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Assessment of Immunologically Relevant Dynamic Tertiary Structural Features of the HIV-1 V3 Loop Crown R2 Sequence by ab initio Folding
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Crystal structure of the anti-viral APOBEC3G catalytic domain and functional implications

Lauren G Holden1, Courtney Prochnow, Y Paul Chang

  • 1Molecular and Computational Biology, University of Southern California, Los Angeles, California 90089, USA.

Nature
|October 14, 2008
PubMed

Insights

The study reveals the high-resolution crystal structure of APOBEC3G-CD2, a protein that restricts viral replication. This structure clarifies the active site and identifies key residues for substrate specificity and DNA binding in the APOBEC family.

Area of Science:

  • Biochemistry
  • Structural Biology
  • Molecular Biology

Background:

  • APOBEC family proteins play crucial roles in various biological processes.
  • APOBEC3G (A3G) is known to restrict the replication of viruses like HIV and HBV through cytidine deamination and RNA binding.

Purpose of the Study:

  • To determine the high-resolution crystal structure of the carboxy-terminal deaminase domain of APOBEC3G (APOBEC3G-CD2).
  • To elucidate the structural basis of APOBEC3G's deaminase activity and substrate specificity.

Main Methods:

  • Purification of APOBEC3G-CD2 from Escherichia coli.
  • High-resolution X-ray crystallography to determine the protein structure.
  • Site-directed mutagenesis to investigate residue function.

Main Results:

  • The crystal structure of APOBEC3G-CD2 reveals a conserved five-stranded beta-sheet core, similar to other deaminases.
  • A distinct 'substrate groove' formed by active-site loops was identified, differing in orientation from previous NMR predictions.
  • Mutational analysis identified key residues essential for substrate specificity, single-stranded DNA binding, and deaminase activity.

Conclusions:

  • The determined structure provides critical insights into the APOBEC3G deaminase mechanism.
  • Understanding the substrate groove and key residues lays the groundwork for deciphering APOBEC family substrate specificity.

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