2A0Q

Structure of thrombin in 400 mM potassium chloride

Summary for 2A0Q

• Entry DOI: 10.2210/pdb2a0q/pdb
• Descriptor: Thrombin, light chain, Thrombin, heavy chain, 2-acetamido-2-deoxy-alpha-D-glucopyranose, ... (6 entities in total)
• Functional Keywords: serine protease, hydrolase
• Biological source: Homo sapiens (human); More
• Total number of polymer chains: 4
• Total formula weight: 66386.65

Authors

Papaconstantinou, M.,Carrell, C.J.,Pineda, A.O.,Bobofchak, K.M.,Mathews, F.S.,Flordellis, C.S.,Maragoudakis, M.E.,Tsopanoglou, N.E.,di Cera, E. (deposition date: 2005-06-16, release date: 2005-07-12, Last modification date: 2024-10-30)

Primary citation

Papaconstantinou, M.E.,Carrell, C.J.,Pineda, A.O.,Bobofchak, K.M.,Mathews, F.S.,Flordellis, C.S.,Maragoudakis, M.E.,Tsopanoglou, N.E.,Di Cera, E.
Thrombin Functions through Its RGD Sequence in a Non-canonical Conformation.
J.Biol.Chem., 280:29393-29396, 2005

PubMed Abstract: Previous studies have suggested that thrombin interacts with integrins in endothelial cells through its RGD (Arg-187, Gly-188, Asp-189) sequence. All existing crystal structures of thrombin show that most of this sequence is buried under the 220-loop and therefore interaction via RGD implies either partial unfolding of the enzyme or its proteolytic digestion. Here, we demonstrate that surface-absorbed thrombin promotes attachment and migration of endothelial cells through interaction with alpha(v)beta(3) and alpha(5)beta(1) integrins. Using site-directed mutants of thrombin we prove that this effect is mediated by the RGD sequence and does not require catalytic activity. The effect is abrogated when residues of the RGD sequence are mutated to Ala and is not observed with proteases like trypsin and tissue-type plasminogen activator, unless the RGD sequence is introduced at position 187-189. The potent inhibitor hirudin does not abrogate the effect, suggesting that thrombin functions through its RGD sequence in a non-canonical conformation. A 1.9-Angstroms resolution crystal structure of free thrombin grown in the presence of high salt (400 mm KCl) shows two molecules in the asymmetric unit, one of which assumes an unprecedented conformation with the autolysis loop shifted 20 Angstroms away from its canonical position, the 220-loop entirely disordered, and the RGD sequence exposed to the solvent.

PubMed: 15998637
DOI: 10.1074/jbc.C500248200

Experimental method

X-RAY DIFFRACTION (1.9 Å)