The ternary complex of antithrombin-anhydrothrombin-heparin reveals the basis of inhibitor specificity.
Antithrombin, the principal physiological inhibitor of the blood coagulation proteinase thrombin, requires heparin as a cofactor. We report the crystal structure of the rate-determining encounter complex formed between antithrombin, anhydrothrombin and an optimal synthetic 16-mer oligosaccharide. The antithrombin reactive center loop projects from the serpin body and adopts a canonical conformation that makes extensive backbone and side chain contacts from P5 to P6' with thrombin's restrictive specificity pockets, including residues in the 60-loop. These contacts rationalize many earlier mutagenesis studies on thrombin specificity. The 16-mer oligosaccharide is just long enough to form the predicted bridge between the high-affinity pentasaccharide-binding site on antithrombin and the highly basic exosite 2 on thrombin, validating the design strategy for this synthetic heparin. The protein-protein and protein-oligosaccharide interactions together explain the basis for heparin activation of antithrombin as a thrombin inhibitor.
Dementiev
Alexey
A
Department of Biochemistry and Molecular Genetics, College of Medicine, University of Illinois at Chicago, 900 S. Ashland, Chicago, Illinois 60607, USA.
Petitou
Maurice
M
Herbert
Jean-Marc
JM
Gettins
Peter G W
PG
D000991:Antithrombins / Q000737:chemistry*; D001665:Binding Sites; D018360:Crystallography, X-Ray; D005343:Fibrinolytic Agents / Q000494:pharmacology*; D006025:Glycosaminoglycans / Q000737:chemistry; D006493:Heparin / Q000737:chemistry*; D006801:Humans; D008956:Models, Chemical; D008958:Models, Molecular; D009844:Oligosaccharides / Q000737:chemistry; D011485:Protein Binding; D011487:Protein Conformation; D017434:Protein Structure, Tertiary; D011506:Proteins / Q000737:chemistry; D013917:Thrombin / Q000737:chemistry*
D000991:Antithrombins; D005343:Fibrinolytic Agents; D006025:Glycosaminoglycans; D009844:Oligosaccharides; D011506:Proteins; D006493:Heparin; D013917:Thrombin