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PDBsum entry 1hys
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Transferase/DNA-RNA hybrid
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PDB id
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1hys
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Contents |
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553 a.a.
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425 a.a.
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214 a.a.
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220 a.a.
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* Residue conservation analysis
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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 structure of HIV-1 reverse transcriptase in complex with a polypurine tract RNA:DNA.
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Authors
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S.G.Sarafianos,
K.Das,
C.Tantillo,
A.D.Clark,
J.Ding,
J.M.Whitcomb,
P.L.Boyer,
S.H.Hughes,
E.Arnold.
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Ref.
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EMBO J, 2001,
20,
1449-1461.
[DOI no: ]
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PubMed id
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Abstract
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We have determined the 3.0 A resolution structure of wild-type HIV-1 reverse
transcriptase in complex with an RNA:DNA oligonucleotide whose sequence includes
a purine-rich segment from the HIV-1 genome called the polypurine tract (PPT).
The PPT is resistant to ribonuclease H (RNase H) cleavage and is used as a
primer for second DNA strand synthesis. The 'RNase H primer grip', consisting of
amino acids that interact with the DNA primer strand, may contribute to RNase H
catalysis and cleavage specificity. Cleavage specificity is also controlled by
the width of the minor groove and the trajectory of the RNA:DNA, both of which
are sequence dependent. An unusual 'unzipping' of 7 bp occurs in the adenine
stretch of the PPT: an unpaired base on the template strand takes the base
pairing out of register and then, following two offset base pairs, an unpaired
base on the primer strand re-establishes the normal register. The structural
aberration extends to the RNase H active site and may play a role in the
resistance of PPT to RNase H cleavage.
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Figure 3.
Figure 3 Stereo view of a ribbon representation of the structure
of HIV-1 RT in complex with the polypurine RNA:DNA. The fingers,
palm, thumb, connection and RNase H subdomains of p66 are
colored blue, red, green, yellow and orange, respectively. The
p51 subunit is colored gray. The RNA template and DNA primer
strands are shown in magenta and blue, respectively.
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Figure 5.
Figure 5 Simulated annealing (F[o] - F[c]) omit electron density
maps contoured at the 2  level
at the polymerase active site (1) (omitting nucleic acid) and of
the unpaired residue of template (2) (omitting unpaired residue
Tem-15-Ade).
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The above figures are
reprinted
from an Open Access publication published by Macmillan Publishers Ltd:
EMBO J
(2001,
20,
1449-1461)
copyright 2001.
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