1SGI

Crystal structure of the anticoagulant slow form of thrombin

Summary for 1SGI

• Entry DOI: 10.2210/pdb1sgi/pdb
• Related: 1SFQ 1SG8 1SGI 1SHH
• Descriptor: thrombin, 2-acetamido-2-deoxy-beta-D-glucopyranose, ... (4 entities in total)
• Functional Keywords: thrombin, allostery, hydrolase
• Biological source: Homo sapiens (human); More
• Total number of polymer chains: 4
• Total formula weight: 68023.69

Authors

Pineda, A.O.,Carrell, C.J.,Bush, L.A.,Prasad, S.,Caccia, S.,Chen, Z.W.,Mathews, F.S.,Di Cera, E. (deposition date: 2004-02-23, release date: 2004-06-08, Last modification date: 2024-10-30)

Primary citation

Pineda, A.O.,Carrell, C.J.,Bush, L.A.,Prasad, S.,Caccia, S.,Chen, Z.W.,Mathews, F.S.,Di Cera, E.
Molecular dissection of na+ binding to thrombin.
J.Biol.Chem., 279:31842-31853, 2004

PubMed Abstract: Na(+) binding near the primary specificity pocket of thrombin promotes the procoagulant, prothrombotic, and signaling functions of the enzyme. The effect is mediated allosterically by a communication between the Na(+) site and regions involved in substrate recognition. Using a panel of 78 Ala mutants of thrombin, we have mapped the allosteric core of residues that are energetically linked to Na(+) binding. These residues are Asp-189, Glu-217, Asp-222, and Tyr-225, all in close proximity to the bound Na(+). Among these residues, Asp-189 shares with Asp-221 the important function of transducing Na(+) binding into enhanced catalytic activity. None of the residues of exosite I, exosite II, or the 60-loop plays a significant role in Na(+) binding and allosteric transduction. X-ray crystal structures of the Na(+)-free (slow) and Na(+)-bound (fast) forms of thrombin, free or bound to the active site inhibitor H-d-Phe-Pro-Arg-chloromethyl-ketone, document the conformational changes induced by Na(+) binding. The slow --> fast transition results in formation of the Arg-187:Asp-222 ion pair, optimal orientation of Asp-189 and Ser-195 for substrate binding, and a significant shift of the side chain of Glu-192 linked to a rearrangement of the network of water molecules that connect the bound Na(+) to Ser-195 in the active site. The changes in the water network and the allosteric core explain the thermodynamic signatures linked to Na(+) binding and the mechanism of thrombin activation by Na(+). The role of the water network uncovered in this study establishes a new paradigm for the allosteric regulation of thrombin and other Na(+)-activated enzymes involved in blood coagulation and the immune response.

PubMed: 15152000
DOI: 10.1074/jbc.M401756200

Experimental method

X-RAY DIFFRACTION (2.3 Å)