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PDBsum entry 1i2f
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* Residue conservation analysis
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Enzyme class:
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E.C.4.6.1.24
- ribonuclease T1.
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Reaction:
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[RNA] containing guanosine + H2O = an [RNA fragment]-3'-guanosine- 3'-phosphate + a 5'-hydroxy-ribonucleotide-3'-[RNA fragment]
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DOI no:
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Biochemistry
40:10140-10149
(2001)
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PubMed id:
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Hydrophobic core manipulations in ribonuclease T1.
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S.De Vos,
J.Backmann,
M.Prévost,
J.Steyaert,
R.Loris.
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ABSTRACT
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Differential scanning calorimetry, urea denaturation, and X-ray crystallography
were combined to study the structural and energetic consequences of refilling an
engineered cavity in the hydrophobic core of RNase T1 with CH(3), SH, and OH
groups. Three valines that cluster together in the major hydrophobic core of T1
were each replaced with Ala, Ser, Thr, and Cys. Compared to the wild-type
protein, all these mutants reduce the thermodynamic stability of the enzyme
considerably. The relative order of stability at all three positions is as
follows: Val > Ala approximately equal to Thr > Ser. The effect of
introducing a sulfhydryl group is more variable. Surprisingly, a Val --> Cys
mutation in a hydrophobic environment can be as or even more destabilizing than
a Val --> Ser mutation. Furthermore, our results reveal that the penalty for
introducing an OH group into a hydrophobic cavity is roughly the same as the
gain obtained from filling the cavity with a CH(3) group. The inverse
equivalence of the behavior of hydroxyl and methyl groups seems to be crucial
for the unique three-dimensional structure of the proteins. The importance of
negative design elements in this context is highlighted.
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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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C.N.Pace,
H.Fu,
K.L.Fryar,
J.Landua,
S.R.Trevino,
B.A.Shirley,
M.M.Hendricks,
S.Iimura,
K.Gajiwala,
J.M.Scholtz,
and
G.R.Grimsley
(2011).
Contribution of hydrophobic interactions to protein stability.
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J Mol Biol,
408,
514-528.
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K.Yura,
S.Sulaiman,
Y.Hatta,
M.Shionyu,
and
M.Go
(2009).
RESOPS: a database for analyzing the correspondence of RNA editing sites to protein three-dimensional structures.
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Plant Cell Physiol,
50,
1865-1873.
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K.Yura,
and
M.Go
(2008).
Correlation between amino acid residues converted by RNA editing and functional residues in protein three-dimensional structures in plant organelles.
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BMC Plant Biol,
8,
79.
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A.Mittermaier,
and
L.E.Kay
(2004).
The response of internal dynamics to hydrophobic core mutations in the SH3 domain from the Fyn tyrosine kinase.
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Protein Sci,
13,
1088-1099.
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J.C.van Swieten,
E.Brusse,
B.M.de Graaf,
E.Krieger,
R.van de Graaf,
I.de Koning,
A.Maat-Kievit,
P.Leegwater,
D.Dooijes,
B.A.Oostra,
and
P.Heutink
(2003).
A mutation in the fibroblast growth factor 14 gene is associated with autosomal dominant cerebellar ataxia [corrected].
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Am J Hum Genet,
72,
191-199.
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K.Takano,
J.M.Scholtz,
J.C.Sacchettini,
and
C.N.Pace
(2003).
The contribution of polar group burial to protein stability is strongly context-dependent.
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J Biol Chem,
278,
31790-31795.
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PDB codes:
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S.R.Brych,
J.Kim,
T.M.Logan,
and
M.Blaber
(2003).
Accommodation of a highly symmetric core within a symmetric protein superfold.
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Protein Sci,
12,
2704-2718.
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PDB codes:
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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
codes are
shown on the right.
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Links
