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PDBsum entry 1tgb
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Hydrolase zymogen (serine proteinase)
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PDB id
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1tgb
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* Residue conservation analysis
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Enzyme class:
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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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J Mol Biol
111:415-438
(1977)
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PubMed id:
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Crystal structure of bovine trypsinogen at 1-8 A resolution. II. Crystallographic refinement, refined crystal structure and comparison with bovine trypsin.
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H.Fehlhammer,
W.Bode,
R.Huber.
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ABSTRACT
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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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P.L.Kastritis,
I.H.Moal,
H.Hwang,
Z.Weng,
P.A.Bates,
A.M.Bonvin,
and
J.Janin
(2011).
A structure-based benchmark for protein-protein binding affinity.
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| |
Protein Sci,
20,
482-491.
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A.A.Stoop,
R.V.Joshi,
C.T.Eggers,
and
C.S.Craik
(2010).
Analysis of an engineered plasma kallikrein inhibitor and its effect on contact activation.
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| |
Biol Chem,
391,
425-433.
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A.D.Vogt,
A.Bah,
and
E.Di Cera
(2010).
Evidence of the E*-E equilibrium from rapid kinetics of Na+ binding to activated protein C and factor Xa.
|
| |
J Phys Chem B,
114,
16125-16130.
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A.Bah,
C.J.Carrell,
Z.Chen,
P.S.Gandhi,
and
E.Di Cera
(2009).
Stabilization of the E* form turns thrombin into an anticoagulant.
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| |
J Biol Chem,
284,
20034-20040.
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PDB code:
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D.Kaiserman,
A.M.Buckle,
P.Van Damme,
J.A.Irving,
R.H.Law,
A.Y.Matthews,
T.Bashtannyk-Puhalovich,
C.Langendorf,
P.Thompson,
J.Vandekerckhove,
K.Gevaert,
J.C.Whisstock,
and
P.I.Bird
(2009).
Structure of granzyme C reveals an unusual mechanism of protease autoinhibition.
|
| |
Proc Natl Acad Sci U S A,
106,
5587-5592.
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|
PDB codes:
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E.Di Cera
(2009).
Serine proteases.
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| |
IUBMB Life,
61,
510-515.
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|
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|
|
E.Persson,
and
O.H.Olsen
(2009).
Activation loop 3 and the 170 loop interact in the active conformation of coagulation factor VIIa.
|
| |
FEBS J,
276,
3099-3109.
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|
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J.A.Huntington
(2009).
Slow thrombin is zymogen-like.
|
| |
J Thromb Haemost,
7,
159-164.
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|
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W.Niu,
Z.Chen,
L.A.Bush-Pelc,
A.Bah,
P.S.Gandhi,
and
E.Di Cera
(2009).
Mutant N143P reveals how Na+ activates thrombin.
|
| |
J Biol Chem,
284,
36175-36185.
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|
PDB codes:
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|
K.D.Rand,
M.D.Andersen,
O.H.Olsen,
T.J.Jørgensen,
H.Ostergaard,
O.N.Jensen,
H.R.Stennicke,
and
E.Persson
(2008).
The origins of enhanced activity in factor VIIa analogs and the interplay between key allosteric sites revealed by hydrogen exchange mass spectrometry.
|
| |
J Biol Chem,
283,
13378-13387.
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M.E.Dumez,
N.Teller,
F.Mercier,
T.Tanaka,
I.Vandenberghe,
M.Vandenbranden,
B.Devreese,
A.Luxen,
J.M.Frère,
A.Matagne,
A.Jacquet,
M.Galleni,
and
A.Chevigné
(2008).
Activation Mechanism of Recombinant Der p 3 Allergen Zymogen: CONTRIBUTION OF CYSTEINE PROTEASE Der p 1 AND EFFECT OF PROPEPTIDE GLYCOSYLATION.
|
| |
J Biol Chem,
283,
30606-30617.
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J.Tóth,
Z.Simon,
P.Medveczky,
L.Gombos,
B.Jelinek,
L.Szilágyi,
L.Gráf,
and
A.Málnási-Csizmadia
(2007).
Site directed mutagenesis at position 193 of human trypsin 4 alters the rate of conformational change during activation: role of local internal viscosity in protein dynamics.
|
| |
Proteins,
67,
1119-1127.
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N.N.Nickerson,
L.Prasad,
L.Jacob,
L.T.Delbaere,
and
M.J.McGavin
(2007).
Activation of the SspA serine protease zymogen of Staphylococcus aureus proceeds through unique variations of a trypsinogen-like mechanism and is dependent on both autocatalytic and metalloprotease-specific processing.
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J Biol Chem,
282,
34129-34138.
