, dna binding, deamination, hydrolase
• Biological source: Homo sapiens (human)
• Cellular location: Cytoplasm: Q9HC16
• Total number of polymer chains: 2
• Total formula weight: 46589.20

Authors

Lu, X.,Zhang, T.,Xu, Z.,Liu, S.,Zhao, B.,Lan, W.,Wang, C.,Ding, J.,Cao, C. (deposition date: 2014-10-29, release date: 2014-12-31, Last modification date: 2024-03-20)

Primary citation

Lu, X.,Zhang, T.,Xu, Z.,Liu, S.,Zhao, B.,Lan, W.,Wang, C.,Ding, J.,Cao, C.
Crystal structure of DNA cytidine deaminase ABOBEC3G catalytic deamination domain suggests a binding mode of full-length enzyme to single-stranded DNA
J.Biol.Chem., 290:4010-4021, 2015

PubMed Abstract: APOBEC3G (A3G) is a DNA cytidine deaminase (CD) that demonstrates antiviral activity against human immunodeficiency virus 1 (HIV-1) and other pathogenic virus. It has an inactive N-terminal CD1 virus infectivity factor (Vif) protein binding domain (A3G-CD1) and an actively catalytic C-terminal CD2 deamination domain (A3G-CD2). Although many studies on the structure of A3G-CD2 and enzymatic properties of full-length A3G have been reported, the mechanism of how A3G interacts with HIV-1 single-stranded DNA (ssDNA) is still not well characterized. Here, we reported a crystal structure of a novel A3G-CD2 head-to-tail dimer (in which the N terminus of the monomer H (head) interacts with the C terminus of monomer T (tail)), where a continuous DNA binding groove was observed. By constructing the A3G-CD1 structural model, we found that its overall fold was almost identical to that of A3G-CD2. We mutated the residues located in or along the groove in monomer H and the residues in A3G-CD1 that correspond to those seated in or along the groove in monomer T. Then, by performing enzymatic assays, we confirmed the reported key elements and the residues in A3G necessary to the catalytic deamination. Moreover, we identified more than 10 residues in A3G essential to DNA binding and deamination reaction. Therefore, this dimer structure may represent a structural model of full-length A3G, which indicates a possible binding mode of A3G to HIV-1 ssDNA.

PubMed: 25542899
DOI: 10.1074/jbc.M114.624262

Experimental method

X-RAY DIFFRACTION (1.8 Å)