3R3G

Structure of human thrombin with residues 145-150 of murine thrombin.

Summary for 3R3G

• Entry DOI: 10.2210/pdb3r3g/pdb
• Related: 1SHH
• Descriptor: Thrombin Light Chain, Thrombin Heavy Chain, 2-acetamido-2-deoxy-beta-D-glucopyranose, ... (5 entities in total)
• Functional Keywords: serine protease, hydrolase
• Biological source: Homo sapiens (human); More
• Total number of polymer chains: 2
• Total formula weight: 33879.64

Authors

Pozzi, N.,Chen, R.,Chen, Z.,Bah, A.,Di Cera, E. (deposition date: 2011-03-15, release date: 2011-05-11, Last modification date: 2023-09-13)

Primary citation

Pozzi, N.,Chen, R.,Chen, Z.,Bah, A.,Di Cera, E.
Rigidification of the autolysis loop enhances Na(+) binding to thrombin.
Biophys.Chem., 159:6-13, 2011

PubMed Abstract: Binding of Na(+) to thrombin ensures high activity toward physiological substrates and optimizes the procoagulant and prothrombotic roles of the enzyme in vivo. Under physiological conditions of pH and temperature, the binding affinity of Na(+) is weak due to large heat capacity and enthalpy changes associated with binding, and the K(d)=80 mM ensures only 64% saturation of the site at the concentration of Na(+) in the blood (140 mM). Residues controlling Na(+) binding and activation have been identified. Yet, attempts to improve the interaction of Na(+) with thrombin and possibly increase catalytic activity under physiological conditions have so far been unsuccessful. Here we report how replacement of the flexible autolysis loop of human thrombin with the homologous rigid domain of the murine enzyme results in a drastic (up to 10-fold) increase in Na(+) affinity and a significant improvement in the catalytic activity of the enzyme. Rigidification of the autolysis loop abolishes the heat capacity change associated with Na(+) binding observed in the wild-type and also increases the stability of thrombin. These findings have general relevance to protein engineering studies of clotting proteases and trypsin-like enzymes.

PubMed: 21536369
DOI: 10.1016/j.bpc.2011.04.003

Experimental method

X-RAY DIFFRACTION (1.75 Å)