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PDBsum entry 2a1d
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Hydrolase/hydrolase inhibitor
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PDB id
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2a1d
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Contents |
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41 a.a.
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259 a.a.
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282 a.a.
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References listed in PDB file
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Key reference
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Title
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Structural basis for reduced staphylocoagulase-Mediated bovine prothrombin activation.
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Authors
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R.Friedrich,
P.Panizzi,
S.Kawabata,
W.Bode,
P.E.Bock,
P.Fuentes-Prior.
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Ref.
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J Biol Chem, 2006,
281,
1188-1195.
[DOI no: ]
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PubMed id
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Abstract
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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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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.
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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.
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The above figures are
reprinted
from an Open Access publication published by the ASBMB:
J Biol Chem
(2006,
281,
1188-1195)
copyright 2006.
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