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Contents |
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* Residue conservation analysis
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Enzyme class 1:
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Chains A, B, C, D:
E.C.2.7.7.-
- ?????
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Enzyme class 2:
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Chains A, B, C, D:
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 3:
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Chains A, B, C, D:
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 4:
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Chains A, B, C, D:
E.C.3.1.-.-
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Enzyme class 5:
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Chains A, B, C, D:
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 6:
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Chains A, B, C, D:
E.C.3.1.26.13
- retroviral ribonuclease H.
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Enzyme class 7:
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Chains A, B, C, D:
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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Science
282:1669-1675
(1998)
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PubMed id:
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Structure of a covalently trapped catalytic complex of HIV-1 reverse transcriptase: implications for drug resistance.
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H.Huang,
R.Chopra,
G.L.Verdine,
S.C.Harrison.
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ABSTRACT
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A combinatorial disulfide cross-linking strategy was used to prepare a stalled
complex of human immunodeficiency virus-type 1 (HIV-1) reverse transcriptase
with a DNA template:primer and a deoxynucleoside triphosphate (dNTP), and the
crystal structure of the complex was determined at a resolution of 3.2
angstroms. The presence of a dideoxynucleotide at the 3'-primer terminus allows
capture of a state in which the substrates are poised for attack on the dNTP.
Conformational changes that accompany formation of the catalytic complex produce
distinct clusters of the residues that are altered in viruses resistant to
nucleoside analog drugs. The positioning of these residues in the neighborhood
of the dNTP helps to resolve some long-standing puzzles about the molecular
basis of resistance. The resistance mutations are likely to influence binding or
reactivity of the inhibitors, relative to normal dNTPs, and the clustering of
the mutations correlates with the chemical structure of the drug.
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Selected figure(s)
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Figure 1.
Fig. 1. RT-DNA tethering reaction. Chemistry of disulfide
bond formation between the side chain of an engineered cysteine
residue (blue) in helix H (gold) of RT to a thiol group in the
minor groove of DNA (activated as the mixed disulfide), which is
tethered to N2 of a dG (green) in the template:primer.
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Figure 6.
Fig. 6. Sites of mutations conferring resistance to various
nucleoside analog drugs. (A) "Front" view, corresponding to the
orientation in Fig. 4. The polypeptide backbone of the fingers
and palm domains (residues 1 to 235) is shown as a red worm, and
locations of resistance mutations are indicated by colored
squares. The substrates are shown in Corey-Pauling-Koltun
representation, with colors as in Fig. 3. The color code for
mutations is as follows: light blue for resistance to ddI, ddC,
and 3TC; blue for resistance to AZT; and violet for cross
resistance to AZT and ddI or ddC. The location of the NNRTI
binding site is shown by an arrow. Side chains of the residues
at which mutations affect dideoxynucleotide sensitivity project
forward: L74 bears on the templating base, and V at this
position will also shift Q151 and R72 and hence the dNTP itself;
M184 contacts the backbone and base at the primer terminus, and
mutation to I or V will also generate a contact to the sugar
ring of the dNTP; K65 contacts the  -phosphate;
and T69D (resistance to ddC) can probably best be explained by
assuming a conformational effect on the fingers loop,
transmitted to the dNTP by contacts from other fingers residues.
(B) "Back" view, from the direction opposite to the one in (A).
Side chains of AZT resistance mutations project toward this
surface. One of the earliest mutations that appears in patients
on AZT monotherapy is K70R. The Lys70 residue projects directly
outward in the current model, but mutation to arginine (with
five hydrogen-bond donors in fixed orientations on the
guanidinium group) could readily induce side-chain
reorientation, with contacts to Asp113 or the -phosphate.
Subsequent appearance of T215Y/F confers higher levels of
resistance. This mutation, likely to affect the rear of the 3'
pocket, is frequently "tuned" by appearance of others: K210W
(which probably stabilizes the alteration at 215), M41L, and
D67N and K219Q (which likely affect the interaction of fingers
and palm and hence the formation of the 3' pocket during the
polymerization cycle) (16). Figure 4A was prepared with GRASP
(50), and Figs. 3, 4B, 5, and 6, with RIBBONS (51).
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The above figures are
reprinted
by permission from the AAAs:
Science
(1998,
282,
1669-1675)
copyright 1998.
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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
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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.
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Nat Struct Mol Biol,
20,
230-236.
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PDB codes:
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A.Engelman,
and
P.Cherepanov
(2012).
The structural biology of HIV-1: mechanistic and therapeutic insights.
|
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Nat Rev Microbiol,
10,
279-290.
