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PDBsum entry 1kvc
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Endoribonuclease
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PDB id
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1kvc
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References listed in PDB file
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Key reference
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Title
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Proposal for new catalytic roles for two invariant residues in escherichia coli ribonuclease hi.
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Authors
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T.Kashiwagi,
D.Jeanteur,
M.Haruki,
K.Katayanagi,
S.Kanaya,
K.Morikawa.
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Ref.
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Protein Eng, 1996,
9,
857-867.
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PubMed id
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Abstract
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Three mutants of Escherichia coli ribonuclease HI, in which an invariant acidic
residue Asp134 was replaced, were crystallized, and their three-dimensional
structures were determined by X-ray crystallography. The D134A mutant is
completely inactive, whereas the other two mutants, D134H and D134N, retain 59
and 90% activities relative to the wild-type, respectively. The overall
structures of these three mutant proteins are identical with that of the
wild-type enzyme, except for local conformational changes of the flexible loops.
The ribonuclease H family has a common active site, which is composed of four
invariant acidic residues (Asp10, Glu48, Asp70 and Asp134 in E.coli ribonuclease
HI), and their relative positions in the mutants, even including the side-chain
atoms, are almost the same as those in the wild-type. The positions of the
delta-polar atoms at residue 134 in the wild-type, as well as D134H and D134N,
coincide well with each other. They are located near the imidazole side chain of
His124, which is assumed to participate in the catalytic reaction, in addition
to the four invariant acidic residues. Combined with the pH profiles of the
enzymatic activities of the two other mutants, H124A and H124A/D134N, the
crystallographic results allow us to propose a new catalytic mechanism of
ribonuclease H, which includes the roles for Asp134 and His124.
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Secondary reference #1
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Title
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Crystal structure of escherichia coli rnase hi in complex with mg2+ at 2.8 a resolution: proof for a single mg(2+)-Binding site.
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Authors
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K.Katayanagi,
M.Okumura,
K.Morikawa.
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Ref.
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Proteins, 1993,
17,
337-346.
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PubMed id
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Secondary reference #2
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Title
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Structural details of ribonuclease h from escherichia coli as refined to an atomic resolution.
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Authors
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K.Katayanagi,
M.Miyagawa,
M.Matsushima,
M.Ishikawa,
S.Kanaya,
H.Nakamura,
M.Ikehara,
T.Matsuzaki,
K.Morikawa.
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Ref.
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J Mol Biol, 1992,
223,
1029-1052.
[DOI no: ]
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PubMed id
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Figure 1.
Figure 1. Crystallographic R-factor versu number of cycles. A number in a circle corrsponds to the stage number in
Table 1. The resolution range is shown below the curve. AF indicates manual rebuildig of the model a the end of a
refinement stage using difference ourier maps of the type (IF.1 - IFc'',l)exp(ia,) and (2lF.J - IF,))exp(ia,). The ootnote of B
indicates that refinement calculation includes indiidual B-factors.
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Figure 8.
Figure 8. Stereo pair showing the hydrophobic interface between ct1 ad aIV. Note the hydrophobic triad interactions
involving repeated leucine residues.
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The above figures are
reproduced from the cited reference
with permission from Elsevier
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Secondary reference #3
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Title
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Structure of ribonuclease h phased at 2 a resolution by mad analysis of the selenomethionyl protein.
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Authors
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W.Yang,
W.A.Hendrickson,
R.J.Crouch,
Y.Satow.
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Ref.
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Science, 1990,
249,
1398-1405.
[DOI no: ]
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PubMed id
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Secondary reference #4
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Title
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Three-Dimensional structure of ribonuclease h from e. Coli.
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Authors
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K.Katayanagi,
M.Miyagawa,
M.Matsushima,
M.Ishikawa,
S.Kanaya,
M.Ikehara,
T.Matsuzaki,
K.Morikawa.
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Ref.
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Nature, 1990,
347,
306-309.
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PubMed id
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