1tqr
From Proteopedia
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| Ligands: | , , , | ||||||
| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
NMR Structure of DNA 17-mer GGAAAATCTCTAGCAGT corresponding to the extremity of the U5 LTR of the HIV-1 genome
Overview
The integration of the human immunodeficiency virus type 1 DNA into the host cell genome is catalysed by the viral integrase (IN). The reaction consists of a 3'-processing [dinucleotide released from each 3' end of the viral long terminal repeat (LTR)] followed by a strand transfer (insertion of the viral genome into the human chromosome). A 17 base pair oligonucleotide d(GGAAAATCTCTAGCAGT), d(ACTGCTAGAGATTTTCC) reproducing the U5-LTR extremity of viral DNA that contains the IN attachment site was analysed by NMR using the classical NOEs and scalar coupling constants in conjunction with a small set of residual dipolar coupling constants (RDCs) measured at the 13C/15N natural abundance. The combination of these two types of parameters in calculations significantly improved the DNA structure determination. The well-known features of A-tracts were clearly identified by RDCs in the first part of the molecule. The binding/cleavage site at the viral DNA end is distinguishable by a loss of regular base stacking and a distorted minor groove that can aid its specific recognition by IN.
About this Structure
1TQR is a Protein complex structure of sequences from [1]. Full crystallographic information is available from OCA.
Reference
Pre-organized structure of viral DNA at the binding-processing site of HIV-1 integrase., Renisio JG, Cosquer S, Cherrak I, El Antri S, Mauffret O, Fermandjian S, Nucleic Acids Res. 2005 Apr 6;33(6):1970-81. Print 2005. PMID:15814814
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