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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:
E.C.2.7.7.48
- RNA-directed Rna polymerase.
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Reaction:
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Nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1)
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Nucleoside triphosphate
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+
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RNA(n)
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=
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diphosphate
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+
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RNA(n+1)
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Enzyme class 2:
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Chains A, B:
E.C.3.4.21.98
- Hepacivirin.
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Reaction:
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Hydrolysis of four peptide bonds in the viral precursor polyprotein, commonly with Asp or Glu in the P6 position, Cys or Thr in P1 and Ser or Ala in P1'.
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Enzyme class 3:
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Chains A, B:
E.C.3.6.1.15
- Nucleoside-triphosphatase.
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Reaction:
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NTP + H2O = NDP + phosphate
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NTP
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+
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H(2)O
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=
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NDP
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+
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phosphate
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Enzyme class 4:
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Chains A, B:
E.C.3.6.4.13
- Rna helicase.
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Reaction:
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ATP + H2O = ADP + phosphate
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ATP
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+
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H(2)O
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=
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ADP
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+
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phosphate
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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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Gene Ontology (GO) functional annotation
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Biochemical function
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nucleic acid binding
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3 terms
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DOI no:
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Nat Struct Biol
4:463-467
(1997)
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PubMed id:
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Structure of the hepatitis C virus RNA helicase domain.
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N.Yao,
T.Hesson,
M.Cable,
Z.Hong,
A.D.Kwong,
H.V.Le,
P.C.Weber.
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ABSTRACT
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Helicases are nucleotide triphosphate (NTP)-dependent enzymes responsible for
unwinding duplex DNA and RNA during genomic replication. The 2.1 A resolution
structure of the HCV helicase from the positive-stranded RNA hepatitis C virus
reveals a molecule with distinct NTPase and RNA binding domains. The structure
supports a mechanism of helicase activity involving initial recognition of the
requisite 3' single-stranded region on the nucleic acid substrate by a conserved
arginine-rich sequence on the RNA binding domain. Comparison of
crystallographically independent molecules shows that rotation of the RNA
binding domain involves conformational changes within a conserved TATPP sequence
and untwisting of an extended antiparallel beta-sheet. Location of the TATPP
sequence at the end of an NTPase domain beta-strand structurally homologous to
the 'switch region' of many NTP-dependent enzymes offers the possibility that
domain rotation is coupled to NTP hydrolysis in the helicase catalytic cycle.
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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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J.Strohmeier,
I.Hertel,
U.Diederichsen,
M.G.Rudolph,
and
D.Klostermeier
(2011).
Changing nucleotide specificity of the DEAD-box helicase Hera abrogates communication between the Q-motif and the P-loop.
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| |
Biol Chem, 392,
357-369.
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PDB codes:
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V.López-Ramírez,
L.D.Alcaraz,
G.Moreno-Hagelsieb,
and
G.Olmedo-Álvarez
(2011).
Phylogenetic Distribution and Evolutionary History of Bacterial DEAD-Box Proteins.
|
| |
J Mol Evol, 72,
413-431.
|
|
|
|
|
|
|
B.Lee,
K.B.Kim,
S.Oh,
J.S.Choi,
J.S.Park,
D.H.Min,
and
D.E.Kim
(2010).
Suppression of hepatitis C virus genome replication in cells with RNA-cleaving DNA enzymes and short-hairpin RNA.
|
| |
Oligonucleotides, 20,
285-296.
|
|
|
|
|
|
|
H.Flechsig,
and
A.S.Mikhailov
(2010).
Tracing entire operation cycles of molecular motor hepatitis C virus helicase in structurally resolved dynamical simulations.
|
| |
Proc Natl Acad Sci U S A, 107,
20875-20880.
|
|
|
|
|
|
|
J.van Ameijde,
A.J.Poot,
L.T.van Wandelen,
A.E.Wammes,
R.Ruijtenbeek,
D.T.Rijkers,
and
R.M.Liskamp
(2010).
Preparation of novel alkylated arginine derivatives suitable for click-cycloaddition chemistry and their incorporation into pseudosubstrate- and bisubstrate-based kinase inhibitors.
|
| |
Org Biomol Chem, 8,
1629-1639.
|
|
|
|
|
|
|
L.Rong,
and
A.S.Perelson
(2010).
Treatment of hepatitis C virus infection with interferon and small molecule direct antivirals: viral kinetics and modeling.
|
| |
Crit Rev Immunol, 30,
131-148.
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|
|
|
|
|
|
S.Despins,
M.Issur,
I.Bougie,
and
M.Bisaillon
(2010).
Deciphering the molecular basis for nucleotide selection by the West Nile virus RNA helicase.
|
| |
Nucleic Acids Res, 38,
5493-5506.
|
|
|
|
|
|
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X.Wang,
K.Zhao,
M.Kirberger,
H.Wong,
G.Chen,
and
J.J.Yang
(2010).
