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* Residue conservation analysis
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PDB id:
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Hydrolase/hydrolase inhibitor
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Title:
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Structure of the ternary microplasmin-staphylokinase-microplasmin complex: a proteinase-cofactor-substrate complex in action
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Structure:
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Plasminogen. Chain: a, b. Fragment: peptidase s1 catalytic domain. Synonym: plasmin heavy chain a, activation peptide, angiostatin, plasmin heavy chain a, short form, plasmin light chain b. Engineered: yes. Staphylokinase. Chain: c. Synonym: sak42d
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Source:
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Homo sapiens. Human. Organism_taxid: 9606. Gene: plg. Expressed in: escherichia coli. Expression_system_taxid: 562. Staphylococcus phage 42d.M. Organism_taxid: 10715
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Biol. unit:
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Tetramer (from
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Resolution:
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2.65Å
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R-factor:
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0.204
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R-free:
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0.287
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Authors:
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M.A.A.Parry,C.Fernandez-Catalan,A.Bergner,R.Huber,K.Hopfner, B.Schlott,K.Guehrs,W.Bode
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Key ref:
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M.A.Parry
et al.
(1998).
The ternary microplasmin-staphylokinase-microplasmin complex is a proteinase-cofactor-substrate complex in action.
Nat Struct Biol,
5,
917-923.
PubMed id:
DOI:
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Date:
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04-Sep-98
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Release date:
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02-Sep-99
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PROCHECK
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Headers
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References
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Enzyme class:
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Chains A, B:
E.C.3.4.21.7
- plasmin.
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Reaction:
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Preferential cleavage: Lys-|-Xaa > Arg-|-Xaa; higher selectivity than trypsin. Converts fibrin into soluble products.
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DOI no:
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Nat Struct Biol
5:917-923
(1998)
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PubMed id:
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The ternary microplasmin-staphylokinase-microplasmin complex is a proteinase-cofactor-substrate complex in action.
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M.A.Parry,
C.Fernandez-Catalan,
A.Bergner,
R.Huber,
K.P.Hopfner,
B.Schlott,
K.H.Gührs,
W.Bode.
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ABSTRACT
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The serine proteinase plasmin is the key fibrinolytic enzyme that dissolves
blood clots and also promotes cell migration and tissue remodeling. Here, we
report the 2.65 A crystal structure of a ternary complex of
microplasmin-staphylokinase bound to a second microplasmin. The staphylokinase
'cofactor' does not affect the active-site geometry of the plasmin 'enzyme', but
instead modifies its subsite specificity by providing additional docking sites
for enhanced presentation of the plasminogen 'substrate' to the 'enzymes's'
active site. The activation loop of the plasmin 'substrate', cleaved in these
crystals, can be reconstructed to show how it runs across the active site of the
plasmin 'enzyme' prior to activation cleavage. This is the first experimental
structure of a productive proteinase-cofactor-macromolecular substrate complex.
Furthermore, it provides a template for the design of improved plasminogen
activators and plasmin inhibitors with considerable therapeutical potential.
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Selected figure(s)
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Figure 4.
Figure 4. Stereo section of the final 2.65 Å 2F[obs] - F[
calc] electron density map (blue) contoured at 1  around
the interface between  Pl
enzyme (green carbons) and SAK (yellow carbons). The view is
similar to the standard orientation shown in Figs 2 and 5. Side
chains from both molecules form an extended network of salt
bridges and charged hydrogen bonds. The strong Arg
175(719)−Glu 46SAK salt bridge is buried from the solvent by
Tyr 44SAK. Furthermore, Arg 43SAK and Tyr 44SAK protrude into
the active site of  Pl,
providing more narrow subsite boundaries. Figure produced with
SETOR^28.
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Figure 5.
Figure 5. Standard view from the Pl
substrate towards the active site of the Pl
enzyme in complex with SAK (shown as a solid surface).
Coloring of the Pl
enzyme is made according to the electrostatic potential. a,
Intact Pg activation loop (Lys 10(557)−Val 21(567)) as modeled
on residues Lys 10(557) and Cys 20(566) of the cleaved substrate
and on the tripeptidyl moiety bound to the Pl
enzyme. b, Cleaved Pg activation loop as seen in the crystal
structure. Only the N- and the C-terminal ends of the cleaved
Pl
substrate (Lys 10(557)−Gly 14(560) and Val 16(562)-Val
21(567)) are shown. Figure produced with GRASP^30.
