The refined 1.9 A crystal structure of human alpha-thrombin: interaction with D-Phe-Pro-Arg chloromethylketone and significance of the Tyr-Pro-Pro-Trp insertion segment.Bode, W., Mayr, I., Baumann, U., Huber, R., Stone, S.R., Hofsteenge, J.
(1989) EMBO J. 8: 3467-3475
- PubMed: 2583108
- Also Cited By: 1DWE, 1DWD, 1DWC, 1DWB
- PubMed Abstract:
- The Electrostatic Properties of Thrombin: Importance for Structural Stabilization and Ligand Binding
Karshikov, A.,Bode, W.
(1993) Semin.Thromb.Hemostasis 19: 334
- Electrostatic Interactions in the Association of Proteins: An Analysis of the Thrombin-Hirudin Complex
Karshikov, A.,Bode, W.,Tulinsky, A.,Stone, S.R.
(1992) Protein Sci. 1: 727
- Geometry of Binding of the Benzamidine-and Arginine-Based Inhibitors N Alpha-(2-Naphthyl-Sulphonyl-Glycyl)-Dl-P-Amidinophe
Bode, W.,Turk, D.,Stuerzebecher, J.
(1990) Eur.J.Biochem. 193: 175
- The Interaction of Thrombin with Fibrinogen. A Structural Basis for its Specificity
Stubbs, M.T.,Oschkinat, H.,Mayr, I.,Huber, R.,Angliker, H.,Stone, S.R.,Bode, W.
(1992) Eur.J.Biochem. 206: 187
- The Spatial Structure of Thrombin as a Guide to its Multiple Sites of Interaction
Bode, W.,Stubbs, M.
(1993) Semin.Thromb.Hemostasis 19: 321
- Refined 2.3 Angstroms X-Ray Crystal Structure of Bovine Thrombin Complexes Formed with the Benzamidine and Arginine-Based Thrombin Inhibitors Napap, 4-Tapap and Mqpa. A Starting Point for Improving Anti-Thrombotics
Brandstetter, H.,Turk, D.,Hoeffken, H.W.,Grosse, D.,Stuerzebecher, J.,Martin, P.D.,Edwards, B.F.P.,Bode, W.
(1992) J.Mol.Biol. 226: 1085
- Human D-Phe-Pro-Arg-Ch2-Alpha-Thrombin Crystallization and Diffraction Data
Skrzypczak-Jankun, E.,Rydel, T.J.,Tulinsky, A.,Fenton II, J.W.,Mann, K.G.
(1989) J.Mol.Biol. 206: 755
- X-Ray Crystal Structures of Human Alpha-Thrombin and of the Human Thrombin-Hirudin Complex
Bode, W.,Huber, R.,Rydel, T.J.,Tulinsky, A.
(1992) Thrombin: Structure and Function --: 3
- Crystal Structure of the Thrombin-Hirudin Complex: A Novel Mode of Serine Protease Inhibition
Gruetter, M.G.,Priestle, J.P.,Rahnel, J.,Grossenbacher, H.,Bode, W.,Hofsteenge, J.,Stone, S.R.
(1990) Embo J. 9: 2361
- The Refined 1.9-Angstroms Crystal Structure of D-Phe-Pro-Arg Chloromethylketone-Inhibited Human Alpha-Thrombin. Structure Analysis, Overall Structure, Electrostatic Properties, Detailed Active-Site Geometry, and Structure-Function Properties
Bode, W.,Turk, D.,Karshikov, A.
(1992) Protein Sci. 1: 426
- Refined Structure of the Hirudin-Thrombin Complex
Rydel, T.J.,Tulinsky, A.,Bode, W.,Huber, R.
(1991) J.Mol.Biol. 221: 583
- The Structure of a Complex of Recombinant Hirudin and Human Alpha-Thrombin
Rydel, T.J.,Ravichandran, K.G.,Tulinsky, A.,Bode, W.,Huber, R.,Roitsch, C.,Fenton II, J.W.
(1990) Science 249: 277
A stoichiometric complex formed between human alpha-thrombin and D-Phe-Pro-Arg chloromethylketone was crystallized in an orthorhombic crystal form. Orientation and position of a starting model derived from homologous modelling were determined by Patt ...
A stoichiometric complex formed between human alpha-thrombin and D-Phe-Pro-Arg chloromethylketone was crystallized in an orthorhombic crystal form. Orientation and position of a starting model derived from homologous modelling were determined by Patterson search methods. The thrombin model was completed in a cyclic modelling-crystallographic refinement procedure to a final R-value of 0.171 for X-ray data to 1.92 A. The structure is in full agreement with published cDNA sequence data. The A-chain, ordered only in its central part, is positioned along the molecular surface opposite to the active site. The B-chain exhibits the characteristic polypeptide fold of trypsin-like proteinases. Several extended insertions form, however, large protuberances; most important for interaction with macromolecular substrates is the characteristic thrombin loop around Tyr60A-Pro60B-Pro60C-Trp60D (chymotrypsinogen numbering) and the enlarged loop around the unique Trp148. The former considerably restricts the active site cleft and seems likely to be responsible for poor binding of most natural proteinase inhibitors to thrombin. The exceptional specificity of D-Phe-Pro-Arg chloromethylketone can be explained by a hydrophobic cage formed by Ile174, Trp215, Leu99, His57, Tyr60A and Trp60D. The narrow active site cleft, with a more polar base and hydrophobic rims, extends towards the arginine-rich surface of loop Lys70-Glu80 that probably represents part of the anionic binding region for hirudin and fibrinogen.
Max-Planck-Institut für Biochemie, Martinsried, FRG.