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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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PDB id:
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| Name: |
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Transferase/DNA-RNA hybrid
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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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Structure:
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5'-r( Up Cp Ap Gp Cp Cp Ap Cp Up Up Up Up Up Ap Ap Ap Ap Gp Ap Ap Ap Ap G)-3'. Chain: e. Engineered: yes. 5'-d( Cp Tp Tp Tp Tp Cp Tp Tp Tp Tp Ap Ap Ap Ap Ap Gp Tp Gp Gp Cp Tp G)-3'. Chain: f. Engineered: yes. HIV-1 reverse transcriptase.
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Source:
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Synthetic: yes. Human immunodeficiency virus 1. Organism_taxid: 11676. Gene: pol. Expressed in: escherichia coli. Expression_system_taxid: 562. Mus musculus. House mouse. Organism_taxid: 10090.
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Biol. unit:
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Tetramer (from
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Resolution:
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3.00Å
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R-factor:
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0.274
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R-free:
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0.316
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Authors:
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S.G.Sarafianos,K.Das,C.Tantillo,A.D.Clark Jr.,J.Ding,J.Whitcomb, P.L.Boyer,S.H.Hughes,E.Arnold
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Key ref:
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S.G.Sarafianos
et al.
(2001).
Crystal structure of HIV-1 reverse transcriptase in complex with a polypurine tract RNA:DNA.
EMBO J,
20,
1449-1461.
PubMed id:
DOI:
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Date:
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22-Jan-01
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Release date:
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26-Mar-01
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PROCHECK
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Headers
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References
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P03366
(POL_HV1B1) -
Gag-Pol polyprotein from Human immunodeficiency virus type 1 group M subtype B (isolate BH10)
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Seq:
Struc:
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1447 a.a.
553 a.a.*
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P03366
(POL_HV1B1) -
Gag-Pol polyprotein from Human immunodeficiency virus type 1 group M subtype B (isolate BH10)
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Seq:
Struc:
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1447 a.a.
425 a.a.*
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Enzyme class 2:
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Chains A, B:
E.C.2.7.7.-
- ?????
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Enzyme class 3:
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Chains A, B:
E.C.2.7.7.49
- RNA-directed Dna polymerase.
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Reaction:
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DNA(n) + a 2'-deoxyribonucleoside 5'-triphosphate = DNA(n+1) + diphosphate
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DNA(n)
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+
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2'-deoxyribonucleoside 5'-triphosphate
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=
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DNA(n+1)
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+
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diphosphate
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Enzyme class 4:
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Chains A, B:
E.C.2.7.7.7
- DNA-directed Dna polymerase.
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Reaction:
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DNA(n) + a 2'-deoxyribonucleoside 5'-triphosphate = DNA(n+1) + diphosphate
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DNA(n)
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+
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2'-deoxyribonucleoside 5'-triphosphate
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=
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DNA(n+1)
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+
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diphosphate
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Enzyme class 5:
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Chains A, B:
E.C.3.1.-.-
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Enzyme class 6:
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Chains A, B:
E.C.3.1.13.2
- exoribonuclease H.
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Reaction:
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Exonucleolytic cleavage to 5'-phosphomonoester oligonucleotides in both 5'- to 3'- and 3'- to 5'-directions.
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Enzyme class 7:
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Chains A, B:
E.C.3.1.26.13
- retroviral ribonuclease H.
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Enzyme class 8:
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Chains A, B:
E.C.3.4.23.16
- HIV-1 retropepsin.
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Reaction:
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Specific for a P1 residue that is hydrophobic, and P1' variable, but often Pro.
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Note, where more than one E.C. class is given (as above), each may
correspond to a different protein domain or, in the case of polyprotein
precursors, to a different mature protein.
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Molecule diagrams generated from .mol files obtained from the
KEGG ftp site
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DOI no:
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EMBO J
20:1449-1461
(2001)
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PubMed id:
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Crystal structure of HIV-1 reverse transcriptase in complex with a polypurine tract RNA:DNA.
|
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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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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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Selected figure(s)
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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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Figures were
selected
by an automated process.
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Literature references that cite this PDB file's key reference
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| |
PubMed id
|
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Reference
|
|
|
|
|
|
M.Lapkouski,
L.Tian,
J.T.Miller,
S.F.Le Grice,
and
W.Yang
(2013).