Analysis and prediction of calcium-binding pockets from apo-protein structures exhibiting calcium-induced localized conformational changes.
|
| |
Protein Sci, 19,
1180-1190.
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Y.R.Chemla
(2010).
Revealing the base pair stepping dynamics of nucleic acid motor proteins with optical traps.
|
| |
Phys Chem Chem Phys, 12,
3080-3095.
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|
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A.Chatterjee,
M.A.Johnson,
P.Serrano,
B.Pedrini,
J.S.Joseph,
B.W.Neuman,
K.Saikatendu,
M.J.Buchmeier,
P.Kuhn,
and
K.Wüthrich
(2009).
Nuclear magnetic resonance structure shows that the severe acute respiratory syndrome coronavirus-unique domain contains a macrodomain fold.
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| |
J Virol, 83,
1823-1836.
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PDB codes:
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C.A.Belon,
and
D.N.Frick
(2009).
Helicase inhibitors as specifically targeted antiviral therapy for hepatitis C.
|
| |
Future Virol, 4,
277-293.
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C.A.Belon,
and
D.N.Frick
(2009).
Fuel specificity of the hepatitis C virus NS3 helicase.
|
| |
J Mol Biol, 388,
851-864.
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D.Klostermeier,
and
M.G.Rudolph
(2009).
A novel dimerization motif in the C-terminal domain of the Thermus thermophilus DEAD box helicase Hera confers substantial flexibility.
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| |
Nucleic Acids Res, 37,
421-430.
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PDB codes:
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H.Tang,
and
H.Grisé
(2009).
Cellular and molecular biology of HCV infection and hepatitis.
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| |
Clin Sci (Lond), 117,
49-65.
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S.H.Ling,
Z.Cheng,
and
H.Song
(2009).
Structural aspects of RNA helicases in eukaryotic mRNA decay.
|
| |
Biosci Rep, 29,
339-349.
|
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|
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T.A.Jennings,
S.G.Mackintosh,
M.K.Harrison,
D.Sikora,
B.Sikora,
B.Dave,
A.J.Tackett,
C.E.Cameron,
and
K.D.Raney
(2009).
NS3 helicase from the hepatitis C virus can function as a monomer or oligomer depending on enzyme and substrate concentrations.
|
| |
J Biol Chem, 284,
4806-4814.
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V.Serebrov,
R.K.Beran,
and
A.M.Pyle
(2009).
Establishing a mechanistic basis for the large kinetic steps of the NS3 helicase.
|
| |
J Biol Chem, 284,
2512-2521.
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A.Garai,
D.Chowdhury,
and
M.D.Betterton
(2008).
Two-state model for helicase translocation and unwinding of nucleic acids.
|
| |
Phys Rev E Stat Nonlin Soft Matter Phys, 77,
061910.
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|
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A.Kumar,
W.S.Joo,
G.Meinke,
S.Moine,
E.N.Naumova,
and
P.A.Bullock
(2008).
Evidence for a structural relationship between BRCT domains and the helicase domains of the replication initiators encoded by the Polyomaviridae and Papillomaviridae families of DNA tumor viruses.
|
| |
J Virol, 82,
8849-8862.
|
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|
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B.Sikora,
Y.Chen,
C.F.Lichti,
M.K.Harrison,
T.A.Jennings,
Y.Tang,
A.J.Tackett,
J.B.Jordan,
J.Sakon,
C.E.Cameron,
and
K.D.Raney
(2008).
Hepatitis C virus NS3 helicase forms oligomeric structures that exhibit optimal DNA unwinding activity in vitro.
|
| |
J Biol Chem, 283,
11516-11525.
|
|
|
|
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|
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L.M.Elles,
and
O.C.Uhlenbeck
(2008).
Mutation of the arginine finger in the active site of Escherichia coli DbpA abolishes ATPase and helicase activity and confers a dominant slow growth phenotype.
|
| |
Nucleic Acids Res, 36,
41-50.
|
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|
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M.Z.Lin,
J.S.Glenn,
and
R.Y.Tsien
(2008).
A drug-controllable tag for visualizing newly synthesized proteins in cells and whole animals.
|
| |
Proc Natl Acad Sci U S A, 105,
7744-7749.
|
|
|
|
|
|
|
R.Perera,
and
R.J.Kuhn
(2008).
Structural proteomics of dengue virus.
|
| |
Curr Opin Microbiol, 11,
369-377.
|
|
|
|
|
|
|
S.Salloum,
C.Oniangue-Ndza,
C.Neumann-Haefelin,
L.Hudson,
S.Giugliano,
M.aus dem Siepen,
J.Nattermann,
U.Spengler,
G.M.Lauer,
M.Wiese,
P.Klenerman,
H.Bright,
N.Scherbaum,
R.Thimme,
M.Roggendorf,
S.Viazov,
and
J.Timm
(2008).
