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PDBsum entry 1n1h
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Transferase/RNA
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PDB id
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1n1h
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Enzyme class:
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E.C.2.7.7.48
- RNA-directed Rna polymerase.
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Reaction:
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RNA(n) + a ribonucleoside 5'-triphosphate = RNA(n+1) + diphosphate
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RNA(n)
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+
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ribonucleoside 5'-triphosphate
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=
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RNA(n+1)
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+
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diphosphate
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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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Cell
111:733-745
(2002)
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PubMed id:
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RNA synthesis in a cage--structural studies of reovirus polymerase lambda3.
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Y.Tao,
D.L.Farsetta,
M.L.Nibert,
S.C.Harrison.
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ABSTRACT
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The reovirus polymerase and those of other dsRNA viruses function within the
confines of a protein capsid to transcribe the tightly packed dsRNA genome
segments. The crystal structure of the reovirus polymerase, lambda3, determined
at 2.5 A resolution, shows a fingers-palm-thumb core, similar to those of other
viral polymerases, surrounded by major N- and C-terminal elaborations, which
create a cage-like structure, with four channels leading to the catalytic site.
This "caged" polymerase has allowed us to visualize the results of
several rounds of RNA polymerization directly in the crystals. A 5' cap binding
site on the surface of lambda3 suggests a template retention mechanism by which
attachment of the 5' end of the plus-sense strand facilitates insertion of the
3' end of the minus-sense strand into the template channel.
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Selected figure(s)
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Figure 1.
Figure 1. Functions and Primary Structure of the Reovirus Polymerase, #3
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Figure 2.
Figure 2. Crystal Structure of #3
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The above figures are
reprinted
by permission from Cell Press:
Cell
(2002,
111,
733-745)
copyright 2002.
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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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S.D.Trask,
S.M.McDonald,
and
J.T.Patton
(2012).
Structural insights into the coupling of virion assembly and rotavirus replication.
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Nat Rev Microbiol,
10,
165-177.
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K.Ruszczyńska-Bartnik,
M.Maciejczyk,
and
R.Stolarski
(2011).
Dynamical insight into Caenorhabditis elegans eIF4E recognition specificity for mono-and trimethylated structures of mRNA 5' cap.
|
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J Mol Model,
17,
727-737.
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B.McClain,
E.Settembre,
B.R.Temple,
A.R.Bellamy,
and
S.C.Harrison
(2010).
X-ray crystal structure of the rotavirus inner capsid particle at 3.8 A resolution.
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J Mol Biol,
397,
587-599.
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PDB code:
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K.Das,
J.M.Aramini,
L.C.Ma,
R.M.Krug,
and
E.Arnold
(2010).
Structures of influenza A proteins and insights into antiviral drug targets.
|
| |
Nat Struct Mol Biol,
17,
530-538.
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|
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L.Cheng,
J.Zhu,
W.H.Hui,
X.Zhang,
B.Honig,
Q.Fang,
and
Z.H.Zhou
(2010).
Backbone model of an aquareovirus virion by cryo-electron microscopy and bioinformatics.
|
| |
J Mol Biol,
397,
852-863.
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PDB code:
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P.Gong,
and
O.B.Peersen
(2010).
Structural basis for active site closure by the poliovirus RNA-dependent RNA polymerase.
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Proc Natl Acad Sci U S A,
107,
22505-22510.
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PDB codes:
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P.J.Kranzusch,
A.D.Schenk,
A.A.Rahmeh,
S.R.Radoshitzky,
S.Bavari,
T.Walz,
and
S.P.Whelan
(2010).
Assembly of a functional Machupo virus polymerase complex.
|
| |
Proc Natl Acad Sci U S A,
107,
20069-20074.
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R.T.Kidmose,
N.N.Vasiliev,
A.B.Chetverin,
G.R.Andersen,
and
C.R.Knudsen
(2010).
Structure of the Qbeta replicase, an RNA-dependent RNA polymerase consisting of viral and host proteins.
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Proc Natl Acad Sci U S A,
107,
10884-10889.
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PDB code:
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J.Pan,
L.Dong,
L.Lin,
W.F.Ochoa,
R.S.Sinkovits,
W.M.Havens,
M.L.Nibert,
T.S.Baker,
S.A.Ghabrial,
and
Y.J.Tao
(2009).
