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PDBsum entry 2p3b
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Hydrolase/hydrolase inhibitor
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PDB id
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2p3b
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References listed in PDB file
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Key reference
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Title
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Structural characterization of b and non-B subtypes of HIV-Protease: insights into the natural susceptibility to drug resistance development.
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Authors
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M.Sanches,
S.Krauchenco,
N.H.Martins,
A.Gustchina,
A.Wlodawer,
I.Polikarpov.
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Ref.
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J Mol Biol, 2007,
369,
1029-1040.
[DOI no: ]
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PubMed id
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Abstract
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Although a majority of HIV-1 infections in Brazil are caused by the subtype B
virus (also prevalent in the United States and Western Europe), viral subtypes F
and C are also found very frequently. Genomic differences between the subtypes
give rise to sequence variations in the encoded proteins, including the HIV-1
protease. The current anti-HIV drugs have been developed primarily against
subtype B and the effects arising from the combination of drug-resistance
mutations with the naturally existing polymorphisms in non-B HIV-1 subtypes are
only beginning to be elucidated. To gain more insights into the structure and
function of different variants of HIV proteases, we have determined a 2.1 A
structure of the native subtype F HIV-1 protease (PR) in complex with the
protease inhibitor TL-3. We have also solved crystal structures of two
multi-drug resistant mutant HIV PRs in complex with TL-3, from subtype B (Bmut)
carrying the primary mutations V82A and L90M, and from subtype F (Fmut) carrying
the primary mutation V82A plus the secondary mutation M36I, at 1.75 A and 2.8 A
resolution, respectively. The proteases Bmut, Fwt and Fmut exhibit sevenfold,
threefold, and 54-fold resistance to TL-3, respectively. In addition, the
structure of subtype B wild type HIV-PR in complex with TL-3 has been
redetermined in space group P6(1), consistent with the other three structures.
Our results show that the primary mutation V82A causes the known effect of
collapsing the S1/S1' pockets that ultimately lead to the reduced inhibitory
effect of TL-3. Our results further indicate that two naturally occurring
polymorphic substitutions in subtype F and other non-B HIV proteases, M36I and
L89M, may lead to early development of drug resistance in patients infected with
non-B HIV subtypes.
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Figure 2.
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Figure 6.
Figure 6. Effects of the mutation V82A on the
inhibitor-binding mode. The inhibitor subsite P1/P1′ is shown
in ball-and-stick representation along with the pocket S1/S1′
in stick representation, for the structures Bwt (red) and Bmut
(green). The broken lines represent hydrogen bonds between the
active site aspartate residues and the oxygen of the diol in the
center of the inhibitor, whereas the asterisks mark residues
that belong to chain B. Due to the asymmetric mode of binding of
the inhibitor, the S1′ pocket, occupied by the P1′ phenyl
side-chain, accommodates one hydroxyl of the central diol, which
is indicated by a dotted circle. Whereas there is no significant
modification in the P1 subsite due to V82A mutation (marked with
a square), in the P1′ a rotation of the Phe ring of the
inhibitor is observed. This rotation decreases the number of
interactions between the inhibitor's side-chain and the S1′
pocket, while the interactions are maintained in the S1 pocket.
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The above figures are
reprinted
by permission from Elsevier:
J Mol Biol
(2007,
369,
1029-1040)
copyright 2007.
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Secondary reference #1
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Title
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Crystallization of a non-B and a b mutant HIV protease.
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Authors
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M.Sanches,
N.H.Martins,
A.Calazans,
R.D.E. .M.Brindeiro,
A.Tanuri,
O.A.Antunes,
I.Polikarpov.
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Ref.
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Acta Crystallogr D Biol Crystallogr, 2004,
60,
1625-1627.
[DOI no: ]
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PubMed id
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Figure 1.
Figure 1 Crystals of Bmut and Fwt proteases. (a) Bmut grown in
condition 1 (used in data collection), (b) Bmut grown in
condition 2, (c) Fwt initial screen obtained at 291 K using 0.8
M ammonium sulfate as precipitant, and (d) Fwt final crystals
(used in data collection).
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The above figure is
reproduced from the cited reference
with permission from the IUCr
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