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* Residue conservation analysis
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Enzyme class 2:
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Chain E:
E.C.3.4.21.62
- subtilisin.
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Reaction:
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Hydrolysis of proteins with broad specificity for peptide bonds, and a preference for a large uncharged residue in P1. Hydrolyzes peptide amides.
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Enzyme class 3:
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Chain I:
E.C.?
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Note, where more than one E.C. class is given (as above), each may
correspond to a different protein domain or, in the case of polyprotein
precursors, to a different mature protein.
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DOI no:
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Biochemistry
27:6582-6598
(1988)
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PubMed id:
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Structural comparison of two serine proteinase-protein inhibitor complexes: eglin-c-subtilisin Carlsberg and CI-2-subtilisin Novo.
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C.A.McPhalen,
M.N.James.
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ABSTRACT
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The crystal structures of the molecular complexes between two serine proteinases
and two of their protein inhibitors have been determined: subtilisin Carlsberg
with the recombinant form of eglin-c from the leech Hirudo medicinalis and
subtilisin Novo with chymotrypsin inhibitor 2 from barley seeds. The structures
have been fully refined by restrained-parameter least-squares methods to
crystallographic R factors (sigma[[Fo[ - [Fc[[/sigma[Fo[) of 0.136 at 1.8-A
resolution and 0.154 at 2.1-A resolution, respectively. The 274 equivalent
alpha-carbon atoms of the enzymes superpose with an rms deviation of 0.53 A.
Sequence changes between the enzymes result in localized structural adjustments.
Functional groups in the active sites superpose with an rms deviation of 0.19 A
for 161 equivalent atoms; this close similarity in the conformation of
active-site residues provides no obvious reason for known differences in
catalytic activity between Carlsberg and Novo. Conformational changes in the
active-site region indicate a small induced fit of enzyme and inhibitor. Some
conformational differences are observed between equivalent active-site residues
of subtilisin Carlsberg and alpha-chymotrypsin. Despite differences in tertiary
architecture, most enzyme-substrate (inhibitor) interactions are maintained.
Subtilisin Carlsberg has a rare cis-peptide bond preceding Thr211 (Gly211 in
Novo). Both enzymes contain tightly bound Ca2+ ions. Site 1 is heptacoordinate
with the oxygen atoms at the vertices of a pentagonal bipyramid. Site 2 in
Carlsberg is probably occupied by a K+ ion in Novo. Conserved water molecules
appear to play important structural roles in the enzyme interior, in the
inhibitor beta-sheet, and at the enzyme-inhibitor interface. The 62 equivalent
alpha-carbon atoms of the inhibitors superpose with an rms deviation of 1.68 A.
Sequence changes result in somewhat different packing of the alpha-helix,
beta-sheet, and reactive-site loop relative to each other. Hydrogen bonds and
electrostatic interactions supporting the conformation of the reactive-site loop
are conserved. The 24 main-chain plus C beta atoms of P4 to P1' overlap with an
rms deviation of 0.19 A. Features contributing to the inhibitory nature of
eglin-c and CI-2 are discussed.
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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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M.J.Whitley,
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Nature,
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PDB code:
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The 1.8 A crystal structure of a proteinase K-like enzyme from a psychrotroph Serratia species.
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PDB code:
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Proteins,
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Plasticity of extended subsites facilitates divergent substrate recognition by Kex2 and furin.
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J Biol Chem,
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E.Ben-Zeev,
and
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Weighted geometric docking: incorporating external information in the rotation-translation scan.
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Proteins,
52,
24-27.
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I.H.Barrette-Ng,
K.K.Ng,
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Structural basis of inhibition revealed by a 1:2 complex of the two-headed tomato inhibitor-II and subtilisin Carlsberg.
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J Biol Chem,
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PDB code:
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J.R.Bradford,
and
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(2003).
Asymmetric mutation rates at enzyme-inhibitor interfaces: implications for the protein-protein docking problem.
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Protein Sci,
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A.Heifetz,
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and
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A clogged gutter mechanism for protease inhibitors.
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| |
Proc Natl Acad Sci U S A,
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PDB code:
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|
E.T.Anderson,
M.G.Wetherell,
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S.B.Olmsted,
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Processing, stability, and kinetic parameters of C5a peptidase from Streptococcus pyogenes.
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Progressive rearrangement of subtilisin Carlsberg into orderly and inflexible conformation with Ca(2+) binding.
