2A1D image
Deposition Date 2005-06-20
Release Date 2005-09-27
Last Version Date 2024-10-30
Entry Detail
PDB ID:
2A1D
Title:
Staphylocoagulase bound to bovine thrombin
Biological Source:
Source Organism:
Staphylococcus aureus (Taxon ID: 1280)
Bos taurus (Taxon ID: 9913)
Host Organism:
Method Details:
Experimental Method:
Resolution:
3.50 Å
R-Value Free:
0.30
R-Value Work:
0.23
Space Group:
C 1 2 1
Macromolecular Entities
Polymer Type:polypeptide(L)
Molecule:thrombin
Gene (Uniprot):F2
Chain IDs:A, D (auth: E)
Chain Length:41
Number of Molecules:2
Biological Source:Bos taurus
Polymer Type:polypeptide(L)
Molecule:thrombin
Gene (Uniprot):F2
Chain IDs:B, E (auth: F)
Chain Length:259
Number of Molecules:2
Biological Source:Bos taurus
Polymer Type:polypeptide(L)
Molecule:Staphylocoagulase
Chain IDs:C (auth: D), F (auth: H)
Chain Length:329
Number of Molecules:2
Biological Source:Staphylococcus aureus
Modified Residue
Compound ID Chain ID Parent Comp ID Details 2D Image
ASN B ASN GLYCOSYLATION SITE
Peptide-like Molecules
PRD_000020
Primary Citation
Structural Basis for Reduced Staphylocoagulase-mediated Bovine Prothrombin Activation
J.Biol.Chem. 281 1188 1195 (2006)
PMID: 16230338 DOI: 10.1074/jbc.M507957200

Abstact

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.

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Primary Citation of related structures