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The above figures are
reprinted
by permission from Macmillan Publishers Ltd:
Nat Struct Biol
(1998,
5,
917-923)
copyright 1998.
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Figures were
selected
by an automated process.
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Literature references that cite this PDB file's key reference
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PubMed id
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Reference
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K.Okada,
S.Ueshima,
H.Matsuno,
N.Nagai,
N.Kawao,
M.Tanaka,
and
O.Matsuo
(2011).
A synthetic peptide derived from staphylokinase enhances plasminogen activation by tissue-type plasminogen activator.
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J Thromb Haemost,
9,
997.
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H.N.David,
B.Haelewyn,
J.J.Risso,
N.Colloc'h,
and
J.H.Abraini
(2010).
Xenon is an inhibitor of tissue-plasminogen activator: adverse and beneficial effects in a rat model of thromboembolic stroke.
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J Cereb Blood Flow Metab,
30,
718-728.
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J.He,
R.Xu,
X.Chen,
K.Jia,
X.Zhou,
and
K.Zhu
(2010).
Simultaneous elimination of T- and B-cell epitope by structure-based mutagenesis of single Glu80 residue within recombinant staphylokinase.
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Acta Biochim Biophys Sin (Shanghai),
42,
209-215.
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J.Potempa,
and
R.N.Pike
(2009).
Corruption of Innate Immunity by Bacterial Proteases.
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J Innate Immun,
1,
70-87.
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J.P.Lopez-Atalaya,
B.D.Roussel,
D.Levrat,
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Y.Hommet,
K.Benchenane,
H.Castel,
J.Leprince,
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H.Vaudry,
K.U.Petersen,
J.S.Santos,
C.Ali,
and
D.Vivien
(2008).
Toward safer thrombolytic agents in stroke: molecular requirements for NMDA receptor-mediated neurotoxicity.
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J Cereb Blood Flow Metab,
28,
1212-1221.
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T.Jin,
M.Bokarewa,
Y.Zhu,
and
A.Tarkowski
(2008).
Staphylokinase reduces plasmin formation by endogenous plasminogen activators.
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Eur J Haematol,
81,
8.
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H.Chen,
W.Mo,
H.Su,
Y.Zhang,
and
H.Song
(2007).
Characterization of a novel bifunctional mutant of staphylokinase with platelet-targeted thrombolysis and antiplatelet aggregation activities.
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BMC Mol Biol,
8,
88.
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N.N.Nickerson,
L.Prasad,
L.Jacob,
L.T.Delbaere,
and
M.J.McGavin
(2007).
Activation of the SspA serine protease zymogen of Staphylococcus aureus proceeds through unique variations of a trypsinogen-like mechanism and is dependent on both autocatalytic and metalloprotease-specific processing.
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J Biol Chem,
282,
34129-34138.
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P.Panizzi,
R.Friedrich,
P.Fuentes-Prior,
K.Richter,
P.E.Bock,
and
W.Bode
(2006).
Fibrinogen substrate recognition by staphylocoagulase.(pro)thrombin complexes.
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J Biol Chem,
281,
1179-1187.
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R.Friedrich,
P.Panizzi,
S.Kawabata,
W.Bode,
P.E.Bock,
and
P.Fuentes-Prior
(2006).
Structural basis for reduced staphylocoagulase-mediated bovine prothrombin activation.
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J Biol Chem,
281,
1188-1195.
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PDB code:
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T.Bae,
T.Baba,
K.Hiramatsu,
and
O.Schneewind
(2006).
Prophages of Staphylococcus aureus Newman and their contribution to virulence.
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Mol Microbiol,
62,
1035-1047.
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F.Carafoli,
D.Y.Chirgadze,
T.L.Blundell,
and
E.Gherardi
(2005).
Crystal structure of the beta-chain of human hepatocyte growth factor-like/macrophage stimulating protein.
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FEBS J,
272,
5799-5807.
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PDB code:
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N.A.Copeland,
and
C.Kleanthous
(2005).
