6WMB

Crystal structure of a soluble variant of full-length human APOBEC3G (pH 8.0)

Summary for 6WMB

• Entry DOI: 10.2210/pdb6wmb/pdb
• Descriptor: APOLIPOPROTEIN B MRNA EDITING ENZYME, CATALYTIC PEPTIDE- LIKE 3G, DNA (5'-D(P*CP*C)-3'), ZINC ION, ... (4 entities in total)
• Functional Keywords: apobec3g, antiviral defense, hydrolase, dna cytidine deaminase, hydrolase-dna complex, hydrolase/dna
• Biological source: Homo sapiens (Human); More
• Total number of polymer chains: 2
• Total formula weight: 43066.53

Authors

Maiti, A.,Matsuo, H. (deposition date: 2020-04-21, release date: 2020-12-23, Last modification date: 2023-10-18)

Primary citation

Maiti, A.,Myint, W.,Delviks-Frankenberry, K.A.,Hou, S.,Kanai, T.,Balachandran, V.,Sierra Rodriguez, C.,Tripathi, R.,Kurt Yilmaz, N.,Pathak, V.K.,Schiffer, C.A.,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., 432:6042-6060, 2020

PubMed Abstract: 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 Å and from these data generated a model structure of wild-type A3G. This model demonstrated that the NTD was rotated 90° 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, 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.

PubMed: 33098858
DOI: 10.1016/j.jmb.2020.10.020

Experimental method

X-RAY DIFFRACTION (3.02 Å)