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PDBsum entry 1rdc
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Hydrolase(endoribonuclease)
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PDB id
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1rdc
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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 structures of ribonuclease hi active site mutants from escherichia coli.
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Authors
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K.Katayanagi,
M.Ishikawa,
M.Okumura,
M.Ariyoshi,
S.Kanaya,
Y.Kawano,
M.Suzuki,
I.Tanaka,
K.Morikawa.
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Ref.
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J Biol Chem, 1993,
268,
22092-22099.
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PubMed id
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Note In the PDB file this reference is
annotated as "TO BE PUBLISHED".
The citation details given above were identified by an automated
search of PubMed on title and author
names, giving a
perfect match.
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Abstract
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In order to investigate the relationships between the three-dimensional
structure and the enzymic activity of E. coli RNase HI, three mutant proteins,
which were completely inactivated by the replacements of three functional
residues, Asp10 by Asn (D10N), Glu48 by Gln (E48Q), and Asp70 by Asn (D70N),
were crystallized. Their three-dimensional structures were determined by x-ray
crystallography. Although the entire backbone structures of these mutants were
not affected by the replacements, very localized conformational changes were
observed around the Mg(2+)-binding site. The substitution of an amide group for
a negatively charged carboxyl group in common induces the formation of new
hydrogen bond networks, presumably due to the cancellation of repulsive forces
between carboxyl side chains with negative charges. These conformational changes
can account for the loss of the enzymic activity in the mutants, and suggest a
possible role for Mg2+ in the hydrolysis. Since the 3 replaced acidic residues
are completely conserved in sequences of reverse transcriptases from
retroviruses, including human immunodeficiency virus, the concepts of the
catalytic mechanism deduced from this structural analysis can also be applied to
RNase H activity in reverse transcriptases.
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Secondary reference #1
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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 #2
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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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