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* Residue conservation analysis
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Enzyme class:
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Chain E:
E.C.3.4.21.4
- trypsin.
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Reaction:
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Preferential cleavage: Arg-|-Xaa, Lys-|-Xaa.
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DOI no:
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Acta Crystallogr D Biol Crystallogr
55:139-148
(1999)
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PubMed id:
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High-resolution structures of three new trypsin-squash-inhibitor complexes: a detailed comparison with other trypsins and their complexes.
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R.Helland,
G.I.Berglund,
J.Otlewski,
W.Apostoluk,
O.A.Andersen,
N.P.Willassen,
A.O.Smalås.
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ABSTRACT
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An anionic trypsin from Atlantic salmon and bovine trypsin have been complexed
with the squash-seed inhibitors, CMTI-I (Cucurbita maxima trypsin inhibitor I,
P1 Arg) and CPTI-II (Cucurbita pepo trypsin inhibitor II, P1 Lys). The crystal
structures of three such complexes have been determined to 1.5-1.8 A resolution
and refined to crystallographic R factors ranging from 17.6 to 19.3%. The two
anionic salmon-trypsin complexes (ST-CPTI and ST-CMTI) and the bovine-trypsin
complex (BT-CPTI) have been compared to other trypsin-inhibitor complexes by
means of general structure and primary and secondary binding features. In all
three new structures, the primary binding residue of the inhibitor binds to
trypsin in the classical manner, but with small differences in the primary and
secondary binding patterns. Lysine in CPTI-II binds deeper in the specificity
pocket of bovine trypsin than lysine in other known lysine-bovine-trypsin
complexes, and anionic salmon trypsin lacks some of the secondary binding
interactions found in the complexes formed between squash inhibitors and bovine
trypsin. The ST-CMTI complex was formed from the reactive-site-cleaved form of
the inhibitor. However, well defined electron density was observed for the
P1-P1' peptide bond, together with a hydrogen-bonding pattern virtually
identical to those of all serine-protease-protein-inhibitor complexes,
indicating a resynthesis of the scissile bond.
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Selected figure(s)
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Figure 1.
Figure 1 Electron density for residues at the N-terminus of
anionic salmon trypsin in complex with the squash-seed inhibitor
CPTI-II. The maps are from simulated annealing where residues 24
and 28 were refined as alanines. The 2F[o] - F[c] map (grey) is
contoured at 1.5  and
the F[o] - F[c] map (black) is contoured at 3 .
Both maps clearly identify residues 24 and 28 as prolines. The
coordinates of the final refined model are superimposed on the
simulated-annealing maps. The figure was produced using
BOBSCRIPT (Kraulis, 1991[Kraulis, P. J. (1991). J. Appl. Cryst.
24, 946-950.]; Esnouf, 1997[Esnouf, R. M. (1997). J. Mol. Graph.
15, 133-138.]).
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Figure 2.
Figure 2 Ribbon-style diagram of the complex between salmon
trypsin (red) and CPTI (blue). The P1 lysine residue of CPTI
penetrating the active site of trypsin is indicated along with
the structurally bound calcium ion (green) of trypsin.
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The above figures are
reprinted
by permission from the IUCr:
Acta Crystallogr D Biol Crystallogr
(1999,
55,
139-148)
copyright 1999.
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Figures were
selected
by an automated process.
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Literature references that cite this PDB file's key reference
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Google scholar
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PubMed id
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Reference
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K.Jagadish,
and
J.A.Camarero
(2010).
Cyclotides, a promising molecular scaffold for peptide-based therapeutics.
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Biopolymers,
94,
611-616.
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J.Austin,
W.Wang,
S.Puttamadappa,
A.Shekhtman,
and
J.A.Camarero
(2009).
Biosynthesis and biological screening of a genetically encoded library based on the cyclotide MCoTI-I.
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Chembiochem,
10,
2663-2670.
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R.Bao,
C.Z.Zhou,
C.Jiang,
S.X.Lin,
C.W.Chi,
and
Y.Chen
(2009).
The ternary structure of the double-headed arrowhead protease inhibitor API-A complexed with two trypsins reveals a novel reactive site conformation.
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J Biol Chem,
284,
26676-26684.
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PDB code:
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A.Heitz,
O.Avrutina,
D.Le-Nguyen,
U.Diederichsen,
J.F.Hernandez,
J.Gracy,
H.Kolmar,
and
L.Chiche
(2008).
Knottin cyclization: Impact on Structure and Dynamics.
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BMC Struct Biol,
8,
54.
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D.Dell'orco,
and
P.G.De Benedetti
(2008).
Quantitative structure-activity relationship analysis of canonical inhibitors of serine proteases.
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J Comput Aided Mol Des,
22,
469-478.
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E.S.Radisky,
J.M.Lee,
C.J.Lu,
and
D.E.Koshland
(2006).
Insights into the serine protease mechanism from atomic resolution structures of trypsin reaction intermediates.
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Proc Natl Acad Sci U S A,
103,
6835-6840.
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PDB codes:
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M.Almlöf,
J.Aqvist,
A.O.Smalås,
and
B.O.Brandsdal
(2006).
Probing the effect of point mutations at protein-protein interfaces with free energy calculations.
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Biophys J,
90,
433-442.
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M.Cemazar,
N.L.Daly,
S.Häggblad,
K.P.Lo,
E.Yulyaningsih,
and
D.J.Craik
(2006).
Knots in rings. The circular knotted protein Momordica cochinchinensis trypsin inhibitor-II folds via a stable two-disulfide intermediate.
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J Biol Chem,
281,
8224-8232.
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K.Kamei,
S.Sato,
N.Hamato,
R.Takano,
K.Ohshima,
R.Yamamoto,
T.Nishino,
H.Kato,
and
S.Hara
(2000).
Effect of P(2)' site tryptophan and P(20)' site deletion of Momordica charantia trypsin inhibitor II on inhibition of proteinases.
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Biochim Biophys Acta,
1480,
6.
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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
