1tqr
From Proteopedia
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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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