Plasmin

 

Human Plasminogen is a serine protease, a member of the Trypsin superfamily. It is a zymogen that can be activated to give the serine protease plasmin. Plasmin hydrolyses fibrin and dissolves blood clots. Plasmin has broad specificity but preferentially cleaves Lys-Xaa to Arg-Xaa amide bonds and can not directly catalyse proteolytic activation of plasminogen - it activates activators instead.

Under physiological conditions, activation is mediated by limited proteolysis carried out by urokinase and tissue-type plasminogen activator.

Like most zymogens, plasminogen has an activation loop which is proteolytically cleaved between Arg 561 and Val 562 when the protein is activated, resulting in conformational changes, including formation of a new solvent-inaccessible salt bridge and a functional active site.

Plasminogen activation is known to play a role in the activation of metalloproteinases and lipoxygenase and is linked to many physiological and pathological processes involved in cell migration such as cancer metastasis, angiogenesis, ovum maturation, embryogenesis, wound healing and pathogen invasion.

The PDB code 1qrz refers to the inactive precursor plasminogen, which is activated by cleavage leading to the opening of the active site. The specificity pocket is similar to that of trypsin, with plasmin showing a preference for cleavage after aliphatic basic residues such as Lysine and Arginine.

 

Reference Protein and Structure

Sequence
P00747 UniProt (3.4.21.7) IPR023317 (Sequence Homologues) (PDB Homologues)
Biological species
Homo sapiens (Human) Uniprot
PDB
1qrz - CATALYTIC DOMAIN OF PLASMINOGEN (2.0 Å) PDBe PDBsum 1qrz
Catalytic CATH Domains
2.40.10.10 CATHdb (see all for 1qrz)
Click To Show Structure

Enzyme Reaction (EC:3.4.21.7)

water
CHEBI:15377ChEBI
+
L-arginyl-L-amino acid
CHEBI:134262ChEBI
→
L-arginine
CHEBI:16467ChEBI
+
alpha-amino acid
CHEBI:33704ChEBI
Alternative enzyme names: Actase, Fibrinase, Fibrinolysin, Serum tryptase, Thrombolysin,

Enzyme Mechanism

Introduction

The reaction proceeds by initial nucleophilic attack on the peptide bond by Ser 741, activated by deprotonation by His 603. This leads to the formation of a tetrahedral intermediate, stabilised by Ser 741 and Gly 742. Subsequent collapse of this intermediate, assisted by protonation of the leaving group by His 603 and Asp 646 leads to an acyl enzyme intermediate. Activation of a water molecule by His 603 and Asp 646 allows this intermediate to by hydrolysed, resulting in the reformation of the catalytically active Serine residue and the release of the product.

Catalytic Residues Roles

UniProt PDB* (1qrz)
Gly761 (main-N) Gly742(197)A (main-N) Stabilises the tetrahedral intermediate through contacts with the oxyanion. electrostatic stabiliser
His622 His603(58)A Activates Ser 741 to allow it to act as a nucleophile. Then protonates the leaving group to allow collapse of the tetrahedral intermediate. Finally activates water to allow it to hydrolyse the acyl enzyme intermediate. proton shuttle (general acid/base)
Asp665 Asp646(101)A Modifies the pKa of His 603 so that it is able to act as an acid-base at physiological pH. modifies pKa, electrostatic stabiliser
Ser760 Ser741(196)A Acts as nucleophile to attack peptide bond and form tetrahedral intermediate, which is stabilised by contacts with the oxyanion hole. It is possible that the main chain amide of this serine contributes to the oxyanion hole (given similarity to other Ser-His-Asp proteins). covalent catalysis, proton shuttle (general acid/base)
*PDB label guide - RESx(y)B(C) - RES: Residue Name; x: Residue ID in PDB file; y: Residue ID in PDB sequence if different from PDB file; B: PDB Chain; C: Biological Assembly Chain if different from PDB. If label is "Not Found" it means this residue is not found in the reference PDB.

