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* Residue conservation analysis
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Enzyme class:
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E.C.3.1.27.5
- Pancreatic ribonuclease.
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Reaction:
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Endonucleolytic cleavage to nucleoside 3'-phosphates and 3'-phosphooligonucleotides ending in C-P or U-P with 2',3'-cyclic phosphate intermediates.
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Gene Ontology (GO) functional annotation
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Cellular component
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extracellular region
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1 term
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Biochemical function
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nucleic acid binding
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6 terms
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Protein Sci
7:1255-1258
(1998)
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PubMed id:
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Crystal structures of two mutants that have implications for the folding of bovine pancreatic ribonuclease A.
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M.A.Pearson,
P.A.Karplus,
R.W.Dodge,
J.H.Laity,
H.A.Scheraga.
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ABSTRACT
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The Tyr92-Pro93 peptide group of bovine pancreatic ribonuclease A (RNase A)
exists in the cis conformation in the native state. From unfolding/refolding
kinetic studies of the disulfide-intact wild-type protein and of a variant in
which Pro93 had been replaced by Ala, it had been suggested that the Tyr92-Ala93
peptide group also exists in the cis conformation in the native state. Here, we
report the crystal structure of the P93A variant. Although there is disorder in
the region of residues 92 and 93, the best structural model contains a cis
peptide at this position, lending support to the results of the kinetics
experiments. We also report the crystal structure of the C[40, 95]A variant,
which is an analog of the major rate-determining three-disulfide intermediate in
the oxidative folding of RNase A, missing the 40-95 disulfide bond. As had been
detected by NMR spectroscopy, the crystal structure of this analog shows
disorder in the region surrounding the missing disulfide. However, the global
chain fold of the remainder of the protein, including the disulfide bond between
Cys65 and Cys72, appears to be unaffected by the mutation.
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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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D.J.Graham,
and
J.L.Greminger
(2010).
On the information expressed in enzyme primary structure: lessons from Ribonuclease A.
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Mol Divers, 14,
673-686.
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B.S.Mamathambika,
and
J.C.Bardwell
(2008).
Disulfide-linked protein folding pathways.
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Annu Rev Cell Dev Biol, 24,
211-235.
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M.Cemazar,
A.Joshi,
N.L.Daly,
A.E.Mark,
and
D.J.Craik
(2008).
The structure of a two-disulfide intermediate assists in elucidating the oxidative folding pathway of a cyclic cystine knot protein.
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Structure, 16,
842-851.
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F.Ding,
K.C.Prutzman,
S.L.Campbell,
and
N.V.Dokholyan
(2006).
Topological determinants of protein domain swapping.
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Structure, 14,
5.
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J.Font,
J.Torrent,
M.Ribó,
D.V.Laurents,
C.Balny,
M.Vilanova,
and
R.Lange
(2006).
Pressure-jump-induced kinetics reveals a hydration dependent folding/unfolding mechanism of ribonuclease A.
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Biophys J, 91,
2264-2274.
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T.U.Schwartz,
D.Schmidt,
S.G.Brohawn,
and
G.Blobel
(2006).
Homodimerization of the G protein SRbeta in the nucleotide-free state involves proline cis/trans isomerization in the switch II region.
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Proc Natl Acad Sci U S A, 103,
6823-6828.
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PDB code:
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D.A.Schultz,
A.M.Friedman,
M.A.White,
and
R.O.Fox
(2005).
The crystal structure of the cis-proline to glycine variant (P114G) of ribonuclease A.
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Protein Sci, 14,
2862-2870.
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PDB code:
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W.J.Wedemeyer,
X.Xu,
E.Welker,
and
H.A.Scheraga
(2002).
Conformational propensities of protein folding intermediates: distribution of species in the 1S, 2S, and 3S ensembles of the [C40A,C95A] mutant of bovine pancreatic ribonuclease A.
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Biochemistry, 41,
1483-1491.
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A.Cao,
E.Welker,
and
H.A.Scheraga
(2001).
Effect of mutation of proline 93 on redox unfolding/folding of bovine pancreatic ribonuclease A.
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Biochemistry, 40,
8536-8541.
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E.Welker,
M.Narayan,
W.J.Wedemeyer,
and
H.A.Scheraga
(2001).
Structural determinants of oxidative folding in proteins.
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Proc Natl Acad Sci U S A, 98,
2312-2316.
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M.Jaskólski,
M.Kozak,
J.Lubkowski,
G.Palm,
and
A.Wlodawer
(2001).
Structures of two highly homologous bacterial L-asparaginases: a case of enantiomorphic space groups.
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Acta Crystallogr D Biol Crystallogr, 57,
369-377.
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PDB codes:
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B.Cigić,
S.W.Dahl,
and
R.H.Pain
(2000).
The residual pro-part of cathepsin C fulfills the criteria required for an intramolecular chaperone in folding and stabilizing the human proenzyme.
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Biochemistry, 39,
12382-12390.
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W.J.Wedemeyer,
E.Welker,
M.Narayan,
and
H.A.Scheraga
(2000).
Disulfide bonds and protein folding.
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Biochemistry, 39,
4207-4216.
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Y.Xiong,
D.Juminaga,
G.V.Swapna,
W.J.Wedemeyer,
H.A.Scheraga,
and
G.T.Montelione
(2000).
Solution NMR evidence for a cis Tyr-Ala peptide group in the structure of [Pro93Ala] bovine pancreatic ribonuclease A.
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Protein Sci, 9,
421-426.
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M.Iwaoka,
W.J.Wedemeyer,
and
H.A.Scheraga
(1999).
Conformational unfolding studies of three-disulfide mutants of bovine pancreatic ribonuclease A and the coupling of proline isomerization to disulfide redox reactions.
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Biochemistry, 38,
2805-2815.
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D.Juminaga,
W.J.Wedemeyer,
and
H.A.Scheraga
(1998).
Proline isomerization in bovine pancreatic ribonuclease A. 1. Unfolding conditions.
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Biochemistry, 37,
11614-11620.
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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