Escape from HLA-B*08-restricted CD8 T cells by hepatitis C virus is associated with fitness costs.
|
| |
J Virol, 82,
11803-11812.
|
|
|
|
|
|
|
S.Wang,
M.T.Overgaard,
Y.Hu,
and
D.B.McKay
(2008).
The Bacillus subtilis RNA helicase YxiN is distended in solution.
|
| |
Biophys J, 94,
L01-L03.
|
|
|
|
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|
|
T.M.Lohman,
E.J.Tomko,
and
C.G.Wu
(2008).
Non-hexameric DNA helicases and translocases: mechanisms and regulation.
|
| |
Nat Rev Mol Cell Biol, 9,
391-401.
|
|
|
|
|
|
|
A.R.Karow,
B.Theissen,
and
D.Klostermeier
(2007).
Authentic interdomain communication in an RNA helicase reconstituted by expressed protein ligation of two helicase domains.
|
| |
FEBS J, 274,
463-473.
|
|
|
|
|
|
|
D.N.Frick,
S.Banik,
and
R.S.Rypma
(2007).
Role of divalent metal cations in ATP hydrolysis catalyzed by the hepatitis C virus NS3 helicase: magnesium provides a bridge for ATP to fuel unwinding.
|
| |
J Mol Biol, 365,
1017-1032.
|
|
|
|
|
|
|
E.Jankowsky,
and
M.E.Fairman
(2007).
RNA helicases--one fold for many functions.
|
| |
Curr Opin Struct Biol, 17,
316-324.
|
|
|
|
|
|
|
G.Wen,
C.Chen,
X.Luo,
Y.Wang,
C.Zhang,
and
Z.Pan
(2007).
Identification and characterization of the NTPase activity of classical swine fever virus (CSFV) nonstructural protein 3 (NS3) expressed in bacteria.
|
| |
Arch Virol, 152,
1565-1573.
|
|
|
|
|
|
|
J.M.Pawlotsky,
S.Chevaliez,
and
J.G.McHutchison
(2007).
The hepatitis C virus life cycle as a target for new antiviral therapies.
|
| |
Gastroenterology, 132,
1979-1998.
|
|
|
|
|
|
|
K.L.Maxwell,
and
L.Frappier
(2007).
Viral proteomics.
|
| |
Microbiol Mol Biol Rev, 71,
398-411.
|
|
|
|
|
|
|
R.B.Guo,
P.Rigolet,
H.Ren,
B.Zhang,
X.D.Zhang,
S.X.Dou,
P.Y.Wang,
M.Amor-Gueret,
and
X.G.Xi
(2007).
Structural and functional analyses of disease-causing missense mutations in Bloom syndrome protein.
|
| |
Nucleic Acids Res, 35,
6297-6310.
|
|
|
|
|
|
|
R.K.Beran,
V.Serebrov,
and
A.M.Pyle
(2007).
The serine protease domain of hepatitis C viral NS3 activates RNA helicase activity by promoting the binding of RNA substrate.
|
| |
J Biol Chem, 282,
34913-34920.
|
|
|
|
|
|
|
R.K.Gaur
(2007).
Helicase: mystery of progression.
|
| |
Mol Biol Rep, 34,
161-164.
|
|
|
|
|
|
|
T.L.Tellinghuisen,
M.J.Evans,
T.von Hahn,
S.You,
and
C.M.Rice
(2007).
Studying hepatitis C virus: making the best of a bad virus.
|
| |
J Virol, 81,
8853-8867.
|
|
|
|
|
|
|
W.Zheng,
J.C.Liao,
B.R.Brooks,
and
S.Doniach
(2007).
Toward the mechanism of dynamical couplings and translocation in hepatitis C virus NS3 helicase using elastic network model.
|
| |
Proteins, 67,
886-896.
|
|
|
|
|
|
|
A.M.Lam,
and
D.N.Frick
(2006).
Hepatitis C virus subgenomic replicon requires an active NS3 RNA helicase.
|
| |
J Virol, 80,
404-411.
|
|
|
|
|
|
|
C.S.Weirich,
J.P.Erzberger,
J.S.Flick,
J.M.Berger,
J.Thorner,
and
K.Weis
(2006).
Activation of the DExD/H-box protein Dbp5 by the nuclear-pore protein Gle1 and its coactivator InsP6 is required for mRNA export.
|
| |
Nat Cell Biol, 8,
668-676.
|
|
|
|
|
|
|
D.N.Frick
(2006).
Step-by-step progress toward understanding the hepatitis C virus RNA helicase.
|
| |
Hepatology, 43,
1392-1395.
|
|
|
|
|
|
|
H.Uhlmann-Schiffler,
C.Jalal,
and
H.Stahl
(2006).
Ddx42p--a human DEAD box protein with RNA chaperone activities.
|
| |
Nucleic Acids Res, 34,
10-22.
|
|
|
|
|
|
|
J.R.Mesters,
J.Tan,
and
R.Hilgenfeld
(2006).
