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PDBsum entry 2fvp
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Transferase/DNA
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PDB id
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2fvp
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References listed in PDB file
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Key reference
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Title
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Crystal structures of oligonucleotides including the integrase processing site of the moloney murine leukemia virus.
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Authors
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S.P.Montaño,
M.L.Coté,
M.J.Roth,
M.M.Georgiadis.
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Ref.
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Nucleic Acids Res, 2006,
34,
5353-5360.
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PubMed id
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Abstract
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In the first step of retroviral integration, integrase cleaves the linear viral
DNA within its long terminal repeat (LTR) immediately 3' to the CA dinucleotide
step, resulting in a reactive 3' OH on one strand and a 5' two base overhang on
the complementary strand. In order to investigate the structural properties of
the 3' end processing site within the Moloney murine leukemia virus (MMLV) LTR
d(TCTTTCATT), a host-guest crystallographic method was employed to determine the
structures of four self-complementary 16 bp oligonucleotides including LTR
sequences (underlined), d(TTTCATTGCAATGAAA), d(CTTTCATTAATGAAAG),
d(TCTTTCATATGAAAGA) and d(CACAATGATCATTGTG), the guests, complexed with the
N-terminal fragment of MMLV reverse transcriptase, the host. The structures of
the LTR-containing oligonucleotides were compared to those of non-LTR
oligonucleotides crystallized in the same lattice. Properties unique to the CA
dinucleotide step within the LTR sequence, independent of its position from the
end of the duplex, include a positive roll angle and negative slide value. This
propensity for the CA dinucleotide step within the MMLV LTR sequence to adopt
only positive roll angles is likely influenced by the more rigid, invariable 3'
and 5' flanking TT dinucleotide steps and may be important for specific
recognition and/or cleavage by the MMLV integrase.
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