1RD3

2.5A Structure of Anticoagulant Thrombin Variant E217K

Summary for 1RD3

• Entry DOI: 10.2210/pdb1rd3/pdb
• Descriptor: Prothrombin, alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-alpha-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-alpha-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose, ... (7 entities in total)
• Functional Keywords: hydrolase
• Biological source: Homo sapiens (human); More
• Total number of polymer chains: 4
• Total formula weight: 70056.48

Authors

Carter, W.J.,Myles, T.,Leung, L.L.,Huntington, J.A. (deposition date: 2003-11-05, release date: 2004-05-04, Last modification date: 2024-11-13)

Primary citation

Carter, W.J.,Myles, T.,Gibbs, C.S.,Leung, L.L.,Huntington, J.A.
Crystal Structure of Anticoagulant Thrombin Variant E217K Provides Insights into Thrombin Allostery
J.Biol.Chem., 279:26387-26394, 2004

PubMed Abstract: Thrombin is the ultimate protease of the blood clotting cascade and plays a major role in its own regulation. The ability of thrombin to exhibit both pro- and anti-coagulant properties has spawned efforts to turn thrombin into an anticoagulant for therapeutic purposes. This quest culminated in the identification of the E217K variant through scanning and saturation mutagenesis. The antithrombotic properties of E217K thrombin are derived from its inability to convert fibrinogen to a fibrin clot while maintaining its thrombomodulin-dependent ability to activate the anticoagulant protein C pathway. Here we describe the 2.5-A crystal structure of human E217K thrombin, which displays a dramatic restructuring of the geometry of the active site. Of particular interest is the repositioning of Glu-192, which hydrogen bonds to the catalytic Ser-195 and which results in the complete occlusion of the active site and the destruction of the oxyanion hole. Substrate binding pockets are further blocked by residues previously implicated in thrombin allostery. We have concluded that the E217K mutation causes the allosteric inactivation of thrombin by destabilizing the Na(+) binding site and that the structure thus may represent the Na(+)-free, catalytically inert "slow" form.

PubMed: 15075325
DOI: 10.1074/jbc.M402364200

Experimental method

X-RAY DIFFRACTION (2.5 Å)