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Catalytic Site Atlas Version 2.2.12
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CSA entry for 1rtf
Original Entry
Title:
Serine protease
Compound:
Two chain tissue plasminogen activator
Mutant:
No
UniProt/Swiss-Prot:
P00750-TPA_HUMAN
EC Class:
3.4.21.68
Other CSA Entries:
Overview of all sites for 1rtf
Homologues of 1rtf
Entries for UniProt/Swiss-Prot: P00750
Entries for EC: 3.4.21.68
Other Databases:
PDB entry: 1rtf
PDBsum entry: 1rtf
UniProt/Swiss-Prot: P00750
IntEnz entry: 3.4.21.68
Literature Report:
Introduction:
Tissue-type plasminogen activator is a serine proteinase of the trypsin-family. It catalyses the activation of the zymogen plasminogen to the fibrin-degrading proteinase plasmin in fibrinolysis.

Human tissue-type plasminogen activator is being studied for therapeutic use in cases such as myocardial infarctions and other thromboembolic disorders.
Mechanism:
Tissue-type plasminogen activator employs a classical serine protease mechanism. Ser 195 acts as a nucleophile to attack the peptide bond and form a tetrahedral intermediate that is stabilised by the backbone NH of Ser 195 and Gly 193. His 57 promotes the nucleophilic attack by deprotonating Ser 195, while Asp 102 functions to modify the pKa of His 57. Collapse of the tetrahedral intermediate with protonation of the departing amine leaving group by His 57 generates an acyl-enzyme intermediate. This is then hydrolysed by a water molecule that is deprotonated by His 57.
Sites:

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Found by:
Literature reference 
PsiBLAST alignment on 1ds2

ResidueChainNumberUniProt numberFunctional part FunctionTargetDescription
HISB 57 0Sidechain
Acid/baseSubstrate
Acid/baseWater
Acid/baseResidue
His 57 acts as a general acid/base catalyst to activate Ser 195 and water to nucleophilic attack and facilitates collapse of the intermediates by proton donation.
Evidence from paper Evidence concerns Evidence type
PubMed ID 8613982 Current protein Conservation of residue
PubMed ID 8613982 Current protein Structural similarity to homologue of known mechanism
PubMed ID 8613982 Current protein Residue is positioned appropriately (ligand position hypothetical)

ResidueChainNumberUniProt numberFunctional part FunctionTargetDescription
ASPB 102 0Sidechain
ElectrostaticResidue
Modifies the pKa of His 57 to allow it to act as a general acid/base catalyst.
Evidence from paper Evidence concerns Evidence type
PubMed ID 8613982 Current protein Residue is positioned appropriately (ligand position hypothetical)
PubMed ID 8613982 Current protein Conservation of residue
PubMed ID 8613982 Current protein Structural similarity to homologue of known mechanism

ResidueChainNumberUniProt numberFunctional part FunctionTargetDescription
GLYB 193 0Backbone amide
ElectrostaticTransition state
Forms part of the oxyanion hole.
Evidence from paper Evidence concerns Evidence type
PubMed ID 8613982 Current protein Residue is positioned appropriately (ligand position hypothetical)
PubMed ID 8613982 Current protein Structural similarity to homologue of known mechanism
PubMed ID 8613982 Current protein Conservation of residue

ResidueChainNumberUniProt numberFunctional part FunctionTargetDescription
SERB 195 0Sidechain, Backbone amide
ElectrostaticTransition state
NucleophileSubstrate
Backbone amide stabilises the transition state and side chain acts as a nucleophile to attack the substrate.
Evidence from paper Evidence concerns Evidence type
PubMed ID 8613982 Current protein Structural similarity to homologue of known mechanism
PubMed ID 8613982 Current protein Conservation of residue
PubMed ID 8613982 Current protein Residue is positioned appropriately (ligand position hypothetical)
References:
1
The 2.3 A crystal structure of the catalytic domain of recombinant two-chain human tissue-type plasminogen activator.
D. Lamba and M. Bauer and R. Huber and S. Fischer and R. Rudolph and U. Kohnert and W. Bode
J Mol Biol 258, (1) 117-35, (1996).
8613982
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