Complexes of HIV-1 RT, NNRTI and RNA/DNA hybrid reveal a structure compatible with RNA degradation.
|
| |
Nat Struct Mol Biol,
20,
230-236.
|
|
|
PDB codes:
|
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|
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|
|
K.Das,
S.E.Martinez,
J.D.Bauman,
and
E.Arnold
(2012).
HIV-1 reverse transcriptase complex with DNA and nevirapine reveals non-nucleoside inhibition mechanism.
|
| |
Nat Struct Mol Biol,
19,
253-259.
|
|
|
PDB codes:
|
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|
|
|
|
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A.Herschhorn,
and
A.Hizi
(2010).
Retroviral reverse transcriptases.
|
| |
Cell Mol Life Sci,
67,
2717-2747.
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|
|
|
|
|
|
A.K.Upadhyay,
T.T.Talele,
and
V.N.Pandey
(2010).
Impact of template overhang-binding region of HIV-1 RT on the binding and orientation of the duplex region of the template-primer.
|
| |
Mol Cell Biochem,
338,
19-33.
|
|
|
|
|
|
|
C.S.Adamson,
and
E.O.Freed
(2010).
Novel approaches to inhibiting HIV-1 replication.
|
| |
Antiviral Res,
85,
119-141.
|
|
|
|
|
|
|
C.Zhang,
N.Ding,
K.Chen,
and
R.Yang
(2010).
Complex positive selection pressures drive the evolution of HIV-1 with different co-receptor tropisms.
|
| |
Sci China Life Sci,
53,
1204-1214.
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|
|
|
|
|
|
J.T.Olimpo,
and
J.J.DeStefano
(2010).
Duplex structural differences and not 2'-hydroxyls explain the more stable binding of HIV-reverse transcriptase to RNA-DNA versus DNA-DNA.
|
| |
Nucleic Acids Res,
38,
4426-4435.
|
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|
|
J.Wang,
R.A.Bambara,
L.M.Demeter,
and
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(2010).
Reduced fitness in cell culture of HIV-1 with nonnucleoside reverse transcriptase inhibitor-resistant mutations correlates with relative levels of reverse transcriptase content and RNase H activity in virions.
|
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J Virol,
84,
9377-9389.
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K.Singh,
B.Marchand,
K.A.Kirby,
E.Michailidis,
and
S.G.Sarafianos
(2010).
Structural Aspects of Drug Resistance and Inhibition of HIV-1 Reverse Transcriptase.
|
| |
Viruses,
2,
606-638.
|
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M.Götte,
J.W.Rausch,
B.Marchand,
S.Sarafianos,
and
S.F.Le Grice
(2010).
Reverse transcriptase in motion: conformational dynamics of enzyme-substrate interactions.
|
| |
Biochim Biophys Acta,
1804,
1202-1212.
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M.Mitchell,
A.Gillis,
M.Futahashi,
H.Fujiwara,
and
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(2010).
Structural basis for telomerase catalytic subunit TERT binding to RNA template and telomeric DNA.
|
| |
Nat Struct Mol Biol,
17,
513-518.
|
|
|
PDB code:
|
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|
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|
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N.Sluis-Cremer,
K.Moore,
J.Radzio,
S.Sonza,
and
G.Tachedjian
(2010).
N348I in HIV-1 reverse transcriptase decreases susceptibility to tenofovir and etravirine in combination with other resistance mutations.
|
| |
AIDS,
24,
317-319.
|
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|
R.Hu,
F.Barbault,
F.Maurel,
M.Delamar,
and
R.Zhang
(2010).
Molecular dynamics simulations of 2-amino-6-arylsulphonylbenzonitriles analogues as HIV inhibitors: interaction modes and binding free energies.
|
| |
Chem Biol Drug Des,
76,
518-526.
|
|
|
|
|
|
|
S.Chung,
M.Wendeler,
J.W.Rausch,
G.Beilhartz,
M.Gotte,
B.R.O'Keefe,
A.Bermingham,
J.A.Beutler,
S.Liu,
X.Zhuang,
and
S.F.Le Grice
(2010).
Structure-activity analysis of vinylogous urea inhibitors of human immunodeficiency virus-encoded ribonuclease H.
|
| |
Antimicrob Agents Chemother,
54,
3913-3921.
|
|
|
|
|
|
|
S.J.Schultz,
M.Zhang,
and
J.J.Champoux
(2010).