Chemical Components

References

  1. Wang X et al. (2000), J Mol Biol, 295, 903-914. Human plasminogen catalytic domain undergoes an unusual conformational change upon activation. DOI:10.1006/jmbi.1999.3397. PMID:10656799.
  2. Millers EK et al. (2013), PLoS One, 8, e54104-. The structure of Human Microplasmin in Complex with Textilinin-1, an Aprotinin-like Inhibitor from the Australian Brown Snake. DOI:10.1371/journal.pone.0054104. PMID:23335990.
  3. Schaller J et al. (2011), Cell Mol Life Sci, 68, 785-801. The plasmin–antiplasmin system: structural and functional aspects. DOI:10.1007/s00018-010-0566-5. PMID:21136135.
  4. Pozzi N et al. (2011), Biochemistry, 50, 10195-10202. Crystal Structures of Prethrombin-2 Reveal Alternative Conformations under Identical Solution Conditions and the Mechanism of Zymogen Activation. DOI:10.1021/bi2015019. PMID:22049947.
  5. Gohara DW et al. (2011), Trends Biotechnol, 29, 577-585. Allostery in trypsin-like proteases suggests new therapeutic strategies. DOI:10.1016/j.tibtech.2011.06.001. PMID:21726912.
  6. Hasumi K et al. (2010), FEBS J, 277, 3675-3687. Small-molecule modulators of zymogen activation in the fibrinolytic and coagulation systems. DOI:10.1111/j.1742-4658.2010.07783.x. PMID:20718867.
  7. Tharp AC et al. (2009), J Biol Chem, 284, 19511-19521. Plasminogen Substrate Recognition by the Streptokinase-Plasminogen Catalytic Complex Is Facilitated by Arg253, Lys256, and Lys257 in the Streptokinase  -Domain and Kringle 5 of the Substrate. DOI:10.1074/jbc.m109.005512. PMID:19473980.
  8. Rossignol P et al. (2004), J Biol Chem, 279, 10346-10356. Protease Nexin-1 Inhibits Plasminogen Activation-induced Apoptosis of Adherent Cells. DOI:10.1074/jbc.m310964200. PMID:14699093.
  9. Terzyan S et al. (2004), Proteins, 56, 277-284. Characterization of Lys-698 to met substitution in human plasminogen catalytic domain. DOI:10.1002/prot.20070. PMID:15211511.
  10. Turner RB et al. (2002), J Biol Chem, 277, 33068-33074. Structural Elements That Govern the Substrate Specificity of the Clot-dissolving Enzyme Plasmin. DOI:10.1074/jbc.m203782200. PMID:12080056.
  11. Budayova-Spano M et al. (2002), Structure, 10, 1509-1519. Monomeric structures of the zymogen and active catalytic domain of complement protease c1r: further insights into the c1 activation mechanism. PMID:12429092.
  12. Budayova-Spano M et al. (2002), EMBO J, 21, 231-239. The crystal structure of the zymogen catalytic domain of complement protease C1r reveals that a disruptive mechanical stress is required to trigger activation of the C1 complex. DOI:10.1093/emboj/21.3.231. PMID:11823416.
  13. Peisach E et al. (1999), Biochemistry, 38, 11180-11188. Crystal Structure of the Proenzyme Domain of Plasminogen†,‡. DOI:10.1021/bi991130r. PMID:10460175.
  14. Jespers L et al. (1999), J Mol Biol, 290, 471-479. Guiding a docking mode by phage display: selection of correlated mutations at the staphylokinase-plasmin interface. DOI:10.1006/jmbi.1999.2887. PMID:10390345.
  15. Parry MA et al. (1998), Nat Struct Biol, 5, 917-923. The ternary microplasmin–staphylokinase–microplasmin complex is a proteinase–cofactor–substrate complex in action. DOI:10.1038/2359. PMID:9783753.
  16. Kirschbaum NE et al. (1990), J Biol Chem, 265, 13669-13676. A unique proteolytic fragment of human fibrinogen containing the A alpha COOH-terminal domain of the native molecule. PMID:2143188.

Step 1.

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Catalytic Residues Roles

Residue Roles
Gly742(197)A (main-N) electrostatic stabiliser
His603(58)A proton shuttle (general acid/base)
Ser741(196)A covalent catalysis, proton shuttle (general acid/base)
Asp646(101)A electrostatic stabiliser, modifies pKa

Chemical Components

Step 1.

Contributors

Atlanta Cook, Craig Porter, Fiona J. E. Morgan, Gemma L. Holliday