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|
|
|
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C.Yi,
B.Chen,
B.Qi,
W.Zhang,
G.Jia,
L.Zhang,
C.J.Li,
A.R.Dinner,
C.G.Yang,
and
C.He
(2012).
Duplex interrogation by a direct DNA repair protein in search of base damage.
|
| |
Nat Struct Mol Biol,
19,
671-676.
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PDB codes:
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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.
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PDB codes:
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T.Nakamura,
Y.Zhao,
Y.Yamagata,
Y.J.Hua,
and
W.Yang
(2012).
Watching DNA polymerase η make a phosphodiester bond.
|
| |
Nature,
487,
196-201.
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PDB codes:
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A.Hachiya,
E.N.Kodama,
M.M.Schuckmann,
K.A.Kirby,
E.Michailidis,
Y.Sakagami,
S.Oka,
K.Singh,
and
S.G.Sarafianos
(2011).
K70Q adds high-level tenofovir resistance to "Q151M complex" HIV reverse transcriptase through the enhanced discrimination mechanism.
|
| |
PLoS One,
6,
e16242.
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|
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H.Chunduri,
C.Crumpacker,
and
P.L.Sharma
(2011).
Reverse transcriptase mutation K65N confers a decreased replication capacity to HIV-1 in comparison to K65R due to a decreased RT processivity.
|
| |
Virology,
414,
34-41.
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|
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H.Chunduri,
D.Rimland,
V.Nurpeisov,
C.S.Crumpacker,
and
P.L.Sharma
(2011).
A Leu to Ile but not Leu to Val change at HIV-1 reverse transcriptase codon 74 in the background of K65R mutation leads to an increased processivity of K65R+L74I enzyme and a replication competent virus.
|
| |
Virol J,
8,
33.
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J.Xie,
P.Zhang,
C.Li,
Q.Huang,
R.Zhou,
and
T.Peng
(2011).
Mechanistic insights into the roles of three linked single-stranded template binding residues of MMLV reverse transcriptase in misincorporation and mispair extension fidelity of DNA synthesis.
|
| |
Gene,
479,
47-56.
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M.Mason,
A.Schuller,
and
E.Skordalakes
(2011).
Telomerase structure function.
|
| |
Curr Opin Struct Biol,
21,
92.
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S.Ibe,
and
W.Sugiura
(2011).
Clinical significance of HIV reverse-transcriptase inhibitor-resistance mutations.
|
| |
Future Microbiol,
6,
295-315.
|
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|
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|
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S.Yang,
M.Froeyen,
E.Lescrinier,
P.Marlière,
and
P.Herdewijn
(2011).
3-Phosphono-L-alanine as pyrophosphate mimic for DNA synthesis using HIV-1 reverse transcriptase.
|
| |
Org Biomol Chem,
9,
111-119.
|
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|
|
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|
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A.Giraut,
and
P.Herdewijn
(2010).
Influence of the linkage between leaving group and nucleoside on substrate efficiency for incorporation in DNA catalyzed by reverse transcriptase.
|
| |
Chembiochem,
11,
1399-1403.
|
|
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|
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A.Giraut,
X.P.Song,
M.Froeyen,
P.Marlière,
and
P.Herdewijn
(2010).
Iminodiacetic-phosphoramidates as metabolic prototypes for diversifying nucleic acid polymerization in vivo.
|
| |
Nucleic Acids Res,
38,
2541-2550.
|
|
|
|
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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.J.Acosta-Hoyos,
and
W.A.Scott
(2010).
The Role of Nucleotide Excision by Reverse Transcriptase in HIV Drug Resistance.
|
| |
Viruses,
2,
372-394.
|
|
|
|
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|
|
A.J.Kandathil,
A.P.Joseph,
R.Kannangai,
N.Srinivasan,
O.C.Abraham,
S.A.Pulimood,
and
G.Sridharan
(2010).
HIV reverse transcriptase: Structural interpretation of drug resistant genetic variants from India.
|
| |
Bioinformation,
4,
36-45.
|
|
|
|
|
|
|
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.
|
|
|
|
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|
|
A.W.Walsh,
D.R.Langley,
R.J.Colonno,
and
D.J.Tenney
(2010).
Mechanistic characterization and molecular modeling of hepatitis B virus polymerase resistance to entecavir.
|
| |
PLoS One,
5,
e9195.
|
|
|
|
|
|
|
G.N.Roviello,
S.Di Gaetano,
D.Capasso,
A.Cesarani,
E.M.Bucci,
and
C.Pedone
(2010).
Synthesis, spectroscopic studies and biological activity of a novel nucleopeptide with Moloney murine leukemia virus reverse transcriptase inhibitory activity.
|
| |
Amino Acids,
38,
1489-1496.
|
|
|
|
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|
|
H.Zhang,
and
F.P.Guengerich
(2010).
