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PDBsum entry 1n6q
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Transferase/immune system/DNA
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PDB id
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1n6q
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Contents |
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558 a.a.
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429 a.a.
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211 a.a.
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225 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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Structures of HIV-1 reverse transcriptase with pre- And post-Translocation aztmp-Terminated DNA.
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Authors
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S.G.Sarafianos,
A.D.Clark,
K.Das,
S.Tuske,
J.J.Birktoft,
P.Ilankumaran,
A.R.Ramesha,
J.M.Sayer,
D.M.Jerina,
P.L.Boyer,
S.H.Hughes,
E.Arnold.
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Ref.
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EMBO J, 2002,
21,
6614-6624.
[DOI no: ]
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PubMed id
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Abstract
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AZT (3'-azido-3'-deoxythymidine) resistance involves the enhanced excision of
AZTMP from the end of the primer strand by HIV-1 reverse transcriptase. This
reaction can occur when an AZTMP-terminated primer is bound at the
nucleotide-binding site (pre-translocation complex N) but not at the 'priming'
site (post-translocation complex P). We determined the crystal structures of N
and P complexes at 3.0 and 3.1 A resolution. These structures provide insight
into the structural basis of AZTMP excision and the mechanism of translocation.
Docking of a dNTP in the P complex structure suggests steric crowding in forming
a stable ternary complex that should increase the relative amount of the N
complex, which is the substrate for excision. Structural differences between
complexes N and P suggest that the conserved YMDD loop is involved in
translocation, acting as a springboard that helps to propel the primer terminus
from the N to the P site after dNMP incorporation.
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Figure 5.
Figure 5 (A) Ribbon representation of superposed polymerase
active sites (same basis of superposition as used for Figure 4)
of complex N and HIV-1 RT/DNA/dNTP ternary complex
[RT(ter)−ddNMP−dTTP complex] (Huang et al., 1998); PDB code
1RTD. Color scheme: side chains of complex N (cyan), primer
strand of complex N (magenta), incoming dNTP of the ternary
complex (yellow), metals A and B in the ternary complex
(yellow). In complex N, the corresponding metals (A' and B') are
either not seen in the structure and may have been released
together with PPi (A'), or are observed (Figure 3) at a position
shifted by  4.7
Å (metal B'). (B) Superposition of polymerase active sites
of the non-terminated [RT(P)−dNMP, green] (Ding et al., 1998;
PDB code 2HMI) and AZTMP-terminated P complex [RT(P)−AZTMP,
white]. The main structural difference is in the inclination of
the terminal nucleotide. (C) Superposition of the polymerase
active sites (aligned using p66 residues 107−112 and
155−215) of complex P (in white) on the RT(ter)−ddNMP/dTTP
ternary complex (in cyan) (Huang et al., 1998); PDB code 1RTD.
The ternary complex YMDD loop is displaced 1.0
Å from its position in the P complex. Steric conflicts (in
red) are mostly between the C5' of the incoming dNTP and the
side chain of Asp185.
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Figure 8.
Figure 8 Schematic relationships among events that affect
excision-based NRTI resistance (dNTP binding, translocation,
excision). Factors that affect any stage will affect the overall
equilibrium. X is an NRTI (red), A is ATP (orange) and dNTP
(cyan) is the cognate nucleotide triphosphate.
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The above figures are
reprinted
from an Open Access publication published by Macmillan Publishers Ltd:
EMBO J
(2002,
21,
6614-6624)
copyright 2002.
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