title: Crystal structure of the thrombin-hirudin complex: a novel mode of serine protease inhibition.
abstract: Thrombin is a serine protease that plays a central role in blood coagulation. It is inhibited by hirudin, a polypeptide of 65 amino acids, through the formation of a tight, noncovalent complex. Tetragonal crystals of the complex formed between human alpha-thrombin and recombinant hirudin (variant 1) have been grown and the crystal structure of this complex has been determined to a resolution of 2.95 A. This structure shows that hirudin inhibits thrombin by a previously unobserved mechanism. In contrast to other inhibitors of serine proteases, the specificity of hirudin is not due to interaction with the primary specificity pocket of thrombin, but rather through binding at sites both close to and distant from the active site. The carboxyl tail of hirudin (residues 48-65) wraps around thrombin along the putative fibrinogen secondary binding site. This long groove extends from the active site cleft and is flanked by the thrombin loops 35-39 and 70-80. Hirudin makes a number of ionic and hydrophobic interactions with thrombin in this area. Furthermore hirudin binds with its N-terminal three residues Val, Val, Tyr to the thrombin active site cleft. Val1 occupies the position P2 and Tyr3 approximately the position P3 of the synthetic inhibitor D-Phe-Pro-ArgCH2Cl. Thus the hirudin polypeptide chain runs in a direction opposite to that expected for fibrinogen and that observed for the substrate-like inhibitor D-Phe-Pro-ArgCH2Cl.
authors.affiliation: Department of Biotechnology, Ciba-Geigy Ltd, CH-4002 Basel, Switzerland.
authors.forename: M G
authors.initials: MG
authors.lastname: Grütter
authors.forename: J P
authors.initials: JP
authors.lastname: Priestle
authors.forename: J
authors.initials: J
authors.lastname: Rahuel
authors.forename: H
authors.initials: H
authors.lastname: Grossenbacher
authors.forename: W
authors.initials: W
authors.lastname: Bode
authors.forename: J
authors.initials: J
authors.lastname: Hofsteenge
authors.forename: S R
authors.initials: SR
authors.lastname: Stone
mesh_terms: D000595:Amino Acid Sequence; D001665:Binding Sites; D003196:Computer Graphics; D003460:Crystallization; D006629:Hirudins / Q000378:metabolism*; D006801:Humans; D008958:Models, Molecular; D008969:Molecular Sequence Data; D009842:Oligopeptides; D011487:Protein Conformation; D015842:Serine Proteinase Inhibitors; D013917:Thrombin / Q000378:metabolism*; D014961:X-Ray Diffraction
chemical_list: D006629:Hirudins; D009842:Oligopeptides; D015842:Serine Proteinase Inhibitors; D013917:Thrombin