Viral enzymes.
|
| |
Curr Opin Struct Biol, 16,
776-786.
|
|
|
|
|
|
|
M.Barhoumi,
N.K.Tanner,
J.Banroques,
P.Linder,
and
I.Guizani
(2006).
Leishmania infantum LeIF protein is an ATP-dependent RNA helicase and an eIF4A-like factor that inhibits translation in yeast.
|
| |
FEBS J, 273,
5086-5100.
|
|
|
|
|
|
|
M.P.Killoran,
and
J.L.Keck
(2006).
Sit down, relax and unwind: structural insights into RecQ helicase mechanisms.
|
| |
Nucleic Acids Res, 34,
4098-4105.
|
|
|
|
|
|
|
N.Appel,
T.Schaller,
F.Penin,
and
R.Bartenschlager
(2006).
From structure to function: new insights into hepatitis C virus RNA replication.
|
| |
J Biol Chem, 281,
9833-9836.
|
|
|
|
|
|
|
S.Dumont,
W.Cheng,
V.Serebrov,
R.K.Beran,
I.Tinoco,
A.M.Pyle,
and
C.Bustamante
(2006).
RNA translocation and unwinding mechanism of HCV NS3 helicase and its coordination by ATP.
|
| |
Nature, 439,
105-108.
|
|
|
|
|
|
|
T.Shibuya,
T.Ã.˜.Tange,
M.E.Stroupe,
and
M.J.Moore
(2006).
Mutational analysis of human eIF4AIII identifies regions necessary for exon junction complex formation and nonsense-mediated mRNA decay.
|
| |
RNA, 12,
360-374.
|
|
|
|
|
|
|
A.D.Kwong,
B.G.Rao,
and
K.T.Jeang
(2005).
Viral and cellular RNA helicases as antiviral targets.
|
| |
Nat Rev Drug Discov, 4,
845-853.
|
|
|
|
|
|
|
C.L.Smith,
and
C.L.Peterson
(2005).
A conserved Swi2/Snf2 ATPase motif couples ATP hydrolysis to chromatin remodeling.
|
| |
Mol Cell Biol, 25,
5880-5892.
|
|
|
|
|
|
|
C.Zhang,
Z.Cai,
Y.C.Kim,
R.Kumar,
F.Yuan,
P.Y.Shi,
C.Kao,
and
G.Luo
(2005).
Stimulation of hepatitis C virus (HCV) nonstructural protein 3 (NS3) helicase activity by the NS3 protease domain and by HCV RNA-dependent RNA polymerase.
|
| |
J Virol, 79,
8687-8697.
|
|
|
|
|
|
|
J.Quer,
J.I.Esteban,
J.Cos,
S.Sauleda,
L.Ocaña,
M.Martell,
T.Otero,
M.Cubero,
E.Palou,
P.Murillo,
R.Esteban,
and
J.Guàrdia
(2005).
Effect of bottlenecking on evolution of the nonstructural protein 3 gene of hepatitis C virus during sexually transmitted acute resolving infection.
|
| |
J Virol, 79,
15131-15141.
|
|
|
|
|
|
|
J.Wu,
A.K.Bera,
R.J.Kuhn,
and
J.L.Smith
(2005).
Structure of the Flavivirus helicase: implications for catalytic activity, protein interactions, and proteolytic processing.
|
| |
J Virol, 79,
10268-10277.
|
|
|
PDB codes:
|
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|
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|
|
S.Rocak,
B.Emery,
N.K.Tanner,
and
P.Linder
(2005).
Characterization of the ATPase and unwinding activities of the yeast DEAD-box protein Has1p and the analysis of the roles of the conserved motifs.
|
| |
Nucleic Acids Res, 33,
999.
|
|
|
|
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|
|
T.Xu,
A.Sampath,
A.Chao,
D.Wen,
M.Nanao,
P.Chene,
S.G.Vasudevan,
and
J.Lescar
(2005).
Structure of the Dengue virus helicase/nucleoside triphosphatase catalytic domain at a resolution of 2.4 A.
|
| |
J Virol, 79,
10278-10288.
|
|
|
PDB codes:
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|
A.M.Lam,
R.S.Rypma,
and
D.N.Frick
(2004).
Enhanced nucleic acid binding to ATP-bound hepatitis C virus NS3 helicase at low pH activates RNA unwinding.
|
| |
Nucleic Acids Res, 32,
4060-4070.
|
|
|
|
|
|
|
B.Hwang,
J.S.Cho,
H.J.Yeo,
J.H.Kim,
K.M.Chung,
K.Han,
S.K.Jang,
and
S.W.Lee
(2004).
Isolation of specific and high-affinity RNA aptamers against NS3 helicase domain of hepatitis C virus.
|
| |
RNA, 10,
1277-1290.
|
|
|
|
|
|
|
D.N.Frick,
R.S.Rypma,
A.M.Lam,
and
B.Gu
(2004).