Atomic structure reveals the unique capsid organization of a dsRNA virus.
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Proc Natl Acad Sci U S A,
106,
4225-4230.
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PDB codes:
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L.P.Sarin,
M.M.Poranen,
N.M.Lehti,
J.J.Ravantti,
M.R.Koivunen,
A.P.Aalto,
A.A.van Dijk,
D.I.Stuart,
J.M.Grimes,
and
D.H.Bamford
(2009).
Insights into the pre-initiation events of bacteriophage phi 6 RNA-dependent RNA polymerase: towards the assembly of a productive binary complex.
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Nucleic Acids Res,
37,
1182-1192.
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L.Zhang,
M.A.Agosto,
T.Ivanovic,
D.S.King,
M.L.Nibert,
and
S.C.Harrison
(2009).
Requirements for the formation of membrane pores by the reovirus myristoylated micro1N peptide.
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J Virol,
83,
7004-7014.
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P.Simister,
M.Schmitt,
M.Geitmann,
O.Wicht,
U.H.Danielson,
R.Klein,
S.Bressanelli,
and
V.Lohmann
(2009).
Structural and functional analysis of hepatitis C virus strain JFH1 polymerase.
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J Virol,
83,
11926-11939.
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PDB code:
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S.M.McDonald,
D.Aguayo,
F.D.Gonzalez-Nilo,
and
J.T.Patton
(2009).
Shared and group-specific features of the rotavirus RNA polymerase reveal potential determinants of gene reassortment restriction.
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J Virol,
83,
6135-6148.
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T.Naito,
A.Kawaguchi,
and
K.Nagata
(2009).
[Function of influenza virus RNA polymerase based on structure].
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Uirusu,
59,
1.
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A.Nikonov,
E.Juronen,
and
M.Ustav
(2008).
Functional characterization of fingers subdomain-specific monoclonal antibodies inhibiting the hepatitis C virus RNA-dependent RNA polymerase.
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J Biol Chem,
283,
24089-24102.
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A.Shatkin,
K.Das,
and
E.Arnold
(2008).
3D jigsaw puzzle in rotavirus assembly.
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Structure,
16,
1601-1602.
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D.F.Zamyatkin,
F.Parra,
J.M.Alonso,
D.A.Harki,
B.R.Peterson,
P.Grochulski,
and
K.K.Ng
(2008).
Structural insights into mechanisms of catalysis and inhibition in Norwalk virus polymerase.
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J Biol Chem,
283,
7705-7712.
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PDB codes:
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I.I.Mendez,
S.G.Weiner,
Y.M.She,
M.Yeager,
and
K.M.Coombs
(2008).
Conformational changes accompany activation of reovirus RNA-dependent RNA transcription.
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J Struct Biol,
162,
277-289.
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K.K.Ng,
J.J.Arnold,
and
C.E.Cameron
(2008).
Structure-function relationships among RNA-dependent RNA polymerases.
|
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Curr Top Microbiol Immunol,
320,
137-156.
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M.M.Poranen,
P.S.Salgado,
M.R.Koivunen,
S.Wright,
D.H.Bamford,
D.I.Stuart,
and
J.M.Grimes
(2008).
Structural explanation for the role of Mn2+ in the activity of phi6 RNA-dependent RNA polymerase.
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Nucleic Acids Res,
36,
6633-6644.
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PDB codes:
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P.Roy
(2008).
Functional mapping of bluetongue virus proteins and their interactions with host proteins during virus replication.
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Cell Biochem Biophys,
50,
143-157.
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P.Roy
(2008).
Bluetongue virus: dissection of the polymerase complex.
|
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J Gen Virol,
89,
1789-1804.
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R.Worch,
and
R.Stolarski
(2008).
Stacking efficiency and flexibility analysis of aromatic amino acids in cap-binding proteins.
|
| |
Proteins,
71,
2026-2037.
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W.Xu,
and
K.M.Coombs
(2008).
Avian reovirus L2 genome segment sequences and predicted structure/function of the encoded RNA-dependent RNA polymerase protein.
|
| |
Virol J,
5,
153.
