2A1D

Staphylocoagulase bound to bovine thrombin

Summary for 2A1D

• Entry DOI: 10.2210/pdb2a1d/pdb
• Related: 1NU7 1NU9
• Related PRD ID: PRD_000020
• Descriptor: thrombin, Staphylocoagulase, D-phenylalanyl-N-[(2S,3S)-6-{[amino(iminio)methyl]amino}-1-chloro-2-hydroxyhexan-3-yl]-L-prolinamide, ... (6 entities in total)
• Functional Keywords: prothrombin activator, hydrolase-hydrolase inhibitor complex, hydrolase/hydrolase inhibitor
• Biological source: Staphylococcus aureus; More
• Total number of polymer chains: 6
• Total formula weight: 147388.57

Authors

Friedrich, R.,Panizzi, P.,Kawabata, S.,Bode, W.,Bock, P.E.,Fuentes-Prior, P. (deposition date: 2005-06-20, release date: 2005-09-27, Last modification date: 2024-10-30)

Primary citation

Friedrich, R.,Panizzi, P.,Kawabata, S.,Bode, W.,Bock, P.E.,Fuentes-Prior, P.
Structural Basis for Reduced Staphylocoagulase-mediated Bovine Prothrombin Activation
J.Biol.Chem., 281:1188-1195, 2006

PubMed Abstract: Staphylocoagulase (SC) is a protein secreted by the human pathogen, Staphylococcus aureus, that activates human prothrombin (ProT) by inducing a conformational change. SC-bound ProT efficiently clots fibrinogen, thus bypassing the physiological blood coagulation pathway. The crystal structure of a fully active SC fragment, SC-(1-325), bound to human prethrombin 2 showed that the SC-(1-325) N terminus inserts into the Ile(16) pocket of prethrombin 2, thereby inducing expression of a functional catalytic site in the cognate zymogen without peptide bond cleavage. As shown here, SC-(1-325) binds to bovine and human ProT with similar affinity but activates the bovine zymogen only very poorly. By contrast to the approximately 2-fold difference in chromogenic substrate kinetic constants between human thrombin and the SC-(1-325).human (pro)thrombin complexes, SC-(1-325).bovine ProT shows a 3,500-fold lower k(cat)/K(m) compared with free bovine thrombin, because of a 47-fold increase in K(m) and a 67-fold decrease in k(cat). The SC-(1-325).bovine ProT complex is approximately 5,800-fold less active compared with its human counterpart. Comparison of human and bovine fibrinogen as substrates of human and bovine thrombin and the SC-(1-325).(pro)thrombin complexes indicates that the species specificity of SC-(1-325) cofactor activity is determined primarily by differences in conformational activation of bound ProT. These results suggest that the catalytic site in the SC-(1-325).bovine ProT complex is incompletely formed. The current crystal structure of SC-(1-325).bovine thrombin reveals that SC would dock similarly to the bovine proenzyme, whereas the bovine (pro)thrombin-characteristic residues Arg(144) and Arg(145) would likely interfere with insertion of the SC N terminus, thus explaining the greatly reduced activation of bovine ProT.

PubMed: 16230338
DOI: 10.1074/jbc.M507957200

Experimental method

X-RAY DIFFRACTION (3.5 Å)