The nonstructural protein 3 protease/helicase requires an intact protease domain to unwind duplex RNA efficiently.
|
| |
J Biol Chem, 279,
1269-1280.
|
|
|
|
|
|
|
D.N.Frick,
R.S.Rypma,
A.M.Lam,
and
C.M.Frenz
(2004).
Electrostatic analysis of the hepatitis C virus NS3 helicase reveals both active and allosteric site locations.
|
| |
Nucleic Acids Res, 32,
5519-5528.
|
|
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|
|
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|
PDB codes:
|
|
|
|
|
|
|
|
J.Scheller,
A.Schürer,
C.Rudolph,
S.Hettwer,
and
W.Kramer
(2000).
MPH1, a yeast gene encoding a DEAH protein, plays a role in protection of the genome from spontaneous and chemically induced damage.
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Genetics, 155,
1069-1081.
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K.Fukuda,
D.Vishnuvardhan,
S.Sekiya,
J.Hwang,
N.Kakiuchi,
K.Taira,
K.Shimotohno,
P.K.Kumar,
and
S.Nishikawa
(2000).
Isolation and characterization of RNA aptamers specific for the hepatitis C virus nonstructural protein 3 protease.
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| |
Eur J Biochem, 267,
3685-3694.
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M.Hicham Alaoui-Ismaili,
C.Gervais,
S.Brunette,
G.Gouin,
M.Hamel,
R.F.Rando,
and
J.Bedard
(2000).
A novel high throughput screening assay for HCV NS3 helicase activity.
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| |
Antiviral Res, 46,
181-193.
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N.Butkiewicz,
N.Yao,
W.Zhong,
J.Wright-Minogue,
P.Ingravallo,
R.Zhang,
J.Durkin,
D.N.Standring,
B.M.Baroudy,
D.V.Sangar,
S.M.Lemon,
J.Y.Lau,
and
Z.Hong
(2000).
Virus-specific cofactor requirement and chimeric hepatitis C virus/GB virus B nonstructural protein 3.
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| |
J Virol, 74,
4291-4301.
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|
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P.Askjaer,
R.Rosendahl,
and
J.Kjems
(2000).
Nuclear export of the DEAD box An3 protein by CRM1 is coupled to An3 helicase activity.
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| |
J Biol Chem, 275,
11561-11568.
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|
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P.Borowski,
K.Resch,
H.Schmitz,
and
M.Heiland
(2000).
A synthetic peptide derived from the non-structural protein 3 of hepatitis C virus serves as a specific substrate for PKC.
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| |
Biol Chem, 381,
19-27.
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P.Leyssen,
E.De Clercq,
and
J.Neyts
(2000).
Perspectives for the treatment of infections with Flaviviridae.
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Clin Microbiol Rev, 13,
67.
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P.McGlynn,
A.A.Mahdi,
and
R.G.Lloyd
(2000).
Characterisation of the catalytically active form of RecG helicase.
|
| |
Nucleic Acids Res, 28,
2324-2332.
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|
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|
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P.Soultanas,
and
D.B.Wigley
(2000).
DNA helicases: 'inching forward'.
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| |
Curr Opin Struct Biol, 10,
124-128.
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S.C.Chang,
J.C.Cheng,
Y.H.Kou,
C.H.Kao,
C.H.Chiu,
H.Y.Wu,
and
M.F.Chang
(2000).
Roles of the AX(4)GKS and arginine-rich motifs of hepatitis C virus RNA helicase in ATP- and viral RNA-binding activity.
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| |
J Virol, 74,
9732-9737.
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S.S.Patel,
and
K.M.Picha
(2000).
Structure and function of hexameric helicases.
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| |
Annu Rev Biochem, 69,
651-697.
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T.Hesson,
A.Mannarino,
and
M.Cable
(2000).
Probing the relationship between RNA-stimulated ATPase and helicase activities of HCV NS3 using 2'-O-methyl RNA substrates.
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| |
Biochemistry, 39,
2619-2625.
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|
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A.Martins,
C.H.Gross,
and
S.Shuman
(1999).
Mutational analysis of vaccinia virus nucleoside triphosphate phosphohydrolase I, a DNA-dependent ATPase of the DExH box family.
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| |
J Virol, 73,
1302-1308.
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A.Urbani,
G.Biasiol,
M.Brunetti,
C.Volpari,
S.Di Marco,
M.Sollazzo,
S.Orrú,
F.D.Piaz,
A.Casbarra,
P.Pucci,
C.Nardi,
P.Gallinari,
R.De Francesco,
and
C.Steinkühler
(1999).
Multiple determinants influence complex formation of the hepatitis C virus NS3 protease domain with its NS4A cofactor peptide.
|
| |
Biochemistry, 38,
5206-5215.
