1TQR

NMR Structure of DNA 17-mer GGAAAATCTCTAGCAGT corresponding to the extremity of the U5 LTR of the HIV-1 genome

Summary for 1TQR

• Entry DOI: 10.2210/pdb1tqr/pdb
• Descriptor: DNA HIV-1 U5 LTR extremity (2 entities in total)
• Functional Keywords: double helix, dna
• Total number of polymer chains: 2
• Total formula weight: 10412.79

Authors

Renisio, J.G.,Cosquer, S.,Cherrak, I.,El Antri, S.,Mauffret, O.,Fermandjian, S. (deposition date: 2004-06-18, release date: 2005-04-19, Last modification date: 2024-05-29)

Primary citation

Renisio, J.G.,Cosquer, S.,Cherrak, I.,El Antri, S.,Mauffret, O.,Fermandjian, S.
Pre-organized structure of viral DNA at the binding-processing site of HIV-1 integrase
NUCLEIC ACIDS RES., 33:1970-1981, 2005

PubMed Abstract: 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.

PubMed: 15814814
DOI: 10.1093/nar/gki346

Experimental method

SOLUTION NMR