Multiple nucleotide preferences determine cleavage-site recognition by the HIV-1 and M-MuLV RNases H.
|
| |
J Mol Biol,
397,
161-178.
|
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|
|
S.Liu,
B.T.Harada,
J.T.Miller,
S.F.Le Grice,
and
X.Zhuang
(2010).
Initiation complex dynamics direct the transitions between distinct phases of early HIV reverse transcription.
|
| |
Nat Struct Mol Biol,
17,
1453-1460.
|
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|
D.M.Himmel,
K.A.Maegley,
T.A.Pauly,
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K.Das,
C.Dharia,
A.D.Clark,
K.Ryan,
M.J.Hickey,
R.A.Love,
S.H.Hughes,
S.Bergqvist,
and
E.Arnold
(2009).
Structure of HIV-1 reverse transcriptase with the inhibitor beta-Thujaplicinol bound at the RNase H active site.
|
| |
Structure,
17,
1625-1635.
|
|
|
PDB codes:
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|
|
J.J.Champoux,
and
S.J.Schultz
(2009).
Ribonuclease H: properties, substrate specificity and roles in retroviral reverse transcription.
|
| |
FEBS J,
276,
1506-1516.
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|
J.M.Seckler,
K.J.Howard,
M.D.Barkley,
and
P.L.Wintrode
(2009).
Solution structural dynamics of HIV-1 reverse transcriptase heterodimer.
|
| |
Biochemistry,
48,
7646-7655.
|
|
|
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|
|
K.A.Delviks-Frankenberry,
G.N.Nikolenko,
F.Maldarelli,
S.Hase,
Y.Takebe,
and
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Subtype-specific differences in the human immunodeficiency virus type 1 reverse transcriptase connection subdomain of CRF01_AE are associated with higher levels of resistance to 3'-azido-3'-deoxythymidine.
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| |
J Virol,
83,
8502-8513.
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H.Y.Yi-Brunozzi,
R.G.Brinson,
J.P.Marino,
D.Fabris,
and
S.F.Le Grice
(2009).
SHAMS: combining chemical modification of RNA with mass spectrometry to examine polypurine tract-containing RNA/DNA hybrids.
|
| |
RNA,
15,
1605-1613.
|
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|
K.Post,
B.Kankia,
S.Gopalakrishnan,
V.Yang,
E.Cramer,
P.Saladores,
R.J.Gorelick,
J.Guo,
K.Musier-Forsyth,
and
J.G.Levin
(2009).
Fidelity of plus-strand priming requires the nucleic acid chaperone activity of HIV-1 nucleocapsid protein.
|
| |
Nucleic Acids Res,
37,
1755-1766.
|
|
|
|
|
|
|
L.L.Dunn,
M.J.McWilliams,
K.Das,
E.Arnold,
and
S.H.Hughes
(2009).
Mutations in the thumb allow human immunodeficiency virus type 1 reverse transcriptase to be cleaved by protease in virions.
|
| |
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83,
12336-12344.
|
|
|
|
|
|
|
R.G.Brinson,
K.B.Turner,
H.Y.Yi-Brunozzi,
S.F.Le Grice,
D.Fabris,
and
J.P.Marino
(2009).
Probing anomalous structural features in polypurine tract-containing RNA-DNA hybrids with neomycin B.
|
| |
Biochemistry,
48,
6988-6997.
|
|
|
|
|
|
|
S.G.Sarafianos,
B.Marchand,
K.Das,
D.M.Himmel,
M.A.Parniak,
S.H.Hughes,
and
E.Arnold
(2009).
Structure and function of HIV-1 reverse transcriptase: molecular mechanisms of polymerization and inhibition.
|
| |
J Mol Biol,
385,
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|
|
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|
|
|
|
S.J.Schultz,
M.Zhang,
and
J.J.Champoux
(2009).
Preferred sequences within a defined cleavage window specify DNA 3' end-directed cleavages by retroviral RNases H.
|
| |
J Biol Chem,
284,
32225-32238.
|
|
|
|
|
|
|
S.T.Rigby,
K.P.Van Nostrand,
A.E.Rose,
R.J.Gorelick,
D.H.Mathews,
and
R.A.Bambara
(2009).
