1UMA

ALPHA-THROMBIN (HIRUGEN) COMPLEXED WITH NA-(N,N-DIMETHYLCARBAMOYL)-ALPHA-AZALYSINE

Summary for 1UMA

• Entry DOI: 10.2210/pdb1uma/pdb
• Descriptor: ALPHA-THROMBIN, HIRUDIN I, 2-acetamido-2-deoxy-beta-D-glucopyranose, ... (6 entities in total)
• Functional Keywords: hydrolase-hydrolase inhibitor complex, serine protease, kringle, alpha-thrombin- hirugen complex, hydrolase/hydrolase inhibitor
• Biological source: Homo sapiens (human); More
• Total number of polymer chains: 3
• Total formula weight: 35897.87

Authors

Nardini, M.,Pesce, A.,Rizzi, M.,Casale, E.,Ferraccioli, R.,Balliano, G.,Milla, P.,Ascenzi, P.,Bolognesi, M. (deposition date: 1996-03-26, release date: 1996-11-08, Last modification date: 2024-10-09)

Primary citation

Nardini, M.,Pesce, A.,Rizzi, M.,Casale, E.,Ferraccioli, R.,Balliano, G.,Milla, P.,Ascenzi, P.,Bolognesi, M.
Human alpha-thrombin inhibition by the active site titrant N alpha-(N,N-dimethylcarbamoyl)-alpha-azalysine p-nitrophenyl ester: a comparative kinetic and X-ray crystallographic study.
J.Mol.Biol., 258:851-859, 1996

PubMed Abstract: Kinetics for the hydrolysis of the chromogenic active site titrant N alpha-(N,N-dimethylcarbamoyl)-alpha-azalysine p-nitrophenyl ester (Dmc-azaLys-ONp) catalyzed by bovine beta-trypsin, bovine alpha-thrombin, human alpha-thrombin, human Lys77-plasmin, human urinary kallikrein, the M(r) 33,000 and M(r) 54,000 species of human urokinase, as well as by porcine pancreatic beta-kallikrein-A and B have been obtained between pH 6.0 and 8.0, at 21.0 degrees C. Moreover, the three dimensional structure of the human alpha-thrombin-(hirugen).Dmc-azaLys acyl.enzyme complex has been analyzed and refined by X-ray crystallography at 2.0 A resolution (R-factor = 0.168). As observed for bovine beta-trypsin, the acylating inhibitor molecule is covalently bound to the Ser195 catalytic residue, filling the human alpha-thrombin S1 primary specificity subsite with its lysyl side-group. However, the carbonyl group of the scissile human alpha-thrombin.Dmc-azaLys acyl bond does not occupy properly the oxyanion binding hole. At variance from the bovine beta-trypsin.Dmc-azaLys acyl.enzyme structure, a second, not covalently bound, inhibitor molecule, partly shielded by the 60-insertion loop of human alpha-thrombin, is contacting the enzyme "aryl-binding site".

PubMed: 8637015
DOI: 10.1006/jmbi.1996.0292

Experimental method

X-RAY DIFFRACTION (2 Å)