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PDBsum entry 1oyr
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Contents |
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* Residue conservation analysis
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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 the phosphorolytic exoribonuclease rnase ph from bacillus subtilis and implications for its quaternary structure and tRNA binding.
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Authors
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L.S.Harlow,
A.Kadziola,
K.F.Jensen,
S.Larsen.
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Ref.
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Protein Sci, 2004,
13,
668-677.
[DOI no: ]
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PubMed id
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Abstract
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RNase PH is a member of the family of phosphorolytic 3' --> 5' exoribonucleases
that also includes polynucleotide phosphorylase (PNPase). RNase PH is involved
in the maturation of tRNA precursors and especially important for removal of
nucleotide residues near the CCA acceptor end of the mature tRNAs. Wild-type and
triple mutant R68Q-R73Q-R76Q RNase PH from Bacillus subtilis have been
crystallized and the structures determined by X-ray diffraction to medium
resolution. Wild-type and triple mutant RNase PH crystallize as a hexamer and
dimer, respectively. The structures contain a rare left-handed beta alpha
beta-motif in the N-terminal portion of the protein. This motif has also been
identified in other enzymes involved in RNA metabolism. The RNase PH structure
and active site can, despite low sequence similarity, be overlayed with the
N-terminal core of the structure and active site of Streptomyces antibioticus
PNPase. The surface of the RNase PH dimer fit the shape of a tRNA molecule.
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Figure 1.
Figure 1. Stereo views of the B. subtilis RNase PH monomer.
(A) Ribbon representation showing the secondary structure
elements with labels and ball-and-stick representation of
sulfate ions. C[  ]positions for
mutated residues Arg68, Arg73, and Arg76 are marked with white
balls. (B) C[ ]trace of the
monomer with dots every 10 residues and labels every 20
residues. This figure and Figure 2 Go- were made
using the program MOLSCRIPT (Kraulis 1991).
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Figure 5.
Figure 5. Close-up stereo view at the active site residues
with sixfold averaged electron density. Nitrogen, oxygen,
sulfur, and carbon atoms are dark gray, medium gray, light gray,
and white, respectively. The 2mF[obs] - DF[calc] total density
is shown with weak line contours at a 1  level and the
mF[obs] - DF[calc] difference density is shown with strong lines
and contoured at 4 . The
carboxylate groups of Asp 181 and Asp 187 are unexpectedly close
but residual density present in between may indicate the
presence of a positive countercharge, for example, a partially
occupied Cd^2+ ion (not included in the model). This figure was
made with BOBSCRIPT (Esnouf 1999).
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The above figures are
reprinted
by permission from the Protein Society:
Protein Sci
(2004,
13,
668-677)
copyright 2004.
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