Effect of N2-guanyl modifications on early steps in catalysis of polymerization by Sulfolobus solfataricus P2 DNA polymerase Dpo4 T239W.
|
| |
J Mol Biol,
395,
1007-1018.
|
|
|
|
|
|
|
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.
|
|
|
|
|
|
|
K.A.Delviks-Frankenberry,
G.N.Nikolenko,
and
V.K.Pathak
(2010).
The "Connection" Between HIV Drug Resistance and RNase H.
|
| |
Viruses,
2,
1476-1503.
|
|
|
|
|
|
|
K.A.Johnson
(2010).
The kinetic and chemical mechanism of high-fidelity DNA polymerases.
|
| |
Biochim Biophys Acta,
1804,
1041-1048.
|
|
|
|
|
|
|
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.
|
|
|
|
|
|
|
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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|
|
|
|
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M.Mitchell,
A.Gillis,
M.Futahashi,
H.Fujiwara,
and
E.Skordalakes
(2010).
Structural basis for telomerase catalytic subunit TERT binding to RNA template and telomeric DNA.
|
| |
Nat Struct Mol Biol,
17,
513-518.
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PDB code:
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M.Mukaide,
Y.Tanaka,
T.Shin-I,
M.F.Yuen,
F.Kurbanov,
O.Yokosuka,
M.Sata,
Y.Karino,
G.Yamada,
K.Sakaguchi,
E.Orito,
M.Inoue,
S.Baqai,
C.L.Lai,
and
M.Mizokami
(2010).
Mechanism of entecavir resistance of hepatitis B virus with viral breakthrough as determined by long-term clinical assessment and molecular docking simulation.
|
| |
Antimicrob Agents Chemother,
54,
882-889.
|
|
|
|
|
|
|
M.W.Kellinger,
and
K.A.Johnson
(2010).
Nucleotide-dependent conformational change governs specificity and analog discrimination by HIV reverse transcriptase.
|
| |
Proc Natl Acad Sci U S A,
107,
7734-7739.
|
|
|
|
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|
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M.Yokoyama,
H.Mori,
and
H.Sato
(2010).
Allosteric regulation of HIV-1 reverse transcriptase by ATP for nucleotide selection.
|
| |
PLoS One,
5,
e8867.
|
|
|
|
|
|
|
P.Gong,
and
O.B.Peersen
(2010).
Structural basis for active site closure by the poliovirus RNA-dependent RNA polymerase.
|
| |
Proc Natl Acad Sci U S A,
107,
22505-22510.
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PDB codes:
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P.R.Daga,
J.Duan,
and
R.J.Doerksen
(2010).
Computational model of hepatitis B virus DNA polymerase: molecular dynamics and docking to understand resistant mutations.
|
| |
Protein Sci,
19,
796-807.
|
|
|
|
|
|
|
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.
|
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|
|
|
|
|
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.
|
|
|
|
|
|
|
S.K.Perumal,
H.Yue,
Z.Hu,
M.M.Spiering,
and
S.J.Benkovic
(2010).
Single-molecule studies of DNA replisome function.
|
| |
Biochim Biophys Acta,
1804,
1094-1112.
|
|
|
|
|
|
|
S.Kim,
C.M.Schroeder,
and
X.S.Xie
(2010).
Single-molecule study of DNA polymerization activity of HIV-1 reverse transcriptase on DNA templates.
|
| |
J Mol Biol,
395,
995.
|
|
|
|
|
|
|
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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S.N.Stumpp,
B.Heyn,
and
S.Brakmann
(2010).
Activity-based selection of HIV-1 reverse transcriptase variants with decreased polymerization fidelity.
|
| |
Biol Chem,
391,
665-674.
|
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|
|
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|
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S.Rasheedi,
M.Suragani,
S.K.Haq,
Sachchidanand,
R.Bhardwaj,
S.E.Hasnain,
and
N.Z.Ehtesham
(2010).
Expression, purification and ligand binding properties of the recombinant translation initiation factor (PeIF5B) from Pisum sativum.
|
| |
Mol Cell Biochem,
344,
33-41.
|
|
|
|
|
|
|
V.A.Braz,
L.A.Holladay,
and
M.D.Barkley
(2010).
Efavirenz binding to HIV-1 reverse transcriptase monomers and dimers.
|
| |
Biochemistry,
49,
601-610.
|
|
|
|
|
|
|
V.Svicher,
C.Alteri,
A.Artese,
F.Forbici,
M.M.Santoro,
D.Schols,
K.Van Laethem,
S.Alcaro,
G.Costa,
C.Tommasi,
M.Zaccarelli,
P.Narciso,
A.Antinori,
F.Ceccherini-Silberstein,
J.Balzarini,
and
C.F.Perno
(2010).