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Proteins,
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P.N.Bryan
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Biochim Biophys Acta,
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Biophys J,
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Deciphering the role of the electrostatic interactions involving Gly70 in eglin C by total chemical protein synthesis.
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Biochemistry,
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Three-dimensional structures of the free and antigen-bound Fab from monoclonal antilysozyme antibody HyHEL-63(,).
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| |
Biochemistry,
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PDB codes:
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B.Ruan,
J.Hoskins,
and
P.N.Bryan
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Rapid folding of calcium-free subtilisin by a stabilized pro-domain mutant.
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Biochemistry,
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and
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Predicted structural alterations in proinsulin during its interactions with prohormone convertases.
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Biochemistry,
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H.A.Gabb,
and
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Use of pair potentials across protein interfaces in screening predicted docked complexes.
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Proteins,
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364-373.
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H.Czapinska,
and
J.Otlewski
(1999).
Structural and energetic determinants of the S1-site specificity in serine proteases.
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Eur J Biochem,
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J.C.Waldner,
S.J.Lahr,
M.H.Edgell,
and
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(1999).
Nonideality and protein thermal denaturation.
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Biopolymers,
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471-479.
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H.M.Gudmundsson,
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(1999).
Properties of a subtilisin-like proteinase from a psychrotrophic Vibrio species comparison with proteinase K and aqualysin I.
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Eur J Biochem,
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Probing intermolecular backbone H-bonding in serine proteinase-protein inhibitor complexes.
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Chem Biol,
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PDB codes:
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F.Martin,
N.Dimasi,
C.Volpari,
C.Perrera,
S.Di Marco,
M.Brunetti,
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Design of selective eglin inhibitors of HCV NS3 proteinase.
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Biochemistry,
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A model for the structure of the P domains in the subtilisin-like prohormone convertases.
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Proc Natl Acad Sci U S A,
95,
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N.C.Rockwell,
and
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(1998).
Interplay between S1 and S4 subsites in Kex2 protease: Kex2 exhibits dual specificity for the P4 side chain.
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Biochemistry,
37,
3386-3391.
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T.Tanaka,
H.Matsuzawa,
and
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Engineering of S2 site of aqualysin I; alteration of P2 specificity by excluding P2 side chain.
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Biochemistry,
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J.R.Martin,
F.A.Mulder,
Y.Karimi-Nejad,
J.van der Zwan,
M.Mariani,
D.Schipper,
and
R.Boelens
(1997).
The solution structure of serine protease PB92 from Bacillus alcalophilus presents a rigid fold with a flexible substrate-binding site.
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Structure,
5,
521-532.
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PDB code:
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|
M.A.Qasim,
P.J.Ganz,
C.W.Saunders,
K.S.Bateman,
M.N.James,
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Interscaffolding additivity. Association of P1 variants of eglin c and of turkey ovomucoid third domain with serine proteinases.
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and
J.A.Leunissen
(1997).
Subtilases: the superfamily of subtilisin-like serine proteases.
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Protein Sci,
6,
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S.Kanka,
K.H.Maurer,
and
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Thermostable variants of subtilisin selected by temperature-gradient gel electrophoresis.
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Electrophoresis,
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B.A.Fields,
F.A.Goldbaum,
W.Dall'Acqua,
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Hydrogen bonding and solvent structure in an antigen-antibody interface. Crystal structures and thermodynamic characterization of three Fv mutants complexed with lysozyme.
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Biochemistry,
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PDB codes:
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I.A.Vakser
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Hydrophilicity of cavities in proteins.
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Proteins,
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Biochemistry,
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C.W.Hilbers,
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Backbone dynamics of the 269-residue protease Savinase determined from 15N-NMR relaxation measurements.
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Eur J Biochem,
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Biochemistry,
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Biosci Rep,
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Biopolymers,
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Molecular modeling of the substrate specificity of prohormone convertases SPC2 and SPC3.
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J Biol Chem,
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Biopolymers,
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and
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Structural basis of substrate specificity in the serine proteases.
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Protein Sci,
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PDB code:
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J.Janin
(1995).
Elusive affinities.
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| |
Proteins,
21,
30-39.
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B.L.Barnett,
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Biotechnology (N Y),
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J Protein Chem,
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T.Gallagher,
G.Gilliland,
L.Wang,
and
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(1995).
The prosegment-subtilisin BPN' complex: crystal structure of a specific 'foldase'.
|
| |
Structure,
3,
907-914.
|
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PDB code:
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|
Y.Yamagata,
K.Isshiki,
and
E.Ichishima
(1995).
