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PDBsum entry 1rdd
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Hydrolase(endoribonuclease)
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PDB id
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1rdd
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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 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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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
percentage match of
88%.
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Abstract
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To obtain more precise insight into the Mg(2+)-binding site essential for RNase
HI catalytic activity, we have determined the crystal structure of E. coli RNase
HI in complex with Mg2+. The analyzed cocrystal, which is not isomorphous with
the Mg(2+)-free crystal previously refined at 1.48 A resolution, was grown at a
high MgSO4 concentration more than 100 mM so that even weakly bound Mg2+ sites
could be identified. The structure was solved by the molecular replacement
method, using the Mg(2+)-free crystal structure as a search model, and was
refined to give a final R-value of 0.190 for intensity data from 10 to 2.8 A,
using the XPLOR and PROLSQ programs. The backbone structures are in their
entirety very similar to each other between the Mg(2+)-bound and the metal-free
crystals, except for minor regions in the enzyme interface with the DNA/RNA
hybrid. The active center clearly revealed a single Mg2+ atom located at a
position almost identical to that previously found by the soaking method.
Although the two metal-ion mechanism had been suggested by another group (Yang,
W., Hendrickson, W.A., Crouch, R.J., Satow, Y. Science 249:1398-1405, 1990) and
partially supported by the crystallographic study of inactive HIV-1 RT RNase H
fragment (Davies, J.F., II, Hostomska, Z., Hostomsky, Z., Jordan, S.R.,
Matthews, D. Science 252:88-95, 1991), the present result excludes the
possibility that RNase HI requires two metal-binding sites for activity. In
contrast to the features in the metal-free enzyme, the side chains of Asn-44 and
Glu-48 are found to form coordinate bonds with Mg2+ in the metal-bound crystal.
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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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