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O.H.Olsen,
K.D.Rand,
H.Østergaard,
and
E.Persson
(2007).
A combined structural dynamics approach identifies a putative switch in factor VIIa employed by tissue factor to initiate blood coagulation.
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Protein Sci,
16,
671-682.
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K.D.Rand,
T.J.Jørgensen,
O.H.Olsen,
E.Persson,
O.N.Jensen,
H.R.Stennicke,
and
M.D.Andersen
(2006).
Allosteric activation of coagulation factor VIIa visualized by hydrogen exchange.
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J Biol Chem,
281,
23018-23024.
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O.Guvench,
D.J.Price,
and
C.L.Brooks
(2005).
Receptor rigidity and ligand mobility in trypsin-ligand complexes.
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Proteins,
58,
407-417.
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C.Hink-Schauer,
E.Estébanez-Perpiñá,
E.Wilharm,
P.Fuentes-Prior,
W.Klinkert,
W.Bode,
and
D.E.Jenne
(2002).
The 2.2-A crystal structure of human pro-granzyme K reveals a rigid zymogen with unusual features.
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J Biol Chem,
277,
50923-50933.
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PDB codes:
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F.X.Gomis-Rüth,
A.Bayés,
G.Sotiropoulou,
G.Pampalakis,
T.Tsetsenis,
V.Villegas,
F.X.Avilés,
and
M.Coll
(2002).
The structure of human prokallikrein 6 reveals a novel activation mechanism for the kallikrein family.
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J Biol Chem,
277,
27273-27281.
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PDB code:
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R.M.Camire
(2002).
Prothrombinase assembly and S1 site occupation restore the catalytic activity of FXa impaired by mutation at the sodium-binding site.
|
| |
J Biol Chem,
277,
37863-37870.
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W.Rocchia,
S.Sridharan,
A.Nicholls,
E.Alexov,
A.Chiabrera,
and
B.Honig
(2002).
Rapid grid-based construction of the molecular surface and the use of induced surface charge to calculate reaction field energies: applications to the molecular systems and geometric objects.
|
| |
J Comput Chem,
23,
128-137.
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A.Pasternak,
A.White,
C.J.Jeffery,
N.Medina,
M.Cahoon,
D.Ringe,
and
L.Hedstrom
(2001).
The energetic cost of induced fit catalysis: Crystal structures of trypsinogen mutants with enhanced activity and inhibitor affinity.
|
| |
Protein Sci,
10,
1331-1342.
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PDB codes:
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S.I.Choi,
H.W.Song,
J.W.Moon,
and
B.L.Seong
(2001).
Recombinant enterokinase light chain with affinity tag: expression from Saccharomyces cerevisiae and its utilities in fusion protein technology.
|
| |
Biotechnol Bioeng,
75,
718-724.
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A.Pasternak,
D.Ringe,
and
L.Hedstrom
(1999).
Comparison of anionic and cationic trypsinogens: the anionic activation domain is more flexible in solution and differs in its mode of BPTI binding in the crystal structure.
|
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Protein Sci,
8,
253-258.
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PDB codes:
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G.Moont,
H.A.Gabb,
and
M.J.Sternberg
(1999).
Use of pair potentials across protein interfaces in screening predicted docked complexes.
|
| |
Proteins,
35,
364-373.
|
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H.Jing,
K.J.Macon,
D.Moore,
L.J.DeLucas,
J.E.Volanakis,
and
S.V.Narayana
(1999).
Structural basis of profactor D activation: from a highly flexible zymogen to a novel self-inhibited serine protease, complement factor D.
|
| |
EMBO J,
18,
804-814.
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PDB code:
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L.C.Petersen,
E.Persson,
and
P.O.Freskgård
(1999).
Thermal effects on an enzymatically latent conformation of coagulation factor VIIa.
|
| |
Eur J Biochem,
261,
124-129.
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A.Pasternak,
X.Liu,
T.Y.Lin,
and
L.Hedstrom
(1998).
Activating a zymogen without proteolytic processing: mutation of Lys15 and Asn194 activates trypsinogen.
|
| |
Biochemistry,
37,
16201-16210.
|
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A.R.Khan,
and
M.N.James
(1998).
Molecular mechanisms for the conversion of zymogens to active proteolytic enzymes.
|
| |
Protein Sci,
7,
815-836.
|
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|
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D.E.Hourcade,
L.M.Mitchell,
and
T.J.Oglesby
(1998).
A conserved element in the serine protease domain of complement factor B.
|
| |
J Biol Chem,
273,
25996-26000.
|
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M.T.Stubbs,
M.Renatus,
and
W.Bode
(1998).
