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2a1d
From Proteopedia
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|PDB= 2a1d |SIZE=350|CAPTION= <scene name='initialview01'>2a1d</scene>, resolution 3.50Å | |PDB= 2a1d |SIZE=350|CAPTION= <scene name='initialview01'>2a1d</scene>, resolution 3.50Å | ||
|SITE= | |SITE= | ||
| - | |LIGAND= <scene name='pdbligand= | + | |LIGAND= <scene name='pdbligand=ARM:DEOXY-METHYL-ARGININE'>ARM</scene>, <scene name='pdbligand=DPN:D-PHENYLALANINE'>DPN</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=NDG:2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE'>NDG</scene> |
| - | |ACTIVITY= [http://en.wikipedia.org/wiki/Thrombin Thrombin], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.21.5 3.4.21.5] | + | |ACTIVITY= <span class='plainlinks'>[http://en.wikipedia.org/wiki/Thrombin Thrombin], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.21.5 3.4.21.5] </span> |
|GENE= | |GENE= | ||
| + | |DOMAIN= | ||
| + | |RELATEDENTRY=[[1nu7|1NU7]], [[1nu9|1NU9]] | ||
| + | |RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2a1d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2a1d OCA], [http://www.ebi.ac.uk/pdbsum/2a1d PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=2a1d RCSB]</span> | ||
}} | }} | ||
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[[Category: Kawabata, S.]] | [[Category: Kawabata, S.]] | ||
[[Category: Panizzi, P.]] | [[Category: Panizzi, P.]] | ||
| - | [[Category: NA]] | ||
| - | [[Category: NDG]] | ||
[[Category: protein-protein complex]] | [[Category: protein-protein complex]] | ||
[[Category: prothrombin activator]] | [[Category: prothrombin activator]] | ||
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 01:46:32 2008'' |
Revision as of 22:46, 30 March 2008
| |||||||
| , resolution 3.50Å | |||||||
|---|---|---|---|---|---|---|---|
| Ligands: | , , , | ||||||
| Activity: | Thrombin, with EC number 3.4.21.5 | ||||||
| Related: | 1NU7, 1NU9
| ||||||
| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
Staphylocoagulase bound to bovine thrombin
Overview
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.
About this Structure
2A1D is a Protein complex structure of sequences from Bos taurus and Staphylococcus aureus. Full crystallographic information is available from OCA.
Reference
Structural basis for reduced staphylocoagulase-mediated bovine prothrombin activation., Friedrich R, Panizzi P, Kawabata S, Bode W, Bock PE, Fuentes-Prior P, J Biol Chem. 2006 Jan 13;281(2):1188-95. Epub 2005 Oct 17. PMID:16230338
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