Subtilisin Sendai from alkalophilic Bacillus sp.: molecular and enzymatic properties of the enzyme and molecular cloning and characterization of the gene, aprS.
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| |
Enzyme Microb Technol,
17,
653-663.
|
|
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|
A.Liljas,
K.Håkansson,
B.H.Jonsson,
and
Y.Xue
(1994).
Inhibition and catalysis of carbonic anhydrase. Recent crystallographic analyses.
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| |
Eur J Biochem,
219,
1.
|
|
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E.Fioretti,
M.Angeletti,
G.Lupidi,
and
M.Coletta
(1994).
Heterotropic modulation of the protease-inhibitor-recognition process. Cations effect the binding properties of alpha-chymotrypsin.
|
| |
Eur J Biochem,
225,
459-465.
|
|
|
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|
G.Lange,
C.Betzel,
S.Branner,
and
K.S.Wilson
(1994).
Crystallographic studies of Savinase, a subtilisin-like proteinase, at pH 10.5.
|
| |
Eur J Biochem,
224,
507-518.
|
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|
J.P.Leis,
and
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(1994).
Engineering proteases with altered specificity.
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| |
Curr Opin Biotechnol,
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403-408.
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K.Huang,
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V.D.Bernard,
R.J.Peanasky,
and
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(1994).
The molecular structure of the complex of Ascaris chymotrypsin/elastase inhibitor with porcine elastase.
|
| |
Structure,
2,
679-689.
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PDB code:
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|
M.A.Miller,
G.W.Han,
and
J.Kraut
(1994).
A cation binding motif stabilizes the compound I radical of cytochrome c peroxidase.
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Proc Natl Acad Sci U S A,
91,
11118-11122.
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PDB codes:
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P.Seufer-Wasserthal,
V.Martichonok,
T.H.Keller,
B.Chin,
R.Martin,
and
J.B.Jones
(1994).
Probing the specificity of the S1 binding site of subtilisin Carlsberg with boronic acids.
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Bioorg Med Chem,
2,
35-48.
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R.J.Siezen,
J.W.Creemers,
and
W.J.Van de Ven
(1994).
Homology modelling of the catalytic domain of human furin. A model for the eukaryotic subtilisin-like proprotein convertases.
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| |
Eur J Biochem,
222,
255-266.
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T.K.Chang,
D.Y.Jackson,
J.P.Burnier,
and
J.A.Wells
(1994).
Subtiligase: a tool for semisynthesis of proteins.
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Proc Natl Acad Sci U S A,
91,
12544-12548.
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T.N.Bhat,
G.A.Bentley,
G.Boulot,
M.I.Greene,
D.Tello,
W.Dall'Acqua,
H.Souchon,
F.P.Schwarz,
R.A.Mariuzza,
and
R.J.Poljak
(1994).
Bound water molecules and conformational stabilization help mediate an antigen-antibody association.
|
| |
Proc Natl Acad Sci U S A,
91,
1089-1093.
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PDB codes:
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|
P.A.Fitzpatrick,
A.C.Steinmetz,
D.Ringe,
and
A.M.Klibanov
(1993).
Enzyme crystal structure in a neat organic solvent.
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| |
Proc Natl Acad Sci U S A,
90,
8653-8657.
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PDB codes:
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|
S.H.Bryant,
and
C.E.Lawrence
(1993).
An empirical energy function for threading protein sequence through the folding motif.
|
| |
Proteins,
16,
92.
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A.L.Morris,
M.W.MacArthur,
E.G.Hutchinson,
and
J.M.Thornton
(1992).
Stereochemical quality of protein structure coordinates.
|
| |
Proteins,
12,
345-364.
|
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|
|
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|
|
A.P.Heiner,
H.J.Berendsen,
and
W.F.van Gunsteren
(1992).
MD simulation of subtilisin BPN' in a crystal environment.
|
| |
Proteins,
14,
451-464.
|
|
|
|
|
|
|
J.S.Finer-Moore,
A.A.Kossiakoff,
J.H.Hurley,
T.Earnest,
and
R.M.Stroud
(1992).
Solvent structure in crystals of trypsin determined by X-ray and neutron diffraction.
|
| |
Proteins,
12,
203-222.
|
|
|
PDB code:
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|
|
|
|
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|
|
L.M.Bech,
S.B.Sørensen,
and
K.Breddam
(1992).