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|
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A.Y.Howe,
R.Chase,
S.S.Taremi,
C.Risano,
B.Beyer,
B.Malcolm,
and
J.Y.Lau
(1999).
A novel recombinant single-chain hepatitis C virus NS3-NS4A protein with improved helicase activity.
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| |
Protein Sci, 8,
1332-1341.
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|
|
C.Lin,
and
J.L.Kim
(1999).
Structure-based mutagenesis study of hepatitis C virus NS3 helicase.
|
| |
J Virol, 73,
8798-8807.
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|
|
C.Schmitt,
C.von Kobbe,
A.Bachi,
N.Panté,
J.P.Rodrigues,
C.Boscheron,
G.Rigaut,
M.Wilm,
B.Séraphin,
M.Carmo-Fonseca,
and
E.Izaurralde
(1999).
Dbp5, a DEAD-box protein required for mRNA export, is recruited to the cytoplasmic fibrils of nuclear pore complex via a conserved interaction with CAN/Nup159p.
|
| |
EMBO J, 18,
4332-4347.
|
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|
C.W.Grassmann,
O.Isken,
and
S.E.Behrens
(1999).
Assignment of the multifunctional NS3 protein of bovine viral diarrhea virus during RNA replication: an in vivo and in vitro study.
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| |
J Virol, 73,
9196-9205.
|
|
|
|
|
|
|
E.Ferrari,
J.Wright-Minogue,
J.W.Fang,
B.M.Baroudy,
J.Y.Lau,
and
Z.Hong
(1999).
Characterization of soluble hepatitis C virus RNA-dependent RNA polymerase expressed in Escherichia coli.
|
| |
J Virol, 73,
1649-1654.
|
|
|
|
|
|
|
E.R.Johnson,
and
D.B.McKay
(1999).
Crystallographic structure of the amino terminal domain of yeast initiation factor 4A, a representative DEAD-box RNA helicase.
|
| |
RNA, 5,
1526-1534.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
H.Ago,
T.Adachi,
A.Yoshida,
M.Yamamoto,
N.Habuka,
K.Yatsunami,
and
M.Miyano
(1999).
Crystal structure of the RNA-dependent RNA polymerase of hepatitis C virus.
|
| |
Structure, 7,
1417-1426.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
H.Li,
S.Clum,
S.You,
K.E.Ebner,
and
R.Padmanabhan
(1999).
The serine protease and RNA-stimulated nucleoside triphosphatase and RNA helicase functional domains of dengue virus type 2 NS3 converge within a region of 20 amino acids.
|
| |
J Virol, 73,
3108-3116.
|
|
|
|
|
|
|
J.Benz,
H.Trachsel,
and
U.Baumann
(1999).
Crystal structure of the ATPase domain of translation initiation factor 4A from Saccharomyces cerevisiae--the prototype of the DEAD box protein family.
|
| |
Structure, 7,
671-679.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
J.Sgouros,
P.H.Gaillard,
and
R.D.Wood
(1999).
A relationship betweena DNA-repair/recombination nuclease family and archaeal helicases.
|
| |
Trends Biochem Sci, 24,
95-97.
|
|
|
|
|
|
|
J.Weigelt,
S.E.Brown,
C.S.Miles,
N.E.Dixon,
and
G.Otting
(1999).
NMR structure of the N-terminal domain of E. coli DnaB helicase: implications for structure rearrangements in the helicase hexamer.
|
| |
Structure, 7,
681-690.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
J.de la Cruz,
D.Kressler,
and
P.Linder
(1999).
Unwinding RNA in Saccharomyces cerevisiae: DEAD-box proteins and related families.
|
| |
Trends Biochem Sci, 24,
192-198.
|
|
|
|
|
|
|
L.E.Mechanic,
M.C.Hall,
and
S.W.Matson
(1999).
Escherichia coli DNA helicase II is active as a monomer.
|
| |
J Biol Chem, 274,
12488-12498.
|
|
|
|
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|
|
M.A.Walker
(1999).
Hepatitis C virus: an overview of current approaches and progress.
|
| |
Drug Discov Today, 4,
518-529.
|
|
|
|
|
|
|
M.K.Levin,
and
S.S.Patel
(1999).
The helicase from hepatitis C virus is active as an oligomer.
|
| |
J Biol Chem, 274,
31839-31846.
|
|
|
|
|
|
|
M.Machius,
L.Henry,
M.Palnitkar,
and
J.Deisenhofer
(1999).
Crystal structure of the DNA nucleotide excision repair enzyme UvrB from Thermus thermophilus.
|
| |
Proc Natl Acad Sci U S A, 96,
11717-11722.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
M.R.Sawaya,
S.Guo,
S.Tabor,
C.C.Richardson,
and
T.Ellenberger
(1999).
Crystal structure of the helicase domain from the replicative helicase-primase of bacteriophage T7.
|
| |
Cell, 99,
167-177.
|
|
|
PDB codes:
|
|
|
|
|
|
|
|
N.Mamiya,
and
H.J.Worman
(1999).
