2KEM

Extended structure of citidine deaminase domain of APOBEC3G

Summary for 2KEM

• Entry DOI: 10.2210/pdb2kem/pdb
• Related: 2JYW 2kbo 3E1U
• Descriptor: DNA dC->dU-editing enzyme APOBEC-3G, ZINC ION (2 entities in total)
• Functional Keywords: helix, sheet, zinc, alternative splicing, antiviral defense, cytoplasm, host-virus interaction, hydrolase, metal-binding, nucleus, polymorphism, ubl conjugation
• Biological source: Homo sapiens (human)
• Cellular location: Cytoplasm: Q9HC16
• Total number of polymer chains: 1
• Total formula weight: 23579.87

Authors

Harjes, E.,Gross, P.J.,Chen, K.,Lu, Y.,Shindo, K.,Nowarski, R.,Gross, J.D.,Kotler, M.,Harris, R.S.,Matsuo, H. (deposition date: 2009-01-30, release date: 2009-06-02, Last modification date: 2024-05-29)

Primary citation

Harjes, E.,Gross, P.J.,Chen, K.M.,Lu, Y.,Shindo, K.,Nowarski, R.,Gross, J.D.,Kotler, M.,Harris, R.S.,Matsuo, H.
An extended structure of the APOBEC3G catalytic domain suggests a unique holoenzyme model
J.Mol.Biol., 389:819-832, 2009

PubMed Abstract: Human APOBEC3G (A3G) belongs to a family of polynucleotide cytidine deaminases. This family includes APOBEC1 and AID, which edit APOB mRNA and antibody gene DNA, respectively. A3G deaminates cytidines to uridines in single-strand DNA and inhibits the replication of human immunodeficiency virus-1, other retroviruses, and retrotransposons. Although the mechanism of A3G-catalyzed DNA deamination has been investigated genetically and biochemically, atomic details are just starting to emerge. Here, we compare the DNA cytidine deaminase activities and NMR structures of two A3G catalytic domain constructs. The longer A3G191-384 protein is considerably more active than the shorter A3G198-384 variant. The longer structure has an alpha1-helix (residues 201-206) that was not apparent in the shorter protein, and it contributes to catalytic activity through interactions with hydrophobic core structures (beta1, beta3, alpha5, and alpha6). Both A3G catalytic domain solution structures have a discontinuous beta2 region that is clearly different from the continuous beta2 strand of another family member, APOBEC2. In addition, the longer A3G191-384 structure revealed part of the N-terminal pseudo-catalytic domain, including the interdomain linker and some of the last alpha-helix. These structured residues (residues 191-196) enabled a novel full-length A3G model by providing physical overlap between the N-terminal pseudo-catalytic domain and the new C-terminal catalytic domain structure. Contrary to predictions, this structurally constrained model suggested that the two domains are tethered by structured residues and that the N- and C-terminal beta2 regions are too distant from each other to participate in this interaction.

PubMed: 19389408
DOI: 10.1016/j.jmb.2009.04.031

Experimental method

SOLUTION NMR