1NQ9

Crystal Structure of Antithrombin in the Pentasaccharide-Bound Intermediate State

Summary for 1NQ9

• Entry DOI: 10.2210/pdb1nq9/pdb
• Related: 1E03 1E04 1E05 1OYH
• Related PRD ID: PRD_900031
• Descriptor: Antithrombin-III, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, 3,4-di-O-methyl-2,6-di-O-sulfo-alpha-D-glucopyranose-(1-4)-2,3-di-O-methyl-beta-D-glucopyranuronic acid-(1-4)-2,3,6-tri-O-sulfo-alpha-D-glucopyranose-(1-4)-3-O-methyl-2-O-sulfo-alpha-L-idopyranuronic acid-(1-4)-methyl 2,3,6-tri-O-sulfo-alpha-D-glucopyranoside, ... (5 entities in total)
• Functional Keywords: thrombin; inhibition; heparin analogue; serine protease inhibitor, blood clotting
• Biological source: Homo sapiens (human); More
• Cellular location: Secreted, extracellular space: P01008
• Total number of polymer chains: 2
• Total formula weight: 103240.48

Authors

Huntington, J.A.,Johnson, D.J.D. (deposition date: 2003-01-21, release date: 2003-09-30, Last modification date: 2024-10-16)

Primary citation

Johnson, D.J.D.,Huntington, J.A.
Crystal Structure of Antithrombin in a Heparin-Bound Intermediate State
Biochemistry, 42:8712-8719, 2003

PubMed Abstract: Antithrombin is activated as an inhibitor of the coagulation proteases through its specific interaction with a heparin pentasaccharide. The binding of heparin induces a global conformational change in antithrombin which results in the freeing of its reactive center loop for interaction with target proteases and a 1000-fold increase in heparin affinity. The allosteric mechanism by which the properties of antithrombin are altered by its interactions with the specific pentasaccharide sequence of heparin is of great interest to the medical and protein biochemistry communities. Heparin binding has previously been characterized as a two-step, three-state mechanism where, after an initial weak interaction, antithrombin undergoes a conformational change to its high-affinity state. Although the native and heparin-activated states have been determined through protein crystallography, the number and magnitude of conformational changes render problematic the task of determining which account for the improved heparin affinity and how the heparin binding region is linked to the expulsion of the reactive center loop. Here we present the structure of an intermediate pentasaccharide-bound conformation of antithrombin which has undergone all of the conformational changes associated with activation except loop expulsion and helix D elongation. We conclude that the basis of the high-affinity state is not improved interaction with the pentasaccharide but a lowering of the global free energy due to conformational changes elsewhere in antithrombin. We suggest a mechanism in which the role of helix D elongation is to lock antithrombin in the five-stranded fully activated conformation.

PubMed: 12873131
DOI: 10.1021/bi034524y

Experimental method

X-RAY DIFFRACTION (2.6 Å)