Hepatitis C virus core protein binds to a DEAD box RNA helicase.
|
| |
J Biol Chem, 274,
15751-15756.
|
|
|
|
|
|
|
N.Yao,
P.Reichert,
S.S.Taremi,
W.W.Prosise,
and
P.C.Weber
(1999).
Molecular views of viral polyprotein processing revealed by the crystal structure of the hepatitis C virus bifunctional protease-helicase.
|
| |
Structure, 7,
1353-1363.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
P.Borowski,
J.Schulze zur Wiesch,
K.Resch,
H.Feucht,
R.Laufs,
and
H.Schmitz
(1999).
Protein kinase C recognizes the protein kinase A-binding motif of nonstructural protein 3 of hepatitis C virus.
|
| |
J Biol Chem, 274,
30722-30728.
|
|
|
|
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|
|
P.Borowski,
R.Kuehl,
O.Mueller,
L.H.Hwang,
J.Schulze Zur Wiesch,
and
H.Schmitz
(1999).
Biochemical properties of a minimal functional domain with ATP-binding activity of the NTPase/helicase of hepatitis C virus.
|
| |
Eur J Biochem, 266,
715-723.
|
|
|
|
|
|
|
P.Gallinari,
C.Paolini,
D.Brennan,
C.Nardi,
C.Steinkühler,
and
R.De Francesco
(1999).
Modulation of hepatitis C virus NS3 protease and helicase activities through the interaction with NS4A.
|
| |
Biochemistry, 38,
5620-5632.
|
|
|
|
|
|
|
S.S.Velankar,
P.Soultanas,
M.S.Dillingham,
H.S.Subramanya,
and
D.B.Wigley
(1999).
Crystal structures of complexes of PcrA DNA helicase with a DNA substrate indicate an inchworm mechanism.
|
| |
Cell, 97,
75-84.
|
|
|
PDB codes:
|
|
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|
|
|
|
|
V.Soriano,
R.Rodríguez-Rosado,
and
J.García-Samaniego
(1999).
Management of chronic hepatitis C in HIV-infected patients.
|
| |
AIDS, 13,
539-546.
|
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|
|
|
Y.Gwack,
H.Yoo,
I.Song,
J.Choe,
and
J.H.Han
(1999).
RNA-Stimulated ATPase and RNA helicase activities and RNA binding domain of hepatitis G virus nonstructural protein 3.
|
| |
J Virol, 73,
2909-2915.
|
|
|
|
|
|
|
C.H.Gross,
and
S.Shuman
(1998).
The nucleoside triphosphatase and helicase activities of vaccinia virus NPH-II are essential for virus replication.
|
| |
J Virol, 72,
4729-4736.
|
|
|
|
|
|
|
C.San Martin,
M.Radermacher,
B.Wolpensinger,
A.Engel,
C.S.Miles,
N.E.Dixon,
and
J.M.Carazo
(1998).
Three-dimensional reconstructions from cryoelectron microscopy images reveal an intimate complex between helicase DnaB and its loading partner DnaC.
|
| |
Structure, 6,
501-509.
|
|
|
|
|
|
|
C.Steinkühler,
G.Biasiol,
M.Brunetti,
A.Urbani,
U.Koch,
R.Cortese,
A.Pessi,
and
R.De Francesco
(1998).
Product inhibition of the hepatitis C virus NS3 protease.
|
| |
Biochemistry, 37,
8899-8905.
|
|
|
|
|
|
|
D.J.Porter
(1998).
Inhibition of the hepatitis C virus helicase-associated ATPase activity by the combination of ADP, NaF, MgCl2, and poly(rU). Two ADP binding sites on the enzyme-nucleic acid complex.
|
| |
J Biol Chem, 273,
7390-7396.
|
|
|
|
|
|
|
D.J.Porter
(1998).
A kinetic analysis of the oligonucleotide-modulated ATPase activity of the helicase domain of the NS3 protein from hepatitis C virus. The first cycle of interaction of ATP with the enzyme is unique.
|
| |
J Biol Chem, 273,
14247-14253.
|
|
|
|
|
|
|
D.J.Porter,
S.A.Short,
M.H.Hanlon,
F.Preugschat,
J.E.Wilson,
D.H.Willard,
and
T.G.Consler
(1998).
Product release is the major contributor to kcat for the hepatitis C virus helicase-catalyzed strand separation of short duplex DNA.
|
| |
J Biol Chem, 273,
18906-18914.
|
|
|
|
|
|
|
H.R.Hotz,
and
B.Schwer
(1998).
Mutational analysis of the yeast DEAH-box splicing factor Prp16.
|
| |
Genetics, 149,
807-815.
|
|
|
|
|
|
|
H.S.Cho,
N.C.Ha,
L.W.Kang,
K.M.Chung,
S.H.Back,
S.K.Jang,
and
B.H.Oh
(1998).