Mutational replacements in subtilisin 309. Val104 has a modulating effect on the P4 substrate preference.
|
| |
Eur J Biochem,
209,
869-874.
|
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|
|
M.Gasset,
M.A.Baldwin,
D.H.Lloyd,
J.M.Gabriel,
D.M.Holtzman,
F.Cohen,
R.Fletterick,
and
S.B.Prusiner
(1992).
Predicted alpha-helical regions of the prion protein when synthesized as peptides form amyloid.
|
| |
Proc Natl Acad Sci U S A,
89,
10940-10944.
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P.Gros,
A.V.Teplyakov,
and
W.G.Hol
(1992).
Effects of eglin-c binding to thermitase: three-dimensional structure comparison of native thermitase and thermitase eglin-c complexes.
|
| |
Proteins,
12,
63-74.
|
|
|
|
|
|
|
R.Bott,
J.Dauberman,
R.Caldwell,
C.Mitchinson,
L.Wilson,
B.Schmidt,
C.Simpson,
S.Power,
P.Lad,
and
I.H.Sagar
(1992).
Using structural comparison as a guide in protein engineering.
|
| |
Ann N Y Acad Sci,
672,
10-19.
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|
R.R.Plaskon,
C.M.Kam,
E.M.Burgess,
J.C.Powers,
and
F.L.Suddath
(1992).
Michaelis complexes of porcine pancreatic elastase with 7-[(alkylcarbamoyl)amino]-4-chloro-3-ethoxyisocoumarins: translational sampling of inhibitor position and kinetic measurements.
|
| |
Proteins,
13,
141-151.
|
|
|
|
|
|
|
S.G.Hyberts,
M.S.Goldberg,
T.F.Havel,
and
G.Wagner
(1992).
The solution structure of eglin c based on measurements of many NOEs and coupling constants and its comparison with X-ray structures.
|
| |
Protein Sci,
1,
736-751.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
T.P.Graycar,
R.R.Bott,
R.M.Caldwell,
J.L.Dauberman,
P.J.Lad,
S.D.Power,
I.H.Sagar,
R.A.Silva,
G.L.Weiss,
and
L.R.Woodhouse
(1992).
Altering the proteolytic activity of subtilisin through protein engineering.
|
| |
Ann N Y Acad Sci,
672,
71-79.
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W.Bode,
and
R.Huber
(1992).
Natural protein proteinase inhibitors and their interaction with proteinases.
|
| |
Eur J Biochem,
204,
433-451.
|
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|
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|
G.Forsberg,
M.Brobjer,
E.Holmgren,
K.Bergdahl,
P.Persson,
K.M.Gautvik,
and
M.Hartmanis
(1991).
Thrombin and H64A subtilisin cleavage of fusion proteins for preparation of human recombinant parathyroid hormone.
|
| |
J Protein Chem,
10,
517-526.
|
|
|
|
|
|
|
O.Herzberg,
and
J.Moult
(1991).
Analysis of the steric strain in the polypeptide backbone of protein molecules.
|
| |
Proteins,
11,
223-229.
|
|
|
|
|
|
|
G.J.Wistow,
and
J.Piatigorsky
(1990).
Gene conversion and splice-site slippage in the argininosuccinate lyases/delta-crystallins of the duck lens: members of an enzyme superfamily.
|
| |
Gene,
96,
263-270.
|
|
|
|
|
|
|
M.Bolognesi,
L.Pugliese,
G.Gatti,
F.Frigerio,
A.Coda,
L.Antolini,
H.P.Schnebli,
E.Menegatti,
G.Amiconi,
and
P.Ascenzi
(1990).
X-ray crystal structure of the bovine alpha-chymotrypsin/eglin c complex at 2.6 A resolution.
|
| |
J Mol Recognit,
3,
163-168.
|
|
|
|
|
|
|
P.Carter,
and
J.A.Wells
(1990).
Functional interaction among catalytic residues in subtilisin BPN'.
|
| |
Proteins,
7,
335-342.
|
|
|
|
|
|
|
W.J.van de Ven,
J.Voorberg,
R.Fontijn,
H.Pannekoek,
A.M.van den Ouweland,
H.L.van Duijnhoven,
A.J.Roebroek,
and
R.J.Siezen
(1990).
Furin is a subtilisin-like proprotein processing enzyme in higher eukaryotes.
|
| |
Mol Biol Rep,
14,
265-275.
|
|
|
|
|
|
|
T.E.Creighton,
and
N.J.Darby
(1989).
Functional evolutionary divergence of proteolytic enzymes and their inhibitors.
|
| |
Trends Biochem Sci,
14,
319-324.
|
|
|
|
|
|
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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