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PDBsum entry 2nug
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Hydrolase/RNA
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PDB id
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2nug
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Contents |
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* Residue conservation analysis
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PDB id:
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Hydrolase/RNA
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Title:
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Crystal structure of rnase iii from aquifex aeolicus complexed with ds-RNA at 1.7-angstrom resolution
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Structure:
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5'-r(p Ap Ap Gp Gp Up Cp Ap Up Up Cp G)-3'. Chain: c, d. Engineered: yes. 5'-r(p Ap Gp Up Gp Gp Cp Cp Up Up Gp C)-3'. Chain: e, f. Engineered: yes. Ribonuclease iii. Chain: a, b. Synonym: rnase iii.
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Source:
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Synthetic: yes. Aquifex aeolicus. Organism_taxid: 63363. Gene: rnc. Expressed in: escherichia coli. Expression_system_taxid: 562.
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Resolution:
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1.70Å
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R-factor:
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0.194
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R-free:
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0.220
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Authors:
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J.H.Gan,G.Shaw,J.E.Tropea,D.S.Waugh,D.L.Court,X.Ji
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Key ref:
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J.Gan
et al.
(2008).
A stepwise model for double-stranded RNA processing by ribonuclease III.
Mol Microbiol,
67,
143-154.
PubMed id:
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Date:
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09-Nov-06
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Release date:
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20-Nov-07
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PROCHECK
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Headers
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References
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O67082
(RNC_AQUAE) -
Ribonuclease 3 from Aquifex aeolicus (strain VF5)
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Seq:
Struc:
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221 a.a.
216 a.a.
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Key: |
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PfamA domain |
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Secondary structure |
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CATH domain |
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A-A-G-G-U-C-A-U-U-C-G
11 bases
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A-G-U-G-G-C-C-U-U-G-C
11 bases
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A-A-G-G-U-C-A-U-U-C-G
11 bases
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A-G-U-G-G-C-C-U-U-G-C
11 bases
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Enzyme class:
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E.C.3.1.26.3
- ribonuclease Iii.
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Reaction:
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Endonucleolytic cleavage to 5'-phosphomonoester.
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Mol Microbiol
67:143-154
(2008)
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PubMed id:
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A stepwise model for double-stranded RNA processing by ribonuclease III.
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J.Gan,
G.Shaw,
J.E.Tropea,
D.S.Waugh,
D.L.Court,
X.Ji.
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ABSTRACT
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RNA interference is mediated by small interfering RNAs produced by members of
the ribonuclease III (RNase III) family represented by bacterial RNase III and
eukaryotic Rnt1p, Drosha and Dicer. For mechanistic studies, bacterial RNase III
has been a valuable model system for the family. Previously, we have shown that
RNase III uses two catalytic sites to create the 2-nucleotide (nt) 3' overhangs
in its products. Here, we present three crystal structures of RNase III in
complex with double-stranded RNA, demonstrating how Mg(2+) is essential for the
formation of a catalytically competent protein-RNA complex, how the use of two
Mg(2+) ions can drive the hydrolysis of each phosphodiester bond, and how
conformational changes in both the substrate and the protein are critical
elements for assembling the catalytic complex. Moreover, we have modelled a
protein-substrate complex and a protein-reaction intermediate (transition state)
complex on the basis of the crystal structures. Together, the crystal structures
and the models suggest a stepwise mechanism for RNase III to execute the
phosphoryl transfer reaction.
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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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K.Kim,
S.H.Sim,
C.O.Jeon,
Y.Lee,
and
K.Lee
(2011).
Base substitutions at scissile bond sites are sufficient to alter RNA-binding and cleavage activity of RNase III.
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FEMS Microbiol Lett,
315,
30-37.
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W.Yang
(2011).
Nucleases: diversity of structure, function and mechanism.
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Q Rev Biophys,
44,
1.
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Z.Shi,
R.H.Nicholson,
R.Jaggi,
and
A.W.Nicholson
(2011).
Characterization of Aquifex aeolicus ribonuclease III and the reactivity epitopes of its pre-ribosomal RNA substrates.
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Nucleic Acids Res,
39,
2756-2768.
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P.Braglia,
K.Heindl,
A.Schleiffer,
J.Martinez,
and
N.J.Proudfoot
(2010).
Role of the RNA/DNA kinase Grc3 in transcription termination by RNA polymerase I.
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EMBO Rep,
11,
758-764.
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R.Stefl,
F.C.Oberstrass,
J.L.Hood,
M.Jourdan,
M.Zimmermann,
L.Skrisovska,
C.Maris,
L.Peng,
C.Hofr,
R.B.Emeson,
and
F.H.Allain
(2010).
The solution structure of the ADAR2 dsRBM-RNA complex reveals a sequence-specific readout of the minor groove.
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Cell,
143,
225-237.
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PDB codes:
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H.S.Soifer,
M.Sano,
K.Sakurai,
P.Chomchan,
P.Saetrom,
M.A.Sherman,
M.A.Collingwood,
M.A.Behlke,
and
J.J.Rossi
(2008).
A role for the Dicer helicase domain in the processing of thermodynamically unstable hairpin RNAs.
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Nucleic Acids Res,
36,
6511-6522.
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K.Zenke,
and
K.H.Kim
(2008).
Functional characterization of the RNase III gene of rock bream iridovirus.
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Arch Virol,
153,
1651-1656.
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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
codes are
shown on the right.
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Links
