5JDU

Crystal structure for human thrombin mutant D189A

Summary for 5JDU

• Entry DOI: 10.2210/pdb5jdu/pdb
• Related: 1SHH
• Descriptor: Thrombin light chain, Thrombin heavy chain, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose, ... (6 entities in total)
• Functional Keywords: serine protease, coagulation, conformational equilibrium, hydrolase
• Biological source: Homo sapiens (Human); More
• Total number of polymer chains: 4
• Total formula weight: 68031.18

Authors

Pozzi, N.,Chen, Z.,Di Cera, E. (deposition date: 2016-04-17, release date: 2016-07-13, Last modification date: 2024-10-30)

Primary citation

Pozzi, N.,Zerbetto, M.,Acquasaliente, L.,Tescari, S.,Frezzato, D.,Polimeno, A.,Gohara, D.W.,Di Cera, E.,De Filippis, V.
Loop Electrostatics Asymmetry Modulates the Preexisting Conformational Equilibrium in Thrombin.
Biochemistry, 55:3984-3994, 2016

PubMed Abstract: Thrombin exists as an ensemble of active (E) and inactive (E*) conformations that differ in their accessibility to the active site. Here we show that redistribution of the E*-E equilibrium can be achieved by perturbing the electrostatic properties of the enzyme. Removal of the negative charge of the catalytic Asp102 or Asp189 in the primary specificity site destabilizes the E form and causes a shift in the 215-217 segment that compromises substrate entrance. Solution studies and existing structures of D102N document stabilization of the E* form. A new high-resolution structure of D189A also reveals the mutant in the collapsed E* form. These findings establish a new paradigm for the control of the E*-E equilibrium in the trypsin fold.

PubMed: 27347732
DOI: 10.1021/acs.biochem.6b00385

Experimental method

X-RAY DIFFRACTION (1.7 Å)