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X.He,
J.Zhou,
M.Bartlam,
R.Zhang,
J.Ma,
Z.Lou,
X.Li,
J.Li,
A.Joachimiak,
Z.Zeng,
R.Ge,
Z.Rao,
and
Y.Liu
(2008).
Crystal structure of the polymerase PA(C)-PB1(N) complex from an avian influenza H5N1 virus.
|
| |
Nature,
454,
1123-1126.
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PDB code:
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X.Lu,
S.M.McDonald,
M.A.Tortorici,
Y.J.Tao,
R.Vasquez-Del Carpio,
M.L.Nibert,
J.T.Patton,
and
S.C.Harrison
(2008).
Mechanism for coordinated RNA packaging and genome replication by rotavirus polymerase VP1.
|
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Structure,
16,
1678-1688.
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PDB codes:
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A.A.Thompson,
R.A.Albertini,
and
O.B.Peersen
(2007).
Stabilization of poliovirus polymerase by NTP binding and fingers-thumb interactions.
|
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J Mol Biol,
366,
1459-1474.
|
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PDB codes:
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C.Ferrer-Orta,
A.Arias,
R.Pérez-Luque,
C.Escarmís,
E.Domingo,
and
N.Verdaguer
(2007).
Sequential structures provide insights into the fidelity of RNA replication.
|
| |
Proc Natl Acad Sci U S A,
104,
9463-9468.
|
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PDB codes:
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D.Garriga,
A.Navarro,
J.Querol-Audí,
F.Abaitua,
J.F.Rodríguez,
and
N.Verdaguer
(2007).
Activation mechanism of a noncanonical RNA-dependent RNA polymerase.
|
| |
Proc Natl Acad Sci U S A,
104,
20540-20545.
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PDB codes:
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H.M.Zhang,
J.Yang,
X.Xin,
J.P.Chen,
and
M.J.Adams
(2007).
Molecular characterization of the largest and smallest genome segments, S1 and S12, of Rice gall dwarf virus.
|
| |
Virus Genes,
35,
815-823.
|
|
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|
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|
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H.Malet,
M.P.Egloff,
B.Selisko,
R.E.Butcher,
P.J.Wright,
M.Roberts,
A.Gruez,
G.Sulzenbacher,
C.Vonrhein,
G.Bricogne,
J.M.Mackenzie,
A.A.Khromykh,
A.D.Davidson,
and
B.Canard
(2007).
Crystal structure of the RNA polymerase domain of the West Nile virus non-structural protein 5.
|
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J Biol Chem,
282,
10678-10689.
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PDB codes:
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J.M.Wehrfritz,
M.Boyce,
S.Mirza,
and
P.Roy
(2007).
Reconstitution of bluetongue virus polymerase activity from isolated domains based on a three-dimensional structural model.
|
| |
Biopolymers,
86,
83-94.
|
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J.Pan,
V.N.Vakharia,
and
Y.J.Tao
(2007).
The structure of a birnavirus polymerase reveals a distinct active site topology.
|
| |
Proc Natl Acad Sci U S A,
104,
7385-7390.
|
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PDB code:
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K.E.Murray,
and
M.L.Nibert
(2007).
Guanidine hydrochloride inhibits mammalian orthoreovirus growth by reversibly blocking the synthesis of double-stranded RNA.
|
| |
J Virol,
81,
4572-4584.
|
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|
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M.Kumar,
H.Jayaram,
R.Vasquez-Del Carpio,
X.Jiang,
Z.F.Taraporewala,
R.H.Jacobson,
J.T.Patton,
and
B.V.Prasad
(2007).
Crystallographic and biochemical analysis of rotavirus NSP2 with nucleotides reveals a nucleoside diphosphate kinase-like activity.
|
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J Virol,
81,
12272-12284.
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PDB codes:
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T.Chen,
and
S.C.Glotzer
(2007).
Simulation studies of a phenomenological model for elongated virus capsid formation.
|
| |
Phys Rev E Stat Nonlin Soft Matter Phys,
75,
051504.
|
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|
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T.L.Yap,
T.Xu,
Y.L.Chen,
H.Malet,
M.P.Egloff,
B.Canard,
S.G.Vasudevan,
and
J.Lescar
(2007).