The role of an activating peptide in protease-mediated suicide of Escherichia coli K12.
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J Biol Chem,
280,
112-117.
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W.Bode
(2005).
The structure of thrombin, a chameleon-like proteinase.
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J Thromb Haemost,
3,
2379-2388.
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D.Kirchhofer,
X.Yao,
M.Peek,
C.Eigenbrot,
M.T.Lipari,
K.L.Billeci,
H.R.Maun,
P.Moran,
L.Santell,
C.Wiesmann,
and
R.A.Lazarus
(2004).
Structural and functional basis of the serine protease-like hepatocyte growth factor beta-chain in Met binding and signaling.
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J Biol Chem,
279,
39915-39924.
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PDB code:
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D.O.Beck,
M.A.Bukys,
L.S.Singh,
K.A.Szabo,
and
M.Kalafatis
(2004).
The contribution of amino acid region ASP695-TYR698 of factor V to procofactor activation and factor Va function.
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J Biol Chem,
279,
3084-3095.
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P.Panizzi,
R.Friedrich,
P.Fuentes-Prior,
W.Bode,
and
P.E.Bock
(2004).
The staphylocoagulase family of zymogen activator and adhesion proteins.
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Cell Mol Life Sci,
61,
2793-2798.
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S.Terzyan,
N.Wakeham,
P.Zhai,
K.Rodgers,
and
X.C.Zhang
(2004).
Characterization of Lys-698-to-Met substitution in human plasminogen catalytic domain.
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Proteins,
56,
277-284.
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PDB code:
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C.Hink-Schauer,
E.Estébanez-Perpiñá,
F.C.Kurschus,
W.Bode,
and
D.E.Jenne
(2003).
Crystal structure of the apoptosis-inducing human granzyme A dimer.
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Nat Struct Biol,
10,
535-540.
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PDB code:
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I.P.Gladysheva,
R.B.Turner,
I.Y.Sazonova,
L.Liu,
and
G.L.Reed
(2003).
Coevolutionary patterns in plasminogen activation.
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Proc Natl Acad Sci U S A,
100,
9168-9172.
|
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R.Friedrich,
P.Panizzi,
P.Fuentes-Prior,
K.Richter,
I.Verhamme,
P.J.Anderson,
S.Kawabata,
R.Huber,
W.Bode,
and
P.E.Bock
(2003).
Staphylocoagulase is a prototype for the mechanism of cofactor-induced zymogen activation.
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Nature,
425,
535-539.
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PDB codes:
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S.C.Wu,
F.J.Castellino,
and
S.L.Wong
(2003).
A fast-acting, modular-structured staphylokinase fusion with Kringle-1 from human plasminogen as the fibrin-targeting domain offers improved clot lysis efficacy.
|
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J Biol Chem,
278,
18199-18206.
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V.Sundram,
J.S.Nanda,
K.Rajagopal,
J.Dhar,
A.Chaudhary,
and
G.Sahni
(2003).
Domain truncation studies reveal that the streptokinase-plasmin activator complex utilizes long range protein-protein interactions with macromolecular substrate to maximize catalytic turnover.
|
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J Biol Chem,
278,
30569-30577.
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I.P.Gladysheva,
I.Y.Sazonova,
S.A.Chowdhry,
L.Liu,
R.B.Turner,
and
G.L.Reed
(2002).
Chimerism reveals a role for the streptokinase Beta -domain in nonproteolytic active site formation, substrate, and inhibitor interactions.
|
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J Biol Chem,
277,
26846-26851.
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M.Budayova-Spano,
W.Grabarse,
N.M.Thielens,
H.Hillen,
M.Lacroix,
M.Schmidt,
J.C.Fontecilla-Camps,
G.J.Arlaud,
and
C.Gaboriaud
(2002).
Monomeric structures of the zymogen and active catalytic domain of complement protease c1r: further insights into the c1 activation mechanism.
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Structure,
10,
1509-1519.
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PDB codes:
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M.Wilkens,
and
S.Krishnaswamy
(2002).
The contribution of factor Xa to exosite-dependent substrate recognition by prothrombinase.
|
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J Biol Chem,
277,
9366-9374.