An active zymogen: unravelling the mystery of tissue-type plasminogen activator.
|
| |
Biol Chem,
379,
95.
|
|
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T.Selwood,
D.R.McCaslin,
and
N.M.Schechter
(1998).
Spontaneous inactivation of human tryptase involves conformational changes consistent with conversion of the active site to a zymogen-like structure.
|
| |
Biochemistry,
37,
13174-13183.
|
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A.J.Gale,
X.Sun,
M.J.Heeb,
and
J.H.Griffin
(1997).
Nonenzymatic anticoagulant activity of the mutant serine protease Ser360Ala-activated protein C mediated by factor Va.
|
| |
Protein Sci,
6,
132-140.
|
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|
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M.Renatus,
M.T.Stubbs,
R.Huber,
P.Bringmann,
P.Donner,
W.D.Schleuning,
and
W.Bode
(1997).
Catalytic domain structure of vampire bat plasminogen activator: a molecular paradigm for proteolysis without activation cleavage.
|
| |
Biochemistry,
36,
13483-13493.
|
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PDB code:
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M.Renatus,
R.A.Engh,
M.T.Stubbs,
R.Huber,
S.Fischer,
U.Kohnert,
and
W.Bode
(1997).
Lysine 156 promotes the anomalous proenzyme activity of tPA: X-ray crystal structure of single-chain human tPA.
|
| |
EMBO J,
16,
4797-4805.
|
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PDB code:
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S.H.Ke,
G.S.Coombs,
K.Tachias,
D.R.Corey,
and
E.L.Madison
(1997).
Optimal subsite occupancy and design of a selective inhibitor of urokinase.
|
| |
J Biol Chem,
272,
20456-20462.
|
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|
|
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|
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S.H.Ke,
K.Tachias,
D.Lamba,
W.Bode,
and
E.L.Madison
(1997).
Identification of a hydrophobic exosite on tissue type plasminogen activator that modulates specificity for plasminogen.
|
| |
J Biol Chem,
272,
1811-1816.
|
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J.L.Markley,
and
W.M.Westler
(1996).
Protonation-state dependence of hydrogen bond strengths and exchange rates in a serine protease catalytic triad: bovine chymotrypsinogen A.
|
| |
Biochemistry,
35,
11092-11097.
|
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|
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J.Otlewski,
A.Sywula,
M.Kolasinski,
and
D.Krowarsch
(1996).
Unfolding kinetics of bovine trypsinogen.
|
| |
Eur J Biochem,
242,
601-607.
|
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|
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K.Tachias,
and
E.L.Madison
(1996).
Converting tissue-type plasminogen activator into a zymogen.
|
| |
J Biol Chem,
271,
28749-28752.
|
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L.Hedstrom,
T.Y.Lin,
and
W.Fast
(1996).
Hydrophobic interactions control zymogen activation in the trypsin family of serine proteases.
|
| |
Biochemistry,
35,
4515-4523.
|
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|
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F.X.Gomis-Rüth,
M.Gómez,
W.Bode,
R.Huber,
and
F.X.Avilés
(1995).
The three-dimensional structure of the native ternary complex of bovine pancreatic procarboxypeptidase A with proproteinase E and chymotrypsinogen C.
|
| |
EMBO J,
14,
4387-4394.
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PDB code:
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J.Wang,
B.Brdar,
and
E.Reich
(1995).
Structure and function of microplasminogen: I. Methionine shuffling, chemical proteolysis, and proenzyme activation.
|
| |
Protein Sci,
4,
1758-1767.
|
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|
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L.A.Collins-Racie,
J.M.McColgan,
K.L.Grant,
E.A.DiBlasio-Smith,
J.M.McCoy,
and
E.R.LaVallie
(1995).
Production of recombinant bovine enterokinase catalytic subunit in Escherichia coli using the novel secretory fusion partner DsbA.
|
| |
Biotechnology (N Y),
13,
982-987.
|
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|
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|
|
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L.Strandberg,
and
E.L.Madison
(1995).
Variants of tissue-type plasminogen activator with substantially enhanced response and selectivity toward fibrin co-factors.
|
| |
J Biol Chem,
270,
23444-23449.
|
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|
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G.Bulaj,
and
J.Otlewski
(1994).
Denaturation of free and complexed bovine trypsinogen with the calcium ion, dipeptide Ile-Val and basic pancreatic trypsin inhibitor (Kunitz).
|
| |
Eur J Biochem,
223,
939-946.
|
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|
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B.Bax,
M.Blaber,
G.Ferguson,
M.J.Sternberg,
and
P.H.Walls
(1993).