Crystal structure of the dengue virus RNA-dependent RNA polymerase catalytic domain at 1.85-angstrom resolution.
|
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J Virol,
81,
4753-4765.
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PDB codes:
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J.Ortín,
and
F.Parra
(2006).
Structure and function of RNA replication.
|
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Annu Rev Microbiol,
60,
305-326.
|
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L.Noad,
J.Shou,
K.M.Coombs,
and
R.Duncan
(2006).
Sequences of avian reovirus M1, M2 and M3 genes and predicted structure/function of the encoded mu proteins.
|
| |
Virus Res,
116,
45-57.
|
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M.A.Agosto,
T.Ivanovic,
and
M.L.Nibert
(2006).
Mammalian reovirus, a nonfusogenic nonenveloped virus, forms size-selective pores in a model membrane.
|
| |
Proc Natl Acad Sci U S A,
103,
16496-16501.
|
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M.A.Tortorici,
B.A.Shapiro,
and
J.T.Patton
(2006).
A base-specific recognition signal in the 5' consensus sequence of rotavirus plus-strand RNAs promotes replication of the double-stranded RNA genome segments.
|
| |
RNA,
12,
133-146.
|
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P.S.Salgado,
M.R.Koivunen,
E.V.Makeyev,
D.H.Bamford,
D.I.Stuart,
and
J.M.Grimes
(2006).
The structure of an RNAi polymerase links RNA silencing and transcription.
|
| |
PLoS Biol,
4,
e434.
|
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PDB codes:
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S.G.Tyack,
M.J.Studdert,
and
M.A.Johnson
(2006).
Sequence and function of canine herpesvirus alpha-transinducing factor and its interaction with an immediate early promoter.
|
| |
Virus Genes,
33,
299-307.
|
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|
|
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|
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L.Gardiner,
B.J.Coyle,
W.C.Chan,
and
P.Soultanas
(2005).
Discovery of antagonist peptides against bacterial helicase-primase interaction in B. stearothermophilus by reverse yeast three-hybrid.
|
| |
Chem Biol,
12,
595-604.
|
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P.Clarke,
R.L.Debiasi,
R.Goody,
C.C.Hoyt,
S.Richardson-Burns,
and
K.L.Tyler
(2005).
Mechanisms of reovirus-induced cell death and tissue injury: role of apoptosis and virus-induced perturbation of host-cell signaling and transcription factor activation.
|
| |
Viral Immunol,
18,
89.
|
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|
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S.Di Marco,
C.Volpari,
L.Tomei,
S.Altamura,
S.Harper,
F.Narjes,
U.Koch,
M.Rowley,
R.De Francesco,
G.Migliaccio,
and
A.Carfí
(2005).
Interdomain communication in hepatitis C virus polymerase abolished by small molecule inhibitors bound to a novel allosteric site.
|
| |
J Biol Chem,
280,
29765-29770.
|
|
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PDB codes:
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T.C.Appleby,
H.Luecke,
J.H.Shim,
J.Z.Wu,
I.W.Cheney,
W.Zhong,
L.Vogeley,
Z.Hong,
and
N.Yao
(2005).
Crystal structure of complete rhinovirus RNA polymerase suggests front loading of protein primer.
|
| |
J Virol,
79,
277-288.
|
|
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PDB code:
|
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X.Zhang,
Y.Ji,
L.Zhang,
S.C.Harrison,
D.C.Marinescu,
M.L.Nibert,
and
T.S.Baker
(2005).
Features of reovirus outer capsid protein mu1 revealed by electron cryomicroscopy and image reconstruction of the virion at 7.0 Angstrom resolution.
|
| |
Structure,
13,
1545-1557.
|
|
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PDB code:
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A.L.Odegard,
K.Chandran,
X.Zhang,
J.S.Parker,
T.S.Baker,
and
M.L.Nibert
(2004).
Putative autocleavage of outer capsid protein micro1, allowing release of myristoylated peptide micro1N during particle uncoating, is critical for cell entry by reovirus.
|
| |
J Virol,
78,
8732-8745.
|
|
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|
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|
|
C.L.Miller,
J.S.Parker,
J.B.Dinoso,
C.D.Piggott,
M.J.Perron,
and
M.L.Nibert
(2004).
