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PDBsum entry 2is3
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References listed in PDB file
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Key reference
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Title
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Crystal structure of rnase t, An exoribonuclease involved in tRNA maturation and end turnover.
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Authors
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Y.Zuo,
H.Zheng,
Y.Wang,
M.Chruszcz,
M.Cymborowski,
T.Skarina,
A.Savchenko,
A.Malhotra,
W.Minor.
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Ref.
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Structure, 2007,
15,
417-428.
[DOI no: ]
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PubMed id
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Abstract
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The 3' processing of most bacterial precursor tRNAs involves exonucleolytic
trimming to yield a mature CCA end. This step is carried out by RNase T, a
member of the large DEDD family of exonucleases. We report the crystal
structures of RNase T from Escherichia coli and Pseudomonas aeruginosa, which
show that this enzyme adopts an opposing dimeric arrangement, with the catalytic
DEDD residues from one monomer closely juxtaposed with a large basic patch on
the other monomer. This arrangement suggests that RNase T has to be dimeric for
substrate specificity, and agrees very well with prior site-directed mutagenesis
studies. The dimeric architecture of RNase T is very similar to the arrangement
seen in oligoribonuclease, another bacterial DEDD family exoribonuclease. The
catalytic residues in these two enzymes are organized very similarly to the
catalytic domain of the third DEDD family exoribonuclease in E. coli, RNase D,
which is monomeric.
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Figure 1.
Figure 1. Structure-Based Multiple Alignment of E. coli and
P. aeruginosa RNase T and Related Nucleases
Structures
included here are: E. coli RNase T (PDB ID code 2IS3); P.
aeruginosa putative RNase T (PDB ID code 2F96); E. coli DNA
polymerase III  epsilon
subunit (PDB ID code 1J53); E. coli oligoribonuclease (PDB ID
code 1YTA); E. coli exonuclease I (PDB ID code 1FXX); three
human 3′–5′ exoribonucleases, PARN (PDB ID code 2A1R),
3′hExo (PDB ID code 1W0H), and ISG20 (PDB ID code 1WLJ); yeast
POP2 protein exonuclease domain (PDB ID code 1UOC); E. coli
RNase D (PDB ID code 1YT3); E. coli DNA polymerase I Klenow
fragment (PDB ID code 2KZZ); and T. gorgonarius DNA polymerase
(PDB ID code 1TGO). The last three belong to the DEDDy subgroup,
while the others have DEDDh folds. Sequence alignments were
initially generated using T-Coffee (http://www.tcoffee.org)
(Notredame et al., 2000), followed by some manual adjustment.
The three conserved Exo motifs are labeled at the bottom with
the DEDD residues marked by red triangles. The NBS basic
residues conserved in RNase T orthologs are highlighted using
blue rectangles. The numbering at the top is based on the E.
coli RNase T sequence, with the secondary structure of P.
aeruginosa RNase T.
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Figure 4.
Figure 4. Close-Up of the DEDDh Active Site in P. aeruginosa
RNase T: Monomer B in Stereo View
The conserved DEDDh
residues are shown as sticks (red and yellow). The Mg ion
located at the B site is shown as a green sphere. Also shown are
a few water molecules (small red spheres) at the active center.
The experimental electron-density map after solvent flattening
is shown contoured at 2σ.
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The above figures are
reprinted
from an Open Access publication published by Cell Press:
Structure
(2007,
15,
417-428)
copyright 2007.
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