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PDBsum entry 1bda
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Hydrolase/hydrolase inhibitor
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PDB id
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1bda
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Contents |
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* Residue conservation analysis
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References listed in PDB file
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Key reference
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Title
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Lysine 156 promotes the anomalous proenzyme activity of tpa: X-Ray crystal structure of single-Chain human tpa.
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Authors
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M.Renatus,
R.A.Engh,
M.T.Stubbs,
R.Huber,
S.Fischer,
U.Kohnert,
W.Bode.
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Ref.
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EMBO J, 1997,
16,
4797-4805.
[DOI no: ]
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PubMed id
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Abstract
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Tissue type plasminogen activator (tPA) is the physiological initiator of
fibrinolysis, activating plasminogen via highly specific proteolysis; plasmin
then degrades fibrin with relatively broad specificity. Unlike other
chymotrypsin family serine proteinases, tPA is proteolytically active in a
single-chain form. This form is also preferred for therapeutic administration of
tPA in cases of acute myocardial infarction. The proteolytic cleavage which
activates most other chymotrypsin family serine proteinases increases the
catalytic efficiency of tPA only 5- to 10-fold. The X-ray crystal structure of
the catalytic domain of recombinant human single-chain tPA shows that Lys156
forms a salt bridge with Asp194, promoting an active conformation in the
single-chain form. Comparisons with the structures of other serine proteinases
that also possess Lys156, such as trypsin, factor Xa and human urokinase
plasminogen activator (uPA), identify a set of secondary interactions which are
required for Lys156 to fulfil this activating role. These findings help explain
the anomalous single-chain activity of tPA and may suggest strategies for design
of new therapeutic plasminogen activators.
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Figure 1.
Figure 1 Stereo ribbon plot of the catalytic domain of sc-tPA in
'standard' orientation. The inhibitor
(dansyl-Glu-Gly-Arg-chloromethylketone) shown by green sticks is
covalently bonded to Ser195 and His57 of the catalytic triad.
Key sc-tPA residues are shown as yellow sticks: Asp102, His57
and Ser195 of the catalytic triad; Asp189 at the base of the S1
specificity pocket; and Asp194 and Lys156 which form a salt
bridge in the activation pocket. The red ribbon shows the
conformation of the N-terminal activation loop which includes
the plasmin cleavage site. Some loops arranged around the active
site are labelled: the mainly disordered 37 loop and the 110
loop to the east; the partially disordered 186 loop to the
south-west is in proximity to the activation loop. The figure
was made with SETOR (Evans, 1993).
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Figure 2.
Figure 2 Stereo plot of the activation domain environment of
sc-tPA involving residues of the activation pocket, the
activation loop and Lys156. Lys156 (blue) stabilizes the active
conformation of sc-tPA via formation of a salt bridge with
Asp194 (red). The strength of this interaction is presumably
increased by the concerted solvent shielding effect of the (red)
activation loop and of the hydrophobic residues Ile16, Phe21 and
His144 (yellow). Lysines 17 and 143, which were considered
potential activators of sc-tPA (Wallén et al., 1983; Petersen et
al., 1990) are also shown (blue). Residues His188, Arg186A and
Asn186F of the 186 loop (yellow) are presumed to be responsible
for the conformational stabilization of this loop.
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The above figures are
reprinted
from an Open Access publication published by Macmillan Publishers Ltd:
EMBO J
(1997,
16,
4797-4805)
copyright 1997.
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Secondary reference #1
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Title
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Catalytic domain structure of vampire bat plasminogen activator: a molecular paradigm for proteolysis without activation cleavage.
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Authors
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M.Renatus,
M.T.Stubbs,
R.Huber,
P.Bringmann,
P.Donner,
W.D.Schleuning,
W.Bode.
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Ref.
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Biochemistry, 1997,
36,
13483-13493.
[DOI no: ]
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PubMed id
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Secondary reference #2
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Title
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The 2.3 a crystal structure of the catalytic domain of recombinant two-Chain human tissue-Type plasminogen activator.
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Authors
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D.Lamba,
M.Bauer,
R.Huber,
S.Fischer,
R.Rudolph,
U.Kohnert,
W.Bode.
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Ref.
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J Mol Biol, 1996,
258,
117-135.
[DOI no: ]
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PubMed id
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Figure 3.
Figure 3. Stereo section of the final electron density map (blue) around the bound benzamidine molecule (center),
superimposed on the t-PA model. Standard view as in Figures 1 and 2. Of the protein structure, only the entrance frame
Trpc215 to Cysc220 (around the benzamidine), the catalytic triad Serc195, Hisc57 and Aspc102 (to the east), and Lysc143
and Tyrc151 (to the south) are displayed; the spherical density east of the benzamidine molecule, which partially hides
the active Ser195, represents the bound phosphate ion. Contouring is at 1.0s. Figure made with O (Jones et al., 1991).
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Figure 5.
Figure 5. Stereo plot of the hypothetical docking complex of the catalytic domain (white connections) and kringle
2 (yellow connections; De Vos et al., 1992) in the covalent two-domain t-PA variant. The domains are superimposed
with a blue (catalytic domain) and a green Connolly surface (kringle 2 domain). This view is approximately rotated
135° from the standard orientation around a horizontal axis, so that the active site is now pointing to the east/back.
Charged side-chains of catalytic domain residues presumably involved in fibrin binding, and kringle 2 residues forming
the lysine binding site are labeled (chymotrypsinogen and kringle nomenclature). The plot was made with MAIN (Turk,
1992).
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The above figures are
reproduced from the cited reference
with permission from Elsevier
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