Crystal structure of RNA helicase from genotype 1b hepatitis C virus. A feasible mechanism of unwinding duplex RNA.
|
| |
J Biol Chem, 273,
15045-15052.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
J.C.Carrington,
P.E.Jensen,
and
M.C.Schaad
(1998).
Genetic evidence for an essential role for potyvirus CI protein in cell-to-cell movement.
|
| |
Plant J, 14,
393-400.
|
|
|
|
|
|
|
J.L.Kim,
K.A.Morgenstern,
J.P.Griffith,
M.D.Dwyer,
J.A.Thomson,
M.A.Murcko,
C.Lin,
and
P.R.Caron
(1998).
Hepatitis C virus NS3 RNA helicase domain with a bound oligonucleotide: the crystal structure provides insights into the mode of unwinding.
|
| |
Structure, 6,
89.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
J.P.Staley,
and
C.Guthrie
(1998).
Mechanical devices of the spliceosome: motors, clocks, springs, and things.
|
| |
Cell, 92,
315-326.
|
|
|
|
|
|
|
L.E.Bird,
H.S.Subramanya,
and
D.B.Wigley
(1998).
Helicases: a unifying structural theme?
|
| |
Curr Opin Struct Biol, 8,
14-18.
|
|
|
|
|
|
|
L.E.Bird,
J.A.Brannigan,
H.S.Subramanya,
and
D.B.Wigley
(1998).
Characterisation of Bacillus stearothermophilus PcrA helicase: evidence against an active rolling mechanism.
|
| |
Nucleic Acids Res, 26,
2686-2693.
|
|
|
|
|
|
|
P.Gallinari,
D.Brennan,
C.Nardi,
M.Brunetti,
L.Tomei,
C.Steinkühler,
and
R.De Francesco
(1998).
Multiple enzymatic activities associated with recombinant NS3 protein of hepatitis C virus.
|
| |
J Virol, 72,
6758-6769.
|
|
|
|
|
|
|
P.J.Masterson,
M.A.Stanley,
A.P.Lewis,
and
M.A.Romanos
(1998).
A C-terminal helicase domain of the human papillomavirus E1 protein binds E2 and the DNA polymerase alpha-primase p68 subunit.
|
| |
J Virol, 72,
7407-7419.
|
|
|
|
|
|
|
S.Korolev,
N.Yao,
T.M.Lohman,
P.C.Weber,
and
G.Waksman
(1998).
Comparisons between the structures of HCV and Rep helicases reveal structural similarities between SF1 and SF2 super-families of helicases.
|
| |
Protein Sci, 7,
605-610.
|
|
|
|
|
|
|
Y.Wang,
and
C.Guthrie
(1998).
PRP16, a DEAH-box RNA helicase, is recruited to the spliceosome primarily via its nonconserved N-terminal domain.
|
| |
RNA, 4,
1216-1229.
|
|
|
|
|
|
|
Z.Wu,
N.Yao,
H.V.Le,
and
P.C.Weber
(1998).
Mechanism of autoproteolysis at the NS2-NS3 junction of the hepatitis C virus polyprotein.
|
| |
Trends Biochem Sci, 23,
92-94.
|
|
|
|
|
|
|
A.Fernández,
H.S.Guo,
P.Sáenz,
L.Simón-Buela,
M.Gómez de Cedrón,
and
J.A.García
(1997).
The motif V of plum pox potyvirus CI RNA helicase is involved in NTP hydrolysis and is essential for virus RNA replication.
|
| |
Nucleic Acids Res, 25,
4474-4480.
|
|
|
|
|
|
|
B.Guenther,
R.Onrust,
A.Sali,
M.O'Donnell,
and
J.Kuriyan
(1997).
Crystal structure of the delta' subunit of the clamp-loader complex of E. coli DNA polymerase III.
|
| |
Cell, 91,
335-345.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
D.W.Kim,
J.Kim,
Y.Gwack,
J.H.Han,
and
J.Choe
(1997).
Mutational analysis of the hepatitis C virus RNA helicase.
|
| |
J Virol, 71,
9400-9409.
|
|
|
|
|
|
|
K.J.Marians
(1997).
Helicase structures: a new twist on DNA unwinding.
|
| |
Structure, 5,
1129-1134.
|
|
|
|
|
|
|
P.A.Bullock
(1997).
The initiation of simian virus 40 DNA replication in vitro.
|
| |
Crit Rev Biochem Mol Biol, 32,
503-568.
|
|
|
|
|
|
The most recent references are shown first.
Citation data come partly from CiteXplore and partly
from an automated harvesting procedure. Note that this is likely to be
only a partial list as not all journals are covered by
either method. However, we are continually building up the citation data
so more and more references will be included with time.
Where a reference describes a PDB structure, the PDB
codes are
shown on the right.
|
|
Links
