3JZ1

Crystal structure of human thrombin mutant N143P in E:Na+ form

Summary for 3JZ1

• Entry DOI: 10.2210/pdb3jz1/pdb
• Related: 1SHH 3BEI 3JZ2
• Descriptor: Thrombin light chain, Thrombin heavy chain, SODIUM ION, ... (7 entities in total)
• Functional Keywords: serine protease, acute phase, blood coagulation, cleavage on pair of basic residues, disease mutation, disulfide bond, gamma-carboxyglutamic acid, glycoprotein, hydrolase, kringle, protease, secreted, zymogen
• Biological source: Homo sapiens (human); More
• Total number of polymer chains: 2
• Total formula weight: 34343.06

Authors

Niu, W.,Chen, Z.,Bush-Pelc, L.A.,Bah, A.,Gandhi, P.S.,Di Cera, E. (deposition date: 2009-09-22, release date: 2009-10-20, Last modification date: 2023-09-06)

Primary citation

Niu, W.,Chen, Z.,Bush-Pelc, L.A.,Bah, A.,Gandhi, P.S.,Di Cera, E.
Mutant N143P reveals how Na+ activates thrombin
J.Biol.Chem., 284:36175-36185, 2009

PubMed Abstract: The molecular mechanism of thrombin activation by Na(+) remains elusive. Its kinetic formulation requires extension of the classical Botts-Morales theory for the action of a modifier on an enzyme to correctly account for the contribution of the E*, E, and E:Na(+) forms. The extended scheme establishes that analysis of k(cat) unequivocally identifies allosteric transduction of Na(+) binding into enhanced catalytic activity. The thrombin mutant N143P features no Na(+)-dependent enhancement of k(cat) yet binds Na(+) with an affinity comparable to that of wild type. Crystal structures of the mutant in the presence and absence of Na(+) confirm that Pro(143) abrogates the important H-bond between the backbone N atom of residue 143 and the carbonyl O atom of Glu(192), which in turn controls the orientation of the Glu(192)-Gly(193) peptide bond and the correct architecture of the oxyanion hole. We conclude that Na(+) activates thrombin by securing the correct orientation of the Glu(192)-Gly(193) peptide bond, which is likely flipped in the absence of cation. Absolute conservation of the 143-192 H-bond in trypsin-like proteases and the importance of the oxyanion hole in protease function suggest that this mechanism of Na(+) activation is present in all Na(+)-activated trypsin-like proteases.

PubMed: 19846563
DOI: 10.1074/jbc.M109.069500

Experimental method

X-RAY DIFFRACTION (1.6 Å)