2B5T

2.1 Angstrom structure of a nonproductive complex between antithrombin, synthetic heparin mimetic SR123781 and two S195A thrombin molecules

Summary for 2B5T

• Entry DOI: 10.2210/pdb2b5t/pdb
• Related: 1NQ9 1T1F 1TB6
• Descriptor: Thrombin, 2-acetamido-2-deoxy-beta-D-glucopyranose, Antithrombin-III, ... (11 entities in total)
• Functional Keywords: blood coagulation, blood clotting
• Biological source: Homo sapiens (human); More
• Total number of polymer chains: 5
• Total formula weight: 128613.87

Authors

Johnson, D.J.,Li, W.,Luis, S.A.,Carrell, R.W.,Huntington, J.A. (deposition date: 2005-09-29, release date: 2006-09-19, Last modification date: 2024-11-13)

Primary citation

Johnson, D.J.,Langdown, J.,Li, W.,Luis, S.A.,Baglin, T.P.,Huntington, J.A.
Crystal structure of monomeric native antithrombin reveals a novel reactive center loop conformation.
J.Biol.Chem., 281:35478-35486, 2006

PubMed Abstract: The poor inhibitory activity of circulating antithrombin (AT) is critical to the formation of blood clots at sites of vascular damage. AT becomes an efficient inhibitor of the coagulation proteases only after binding to a specific heparin pentasaccharide, which alters the conformation of the reactive center loop (RCL). The molecular basis of this activation event lies at the heart of the regulation of hemostasis and accounts for the anticoagulant properties of the low molecular weight heparins. Although several structures of AT have been solved, the conformation of the RCL in native AT remains unknown because of the obligate crystal contact between the RCL of native AT and its latent counterpart. Here we report the crystallographic structure of a variant of AT in its monomeric native state. The RCL shifted approximately 20 A, and a salt bridge was observed between the P1 residue (Arg-393) and Glu-237. This contact explains the effect of mutations at the P1 position on the affinity of AT for heparin and also the properties of AT-Truro (E237K). The relevance of the observed conformation was verified through mutagenesis studies and by solving structures of the same variant in different crystal forms. We conclude that the poor inhibitory activity of the circulating form of AT is partially conferred by intramolecular contacts that restrain the RCL, orient the P1 residue away from attacking proteases, and additionally block the exosite utilized in protease recognition.

PubMed: 16973611
DOI: 10.1074/jbc.M607204200

Experimental method

X-RAY DIFFRACTION (2.1 Å)