Different evolution of genotypic resistance profiles to emtricitabine versus lamivudine in tenofovir-containing regimens.
|
| |
J Acquir Immune Defic Syndr,
55,
336-344.
|
|
|
|
|
|
|
X.Ding,
L.Jiang,
C.Ke,
Z.Yang,
C.Lei,
K.Cao,
J.Xu,
L.Xu,
X.Yang,
Y.Zhang,
P.Huang,
W.Huang,
X.Zhu,
Z.He,
L.Liu,
J.Li,
J.Yuan,
J.Wu,
X.Tang,
and
M.Li
(2010).
Amino acid sequence analysis and identification of mutations under positive selection in hemagglutinin of 2009 influenza A (H1N1) isolates.
|
| |
Virus Genes,
41,
329-340.
|
|
|
|
|
|
|
X.Tu,
K.Das,
Q.Han,
J.D.Bauman,
A.D.Clark,
X.Hou,
Y.V.Frenkel,
B.L.Gaffney,
R.A.Jones,
P.L.Boyer,
S.H.Hughes,
S.G.Sarafianos,
and
E.Arnold
(2010).
Structural basis of HIV-1 resistance to AZT by excision.
|
| |
Nat Struct Mol Biol,
17,
1202-1209.
|
|
|
PDB codes:
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Y.Qi,
M.C.Spong,
K.Nam,
M.Karplus,
and
G.L.Verdine
(2010).
Entrapment and structure of an extrahelical guanine attempting to enter the active site of a bacterial DNA glycosylase, MutM.
|
| |
J Biol Chem,
285,
1468-1478.
|
|
|
PDB codes:
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|
|
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|
|
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A.Alian,
S.L.Griner,
V.Chiang,
M.Tsiang,
G.Jones,
G.Birkus,
R.Geleziunas,
A.D.Leavitt,
and
R.M.Stroud
(2009).
Catalytically-active complex of HIV-1 integrase with a viral DNA substrate binds anti-integrase drugs.
|
| |
Proc Natl Acad Sci U S A,
106,
8192-8197.
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B.A.Mulder,
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V.K.Batra,
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Structure,
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PDB codes:
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D.W.Gohara,
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J Virol,
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PDB code:
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G.A.Locatelli,
G.Campiani,
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Nature,
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PDB code:
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G.N.Nikolenko,
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PDB code:
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Proc Natl Acad Sci U S A,
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PDB codes:
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K.L.White,
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Structure,
12,
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PDB codes:
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R.A.Love,
K.A.Maegley,
X.Yu,
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The crystal structure of the RNA-dependent RNA polymerase from human rhinovirus: a dual function target for common cold antiviral therapy.
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Structure,
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PDB codes:
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R.L.Crowther,
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Structural and energetic characterization of nucleic acid-binding to the fingers domain of Moloney murine leukemia virus reverse transcriptase.
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Proteins,
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PDB code:
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S.Crowder,
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Structure,
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S.J.Johnson,
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Structures of mismatch replication errors observed in a DNA polymerase.
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Cell,
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PDB codes:
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S.Tuske,
S.G.Sarafianos,
A.D.Clark,
J.Ding,
L.K.Naeger,
K.L.White,
M.D.Miller,
C.S.Gibbs,
P.L.Boyer,
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Structures of HIV-1 RT-DNA complexes before and after incorporation of the anti-AIDS drug tenofovir.
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Nat Struct Mol Biol,
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PDB codes:
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T.A.Steitz,
and
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Accuracy, lesion bypass, strand displacement and translocation by DNA polymerases.
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Philos Trans R Soc Lond B Biol Sci,
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Y.W.Yin,
and
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The structural mechanism of translocation and helicase activity in T7 RNA polymerase.
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Cell,
116,
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PDB codes:
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Z.Zhou,
and
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Relative free energy of binding and binding mode calculations of HIV-1 RT inhibitors based on dock-MM-PB/GS.
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Proteins,
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A.Bashan,
R.Zarivach,
F.Schluenzen,
I.Agmon,
J.Harms,
T.Auerbach,
D.Baram,
R.Berisio,
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M.Kessler,
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Ribosomal crystallography: peptide bond formation and its inhibition.
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Biopolymers,
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19-41.
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A.M.DeLucia,
N.D.Grindley,
and
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only a partial list as not all journals are covered by
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Where a reference describes a PDB structure, the PDB
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shown on the right.
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