Experimental Data Snapshot
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(2003) Nature 425: 535-539
Many bacterial pathogens secrete proteins that activate host trypsinogen-like enzyme precursors, most notably the proenzymes of the blood coagulation and fibrinolysis systems. Staphylococcus aureus, an important human pathogen implicated in sepsis and endocarditis, secretes the cofactor staphylocoagulase, which activates prothrombin, without the usual proteolytic cleavages, to directly initiate blood clotting. Here we present the 2.2 A crystal structures of human alpha-thrombin and prethrombin-2 bound to a fully active staphylocoagulase variant. The cofactor consists of two domains, each with three-helix bundles; this is a novel fold that is distinct from known serine proteinase activators, particularly the streptococcal plasminogen activator streptokinase. The staphylocoagulase fold is conserved in other bacterial plasma-protein-binding factors and extracellular-matrix-binding factors. Kinetic studies confirm the importance of isoleucine 1 and valine 2 at the amino terminus of staphylocoagulase for zymogen activation. In addition to making contacts with the 148 loop and (pro)exosite I of prethrombin-2, staphylocoagulase inserts its N-terminal peptide into the activation pocket of bound prethrombin-2, allosterically inducing functional catalytic machinery. These investigations demonstrate unambiguously the validity of the zymogen-activation mechanism known as 'molecular sexuality'.
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Biological assembly 1 assigned by authors and generated by PISA (software)
 Explore in 3D: Structure |Sequence Annotations |Validation Report |Ligand Interaction (0ZJ)
Biological assembly 2 assigned by authors and generated by PISA (software)
Macromolecule Content 
Entity ID: 1 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Thrombin light and heavy chains | A, C [auth D] | 291 | Homo sapiens | Mutation(s): 0  EC: 3.4.21.5 | ![]() |
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for P00734 (Homo sapiens) Explore P00734  Go to UniProtKB:  P00734 | |||||
PHAROS:  P00734 GTEx:  ENSG00000180210  | |||||
Entity Groups  | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | P00734 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Entity ID: 2 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Staphylocoagulase | B [auth C], D [auth F] | 281 | Staphylococcus aureus | Mutation(s): 0  | ![]() |
UniProt | |||||
Find proteins for Q846V4 (Staphylococcus aureus) Explore Q846V4  Go to UniProtKB:  Q846V4 | |||||
Entity Groups  | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | Q846V4 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Entity ID: 3 | |||||
|---|---|---|---|---|---|
| ID | Chains | Name | Type/Class | 2D Diagram | 3D Interactions |
| PRD_000377 (0ZJ) Query on PRD_000377 | E [auth A], K [auth D] | N(alpha)-((acetylthio)acetyl)-phenylalanyl-prolyl-arginine chloromethyl ketone | Peptide-like / Inhibitor | ||
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 181.16 | α = 90 |
| b = 102.34 | β = 129.91 |
| c = 135.54 | γ = 90 |
| Software Name | Purpose |
|---|---|
| CNS | refinement |
| DENZO | data reduction |
| SCALEPACK | data scaling |
| CNS | phasing |
RCSB PDB Core Operations are funded by theU.S. National Science Foundation (DBI-2321666), theUS Department of Energy (DE-SC0019749), and theNational Cancer Institute,National Institute of Allergy and Infectious Diseases, andNational Institute of General Medical Sciences of theNational Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.