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R.B.Turner,
L.Liu,
I.Y.Sazonova,
and
G.L.Reed
(2002).
Structural elements that govern the substrate specificity of the clot-dissolving enzyme plasmin.
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J Biol Chem,
277,
33068-33074.
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Y.Chen,
G.Song,
F.Jiang,
L.Feng,
X.Zhang,
Y.Ding,
M.Bartlam,
A.Yang,
X.Ma,
S.Ye,
Y.Liu,
H.Tang,
H.Song,
and
Z.Rao
(2002).
Crystal structure of a staphylokinase: variant a model for reduced antigenicity.
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Eur J Biochem,
269,
705-711.
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PDB codes:
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C.Eigenbrot,
D.Kirchhofer,
M.S.Dennis,
L.Santell,
R.A.Lazarus,
J.Stamos,
and
M.H.Ultsch
(2001).
The factor VII zymogen structure reveals reregistration of beta strands during activation.
|
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Structure,
9,
627-636.
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PDB code:
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K.Lähteenmäki,
P.Kuusela,
and
T.K.Korhonen
(2001).
Bacterial plasminogen activators and receptors.
|
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FEMS Microbiol Rev,
25,
531-552.
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M.Murakami,
T.Towatari,
M.Ohuchi,
M.Shiota,
M.Akao,
Y.Okumura,
M.A.Parry,
and
H.Kido
(2001).
Mini-plasmin found in the epithelial cells of bronchioles triggers infection by broad-spectrum influenza A viruses and Sendai virus.
|
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Eur J Biochem,
268,
2847-2855.
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S.Masmoudi,
S.E.Antonarakis,
T.Schwede,
A.M.Ghorbel,
M.Gratri,
M.P.Pappasavas,
M.Drira,
A.Elgaied-Boulila,
M.Wattenhofer,
C.Rossier,
H.S.Scott,
H.Ayadi,
and
M.Guipponi
(2001).
Novel missense mutations of TMPRSS3 in two consanguineous Tunisian families with non-syndromic autosomal recessive deafness.
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Hum Mutat,
18,
101-108.
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K.Okada,
S.Ueshima,
M.Tanaka,
H.Fukao,
and
O.Matsuo
(2000).
Analysis of plasminogen activation by the plasmin-staphylokinase complex in plasma of alpha2-antiplasmin-deficient mice.
|
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Blood Coagul Fibrinolysis,
11,
645-655.
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L.K.Rasmussen,
T.E.Petersen,
M.Etzerodt,
and
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(2000).
Kinetic and structural characterization of a two-domain streptokinase: dissection of domain functionality.
|
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Biochemistry,
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6440-6448.
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P.D.Boxrud,
W.P.Fay,
and
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(2000).
Streptokinase binds to human plasmin with high affinity, perturbs the plasmin active site, and induces expression of a substrate recognition exosite for plasminogen.
|
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J Biol Chem,
275,
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S.Wang,
G.L.Reed,
and
L.Hedstrom
(2000).
Zymogen activation in the streptokinase-plasminogen complex. Ile1 is required for the formation of a functional active site.
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Eur J Biochem,
267,
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Function of the central domain of streptokinase in substrate plasminogen docking and processing revealed by site-directed mutagenesis.
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| |
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W.Bode,
and
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(1999).
Coagulation factor IXa: the relaxed conformation of Tyr99 blocks substrate binding.
|
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Structure,
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PDB code:
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R.G.Miele,
M.Prorok,
V.A.Costa,
and
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(1999).
Glycosylation of asparagine-28 of recombinant staphylokinase with high-mannose-type oligosaccharides results in a protein with highly attenuated plasminogen activator activity.
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| |
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S.Wang,
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and
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Deletion of Ile1 changes the mechanism of streptokinase: evidence for the molecular sexuality hypothesis.
|
| |
Biochemistry,
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C.T.Esmon,
and
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Switching serine protease specificity.
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Nat Struct Biol,
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The most recent references are shown first.
Citation data come partly from CiteXplore and partly
from an automated harvesting procedure. Note that this is likely to be
only a partial list as not all journals are covered by
either method. However, we are continually building up the citation data
so more and more references will be included with time.
Where a reference describes a PDB structure, the PDB
code is
shown on the right.
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Links