Increased ubiquitination and other covariant phenotypes attributed to a strain- and temperature-dependent defect of reovirus core protein mu2.
|
| |
J Virol,
78,
10291-10302.
|
|
|
|
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|
|
J.Kim,
J.S.Parker,
K.E.Murray,
and
M.L.Nibert
(2004).
Nucleoside and RNA triphosphatase activities of orthoreovirus transcriptase cofactor mu2.
|
| |
J Biol Chem,
279,
4394-4403.
|
|
|
|
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|
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K.H.Choi,
J.M.Groarke,
D.C.Young,
R.J.Kuhn,
J.L.Smith,
D.C.Pevear,
and
M.G.Rossmann
(2004).
The structure of the RNA-dependent RNA polymerase from bovine viral diarrhea virus establishes the role of GTP in de novo initiation.
|
| |
Proc Natl Acad Sci U S A,
101,
4425-4430.
|
|
|
PDB codes:
|
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|
|
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|
|
M.Boyce,
J.Wehrfritz,
R.Noad,
and
P.Roy
(2004).
Purified recombinant bluetongue virus VP1 exhibits RNA replicase activity.
|
| |
J Virol,
78,
3994-4002.
|
|
|
|
|
|
|
P.S.Salgado,
E.V.Makeyev,
S.J.Butcher,
D.H.Bamford,
D.I.Stuart,
and
J.M.Grimes
(2004).
The structural basis for RNA specificity and Ca2+ inhibition of an RNA-dependent RNA polymerase.
|
| |
Structure,
12,
307-316.
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|
PDB codes:
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P.Yin,
N.D.Keirstead,
T.J.Broering,
M.M.Arnold,
J.S.Parker,
M.L.Nibert,
and
K.M.Coombs
(2004).
Comparisons of the M1 genome segments and encoded mu2 proteins of different reovirus isolates.
|
| |
Virol J,
1,
6.
|
|
|
|
|
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|
S.C.Harrison
(2004).
Whither structural biology?
|
| |
Nat Struct Mol Biol,
11,
12-15.
|
|
|
|
|
|
|
S.Cheek,
Y.Qi,
S.S.Krishna,
L.N.Kinch,
and
N.V.Grishin
(2004).
4SCOPmap: automated assignment of protein structures to evolutionary superfamilies.
|
| |
BMC Bioinformatics,
5,
197.
|
|
|
|
|
|
|
S.Crowder,
and
K.Kirkegaard
(2004).
Complete three-dimensional structures of picornaviral RNA-dependent RNA polymerases.
|
| |
Structure,
12,
1336-1339.
|
|
|
|
|
|
|
T.J.Broering,
J.Kim,
C.L.Miller,
C.D.Piggott,
J.B.Dinoso,
M.L.Nibert,
and
J.S.Parker
(2004).
Reovirus nonstructural protein mu NS recruits viral core surface proteins and entering core particles to factory-like inclusions.
|
| |
J Virol,
78,
1882-1892.
|
|
|
|
|
|
|
K.Chandran,
and
M.L.Nibert
(2003).
Animal cell invasion by a large nonenveloped virus: reovirus delivers the goods.
|
| |
Trends Microbiol,
11,
374-382.
|
|
|
|
|
|
|
P.Sliz,
S.C.Harrison,
and
G.Rosenbaum
(2003).
How does radiation damage in protein crystals depend on X-ray dose?
|
| |
Structure,
11,
13-19.
|
|
|
|
|
|
|
X.Xu,
Y.Liu,
S.Weiss,
E.Arnold,
S.G.Sarafianos,
and
J.Ding
(2003).
Molecular model of SARS coronavirus polymerase: implications for biochemical functions and drug design.
|
| |
Nucleic Acids Res,
31,
7117-7130.
|
|
|
PDB code:
|
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|
X.Zhang,
S.B.Walker,
P.R.Chipman,
M.L.Nibert,
and
T.S.Baker
(2003).
Reovirus polymerase lambda 3 localized by cryo-electron microscopy of virions at a resolution of 7.6 A.
|
| |
Nat Struct Biol,
10,
1011-1018.
|
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PDB code:
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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
code is
shown on the right.
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Links
