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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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Contents |
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* Residue conservation analysis
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Enzyme class:
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E.C.3.1.26.4
- ribonuclease H.
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Reaction:
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Endonucleolytic cleavage to 5'-phosphomonoester.
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J Biol Chem
268:22092-22099
(1993)
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PubMed id:
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Crystal structures of ribonuclease HI active site mutants from Escherichia coli.
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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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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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Literature references that cite this PDB file's key reference
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PubMed id
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Reference
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S.Azzi,
V.Parissi,
R.G.Maroun,
P.Eid,
O.Mauffret,
and
S.Fermandjian
(2010).
The HIV-1 integrase α4-helix involved in LTR-DNA recognition is also a highly antigenic peptide element.
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PLoS One,
5,
e16001.
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A.Muroya,
D.Tsuchiya,
M.Ishikawa,
M.Haruki,
M.Morikawa,
S.Kanaya,
and
K.Morikawa
(2001).
Catalytic center of an archaeal type 2 ribonuclease H as revealed by X-ray crystallographic and mutational analyses.
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Protein Sci,
10,
707-714.
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PDB code:
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E.R.Goedken,
J.L.Keck,
J.M.Berger,
and
S.Marqusee
(2000).
Divalent metal cofactor binding in the kinetic folding trajectory of Escherichia coli ribonuclease HI.
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Protein Sci,
9,
1914-1921.
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PDB code:
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A.Saito,
H.Iwasaki,
M.Ariyoshi,
K.Morikawa,
and
H.Shinagawa
(1995).
Identification of four acidic amino acids that constitute the catalytic center of the RuvC Holliday junction resolvase.
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Proc Natl Acad Sci U S A,
92,
7470-7474.
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M.Haruki,
E.Noguchi,
C.Nakai,
Y.Y.Liu,
M.Oobatake,
M.Itaya,
and
S.Kanaya
(1994).
Investigating the role of conserved residue Asp134 in Escherichia coli ribonuclease HI by site-directed random mutagenesis.
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Eur J Biochem,
220,
623-631.
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K.Katayanagi,
M.Okumura,
and
K.Morikawa
(1993).
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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Proteins,
17,
337-346.
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PDB code:
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The most recent references are shown first.
Citation data come partly from CiteXplore and partly
from an automated harvesting procedure. Note that this is likely to be
only a partial list as not all journals are covered by
either method. However, we are continually building up the citation data
so more and more references will be included with time.
Where a reference describes a PDB structure, the PDB
code is
shown on the right.
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Links
