These results suggest that dimerization of the C-terminal domain of IN is important for correct multimerization of IN. Amino acid substitution of residues located in the hydrophobic dimer interface, such as L241A and L242A, results in the loss of oligomerization of IN consequently, the levels of 3′ processing, DNA strand transfer, and intramolecular disintegration are strongly reduced. We also analyzed mutant proteins representing portions of the full-length IN protein. We found that two amino acid residues, arginine 262 and leucine 234, contribute to DNA binding in the context of IN220–270, as indicated by protein- DNA UV cross-link analysis. Based on the structure of IN220–270, we studied the role of 15 amino acid residues potentially involved in DNA binding and oligomerization by mutational analysis. The overall fold of the C-terminal domain of HIV-1 IN is similar to those of Src homology region 3 domains. The structure of the minimal region required for DNA binding (IN220–270) has been solved by nuclear magnetic resonance spectroscopy.
The C-terminal domain of human immunodeficiency virus type 1 (HIV-1) integrase (IN) is a dimer that binds to DNA in a nonspecific manner. Structure-Based Mutational Analysis of the C-Terminal DNA-Binding Domain of Human Immunodeficiency Virus Type 1 Integrase: Critical Residues for Protein Oligomerization and DNA Binding A model for the protein– DNA complex is proposed that accounts for this specificity.
Using chemical shift perturbation experiments, the DNA-binding surface is mapped to the first hairpin region encompassing the conserved glycine–valine–glycine residues followed by lysine–arginine–arginine, a positively charged surface patch and the second hairpin region consisting of glycine–isoleucine–serine. The domain binds to a single-stranded–double-stranded junction DNA, with a strong specificity towards looped duplex DNA that contains at least six unpaired bases per loop (‘bubble DNA’). The Uvr C CTD is shown to mediate structure-specific DNA binding. The structure shows two helix–hairpin–helix (HhH) motifs connected by a small connector helix. We have determined the three-dimensional structure of the Uvr C CTD using heteronuclear NMR techniques. The C-terminal domain of the Uvr C protein (Uvr C CTD) is essential for 5′ incision in the prokaryotic nucleotide excision repair process.
Solution structure and DNA-binding properties of the C-terminal domain of Uvr C from E.coli
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