Factors that determine the efficiency of HIV-1 strand transfer initiated at a specific site.
|
| |
J Mol Biol,
394,
694-707.
|
|
|
|
|
|
|
A.F.Santos,
R.B.Lengruber,
E.A.Soares,
A.Jere,
E.Sprinz,
A.M.Martinez,
J.Silveira,
F.S.Sion,
V.K.Pathak,
and
M.A.Soares
(2008).
Conservation patterns of HIV-1 RT connection and RNase H domains: identification of new mutations in NRTI-treated patients.
|
| |
PLoS ONE,
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|
A.Hachiya,
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Amino acid mutation N348I in the connection subdomain of human immunodeficiency virus type 1 reverse transcriptase confers multiclass resistance to nucleoside and nonnucleoside reverse transcriptase inhibitors.
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| |
J Virol,
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M.Götte,
and
S.F.Le Grice
(2008).
Examining the ribonuclease H primer grip of HIV-1 reverse transcriptase by charge neutralization of RNA/DNA hybrids.
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| |
Nucleic Acids Res,
36,
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|
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D.M.Held,
and
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(2008).
Novel bimodular DNA aptamers with guanosine quadruplexes inhibit phylogenetically diverse HIV-1 reverse transcriptases.
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| |
Nucleic Acids Res,
36,
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and
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(2008).
A new role for HIV nucleocapsid protein in modulating the specificity of plus strand priming.
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| |
Virology,
378,
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E.A.Abbondanzieri,
G.Bokinsky,
J.W.Rausch,
J.X.Zhang,
S.F.Le Grice,
and
X.Zhuang
(2008).
Dynamic binding orientations direct activity of HIV reverse transcriptase.
|
| |
Nature,
453,
184-189.
|
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|
|
|
E.Arnold,
and
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(2008).
Molecular biology: an HIV secret uncovered.
|
| |
Nature,
453,
169-170.
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|
E.P.Tchesnokov,
A.Obikhod,
R.F.Schinazi,
and
M.Götte
(2008).
Delayed Chain Termination Protects the Anti-hepatitis B Virus Drug Entecavir from Excision by HIV-1 Reverse Transcriptase.
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J Biol Chem,
283,
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H.Y.Yi-Brunozzi,
R.G.Brinson,
D.M.Brabazon,
D.Lener,
S.F.Le Grice,
and
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(2008).
High-resolution NMR analysis of the conformations of native and base analog substituted retroviral and LTR-retrotransposon PPT primers.
|
| |
Chem Biol,
15,
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|
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J.D.Podlevsky,
C.J.Bley,
R.V.Omana,
X.Qi,
and
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(2008).
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|
| |
Nucleic Acids Res,
36,
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|
|
|
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|
J.Oh,
M.J.McWilliams,
J.G.Julias,
and
S.H.Hughes
(2008).
Mutations in the U5 region adjacent to the primer binding site affect tRNA cleavage by human immunodeficiency virus type 1 reverse transcriptase in vivo.
|
| |
J Virol,
82,
719-727.
|
|
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|
|
|
|
K.B.Turner,
R.G.Brinson,
H.Y.Yi-Brunozzi,
J.W.Rausch,
J.T.Miller,
S.F.Le Grice,
J.P.Marino,
and
D.Fabris
(2008).
Structural probing of the HIV-1 polypurine tract RNA:DNA hybrid using classic nucleic acid ligands.
|
| |
Nucleic Acids Res,
36,
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|
|
|
|
|
|
|
K.W.Chang,
J.Oh,
W.G.Alvord,
and
S.H.Hughes
(2008).
The effects of alternate polypurine tracts (PPTs) and mutations of sequences adjacent to the PPT on viral replication and cleavage specificity of the Rous sarcoma virus reverse transcriptase.
|
| |
J Virol,
82,
8592-8604.
|
|
|
|
|
|
|
M.Ehteshami,
G.L.Beilhartz,
B.J.Scarth,
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PDB codes:
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J.W.Noah,
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PDB codes:
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S.A.Gaidamakov,
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PDB code:
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PDB code:
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PDB codes:
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B.Sharma,
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PDB code:
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PDB codes:
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Where a reference describes a PDB structure, the PDB
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|
| |
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