Prediction of the three-dimensional structures of the nerve growth factor and epidermal growth factor binding proteins (kallikreins) and an hypothetical structure of the high molecular weight complex of epidermal growth factor with its binding protein.
|
| |
Protein Sci,
2,
1229-1241.
|
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|
|
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.
|
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PDB code:
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|
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S.J.Prestrelski,
D.M.Byler,
and
M.N.Liebman
(1992).
Generation of a substructure library for the description and classification of protein secondary structure. II. Application to spectra-structure correlations in Fourier transform infrared spectroscopy.
|
| |
Proteins,
14,
440-450.
|
|
|
|
|
|
|
W.Bode,
and
R.Huber
(1992).
Natural protein proteinase inhibitors and their interaction with proteinases.
|
| |
Eur J Biochem,
204,
433-451.
|
|
|
|
|
|
|
T.Earnest,
E.Fauman,
C.S.Craik,
and
R.Stroud
(1991).
1.59 A structure of trypsin at 120 K: comparison of low temperature and room temperature structures.
|
| |
Proteins,
10,
171-187.
|
|
|
PDB code:
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|
|
T.K.Vu,
D.T.Hung,
V.I.Wheaton,
and
S.R.Coughlin
(1991).
Molecular cloning of a functional thrombin receptor reveals a novel proteolytic mechanism of receptor activation.
|
| |
Cell,
64,
1057-1068.
|
|
|
|
|
|
|
J.R.Vasquez,
L.B.Evnin,
J.N.Higaki,
and
C.S.Craik
(1989).
An expression system for trypsin.
|
| |
J Cell Biochem,
39,
265-276.
|
|
|
|
|
|
|
J.S.Miller,
E.H.Westin,
and
L.B.Schwartz
(1989).
Cloning and characterization of complementary DNA for human tryptase.
|
| |
J Clin Invest,
84,
1188-1195.
|
|
|
|
|
|
|
T.M.Harrison,
M.A.Chidgey,
W.J.Brammar,
and
G.J.Adams
(1989).
The pro-peptide is not necessary for active renin secretion from transfected mammalian cells.
|
| |
Proteins,
5,
259-265.
|
|
|
|
|
|
|
T.L.Burgess,
C.S.Craik,
L.Matsuuchi,
and
R.B.Kelly
(1987).
In vitro mutagenesis of trypsinogen: role of the amino terminus in intracellular protein targeting to secretory granules.
|
| |
J Cell Biol,
105,
659-668.
|
|
|
|
|
|
|
A.Light,
C.T.Duda,
T.W.Odorzynski,
and
W.G.Moore
(1986).
Refolding of serine proteinases.
|
| |
J Cell Biochem,
31,
19-26.
|
|
|
|
|
|
|
B.J.Stevenson,
O.Hagenbüchle,
and
P.K.Wellauer
(1986).
Sequence organisation and transcriptional regulation of the mouse elastase II and trypsin genes.
|
| |
Nucleic Acids Res,
14,
8307-8330.
|
|
|
|
|
|
|
K.W.Watt,
P.J.Lee,
T.M'Timkulu,
W.P.Chan,
and
R.Loor
(1986).
Human prostate-specific antigen: structural and functional similarity with serine proteases.
|
| |
Proc Natl Acad Sci U S A,
83,
3166-3170.
|
|
|
|
|
|
|
C.A.Davis,
D.C.Riddell,
M.J.Higgins,
J.J.Holden,
and
B.N.White
(1985).
A gene family in Drosophila melanogaster coding for trypsin-like enzymes.
|
| |
Nucleic Acids Res,
13,
6605-6619.
|
|
|
|
|
|
|
G.D.Rose,
W.B.Young,
and
L.M.Gierasch
(1983).
Interior turns in globular proteins.
|
| |
Nature,
304,
654-657.
|
|
|
|
|
|
|
W.F.van Gunsteren,
H.J.Berendsen,
J.Hermans,
W.G.Hol,
and
J.P.Postma
(1983).
Computer simulation of the dynamics of hydrated protein crystals and its comparison with x-ray data.
|
| |
Proc Natl Acad Sci U S A,
80,
4315-4319.
|
|
|
|
|
|
|
J.L.Finney,
B.J.Gellatly,
I.C.Golton,
and
J.Goodfellow
(1980).
Solvent effects and polar interactions in the structural stability and dynamics of globular proteins.
|
| |
Biophys J,
32,
17-33.
|
|
|
|
|
|
|
M.Faraggi,
M.H.Klapper,
and
L.M.Dorfman
(1978).
Application of pulse radiolysis to the study of proteins: chymotrypsin and trypsin.
|
| |
Biophys J,
24,
307-317.
|
|
|
|
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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
