The Structure of a Complex of Recombinant Hirudin and Human α-Thrombin

• Published in: Science (American Association for the Advancement of Science) Vol. 249; no. 4966; pp. 277 - 280
• Main Authors: Rydel, Timothy J., Ravichandran, K. G., Tulinsky, A., Bode, Wolfram, Huber, Robert, Roitsch, Carolyn, Fenton, John W.
• Format: Journal Article
• Language: English
• Published: Washington, DC American Society for the Advancement of Science 20.07.1990; American Association for the Advancement of Science
• Subjects: Active sites; alpha -thrombin; Amino Acid Sequence; Atomic interactions; Atoms; Binding Sites; Biochemistry; Biological and medical sciences; Chemical inhibitors; Crystal structure; Crystalline structure; Disulfides; Fundamental and applied biological sciences. Psychology; Glycoproteins; Hirudins - metabolism; Humans; Hydrogen bonds; Models, Molecular; Molecular biophysics; Molecular Sequence Data; Molecules; Nitrogen; Protein Binding; Protein Conformation; Recombinant Proteins - metabolism; Rotation; Structure in molecular biology; Thrombin; Thrombin - metabolism; X-ray crystallography; X-Ray Diffraction; Enzyme; Enzyme inhibitor; Thrombin; Molecular complex; NMR spectrometry; Recombinant protein; Computer aid; Crystalline structure
• ISSN: 0036-8075; 1095-9203
• DOI: 10.1126/science.2374926

The crystallographic structure of a recombinant hirudin-thrombin complex has been solved at 2.3 angstrom (Å) resolution. Hirudin consists of an NH$_2$-terminal globular domain and a long (39 Å) COOH-terminal extended domain. Residues Ile$^1$ to Tyr$^3$ of hirudin form a parallel β-strand with Ser$^{214}$ to Glu$^{217}$ of thrombin with the nitrogen atom of Ile$^1$ making a hydrogen bond with Ser$^{195}$ Oγ atom of the catalytic site, but the specificity pocket of thrombin is not involved in the interaction. The COOH-terminal segment makes numerous electrostatic interactions with an anion-binding exosite of thrombin, whereas the last five residues are in a helical loop that forms many hydrophobic contacts. In all, 27 of the 65 residues of hirudin have contacts less than 4.0 Å with thrombin (10 ion pairs and 23 hydrogen bonds). Such abundant interactions may account for the high affinity and specificity of hirudin.