5TO3

Crystal structure of thrombin mutant W215A/E217A fused to EGF456 of thrombomodulin via a 31-residue linker and bound to PPACK

Summary for 5TO3

• Entry DOI: 10.2210/pdb5to3/pdb
• Related: 1DX5
• Related PRD ID: PRD_000020
• Descriptor: Prothrombin, Prothrombin,Thrombomodulin, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-beta-D-mannopyranose-(1-4)-beta-D-mannopyranose-(1-4)-alpha-D-mannopyranose-(1-4)-[beta-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, ... (8 entities in total)
• Functional Keywords: hydrolase, autoactivation, thrombin-thrombomodulin fusion protein
• Biological source: Homo sapiens (Human); More
• Total number of polymer chains: 2
• Total formula weight: 52180.71

Authors

Barranco-Medina, S.,Murphy, M.,Pelc, L.,Chen, Z.,Di Cera, E.,Pozzi, N. (deposition date: 2016-10-16, release date: 2017-03-29, Last modification date: 2024-10-23)

Primary citation

Barranco-Medina, S.,Murphy, M.,Pelc, L.,Chen, Z.,Di Cera, E.,Pozzi, N.
Rational Design of Protein C Activators.
Sci Rep, 7:44596-44596, 2017

PubMed Abstract: In addition to its procoagulant and proinflammatory functions mediated by cleavage of fibrinogen and PAR1, the trypsin-like protease thrombin activates the anticoagulant protein C in a reaction that requires the cofactor thrombomodulin and the endothelial protein C receptor. Once in the circulation, activated protein C functions as an anticoagulant, anti-inflammatory and regenerative factor. Hence, availability of a protein C activator would afford a therapeutic for patients suffering from thrombotic disorders and a diagnostic tool for monitoring the level of protein C in plasma. Here, we present a fusion protein where thrombin and the EGF456 domain of thrombomodulin are connected through a peptide linker. The fusion protein recapitulates the functional and structural properties of the thrombin-thrombomodulin complex, prolongs the clotting time by generating pharmacological quantities of activated protein C and effectively diagnoses protein C deficiency in human plasma. Notably, these functions do not require exogenous thrombomodulin, unlike other anticoagulant thrombin derivatives engineered to date. These features make the fusion protein an innovative step toward the development of protein C activators of clinical and diagnostic relevance.

PubMed: 28294177
DOI: 10.1038/srep44596

Experimental method

X-RAY DIFFRACTION (2.34 Å)