PDBsum entry 2a1d

Hydrolase/hydrolase inhibitor

PDB id: 2a1d

Contents

Protein chains

41 a.a. *

259 a.a. *

282 a.a. *

Ligands

0G6 ×2

NAG

Metals

_NA ×2

* Residue conservation analysis

PDB id:

2a1d

Name:

Hydrolase/hydrolase inhibitor

Title:

Staphylocoagulase bound to bovine thrombin

Structure:

Thrombin. Chain: a, e. Fragment: thrombin light chain. Synonym: coagulation factor ii. Thrombin. Chain: b, f. Fragment: thrombin heavy chain. Synonym: coagulation factor ii. Staphylocoagulase.

Source:

Bos taurus. Cattle. Organism_taxid: 9913. Staphylococcus aureus. Organism_taxid: 1280. Expressed in: escherichia coli. Expression_system_taxid: 562

Biol. unit:

Trimer (from PQS)

Resolution:

3.50Å R-factor: 0.233 R-free: 0.306

Authors:

R.Friedrich,P.Panizzi,S.Kawabata,W.Bode,P.E.Bock,P.Fuentes-Prior

Key ref:

R.Friedrich et al. (2006). Structural basis for reduced staphylocoagulase-mediated bovine prothrombin activation. J Biol Chem, 281, 1188-1195. PubMed id: 16230338 DOI: 10.1074/jbc.M507957200

Date:

20-Jun-05 Release date: 27-Sep-05

Protein chains

P00735  (THRB_BOVIN) -  Prothrombin from Bos taurus

Seq: 625 a.a.

Struc: 41 a.a.

Protein chains

P00735  (THRB_BOVIN) -  Prothrombin from Bos taurus

Seq: 625 a.a.

Struc: 259 a.a.

Protein chains

P17855  (STC2_STAAU) -  Staphylocoagulase from Staphylococcus aureus

Seq: 715 a.a.

Struc: 282 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

Enzyme reactions

• Enzyme class: Chains A, B, E, F: E.C.3.4.21.5 - thrombin.
• Reaction: Preferential cleavage: Arg-|-Gly; activates fibrinogen to fibrin and releases fibrinopeptide A and B.

DOI no: 10.1074/jbc.M507957200

J Biol Chem 281:1188-1195 (2006)

PubMed id: 16230338

Structural basis for reduced staphylocoagulase-mediated bovine prothrombin activation.

R.Friedrich, P.Panizzi, S.Kawabata, W.Bode, P.E.Bock, P.Fuentes-Prior.

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.

Selected figure(s)

Figure 3.
Crystal structure of the SC-(1-325)·bovineα-thrombin complex. The thrombin moiety is shown as a solid surface colored according to the electrostatic surface potential, from strongly negative (deep red) to strongly positive (deep blue). The boomerang-shaped SC molecule is comprised of the N-terminal domain D1 (helices α[1]^D1 to α[3]^D1) and the C-terminal domain D2 (helices α[1]^D2 to α[6]^D2) and is represented as a green ribbon. The anion-binding exosite I, the active site (Ser^195), and the 148 loop (Trp^148) of bovine α-thrombin are labeled. The N terminus of SC (defined from ^SCSer^7 onwards) is placed close to the Ile^16 activation pocket of thrombin but is disordered in the complexes with bovine and human thrombin and extends away from the enzyme surface.

Figure 4.
Structural characterization of SC-(1-325). A, the two major helix bundles α[1]^D1-α[3]^D1 (yellow) and α[1]^D2-α[3]^D2 (orange), which are shown superimposed here, are structurally related. Side chains of all topologically equivalent residues conserved in both domains are shown with all their non-hydrogen atoms and labeled. B, close-up of the D1-D2 interdomain interface, with important residues shown with their full side chains. Notice the multiple contacts between polar/charged side chains (e.g. ^SCGlu^54-^SCArg^209), which separate the strictly conserved ^SCLeu^146 side chain from bulk solvent.

The above figures are reprinted from an Open Access publication published by the ASBMB: J Biol Chem (2006, 281, 1188-1195) copyright 2006.

Figures were selected by an automated process.