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Plasminogen PDB id
1pkr
Jmol
Contents
Protein chain
80 a.a. *
Metals
_CL ×2
Waters ×71
* Residue conservation analysis
PDB id:
1pkr
Name: Plasminogen
Title: The structure of recombinant plasminogen kringle 1 and the fibrin binding site
Structure: Plasminogen. Chain: a. Engineered: yes
Source: Homo sapiens. Human. Organism_taxid: 9606
Resolution:
2.48Å     R-factor:   0.159    
Authors: T.-P.Wu,A.Tulinsky
Key ref: T.P.Wu et al. (1994). The structure of recombinant plasminogen kringle 1 and the fibrin binding site. Blood Coagul Fibrinolysis, 5, 157-166. PubMed id: 8054447
Date:
03-Aug-93     Release date:   31-Jan-94    
PROCHECK
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 Headers
 References

Protein chain
Pfam   ArchSchema ?
P00747  (PLMN_HUMAN) -  Plasminogen
Seq:
Struc: 		 
Seq:
Struc: 		810 a.a.
80 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.3.4.21.7  - Plasmin.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Preferential cleavage: Lys-|-Xaa > Arg-|-Xaa; higher selectivity than trypsin. Converts fibrin into soluble products.
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     blood coagulation   2 terms 
  Biochemical function     calcium ion binding     2 terms  

 

 
Blood Coagul Fibrinolysis 5:157-166 (1994)
PubMed id: 8054447  
 
 
The structure of recombinant plasminogen kringle 1 and the fibrin binding site.
T.P.Wu, K.P.Padmanabhan, A.Tulinsky.
 
  ABSTRACT  
 
The structure of recombinant (Hoover et al. Biochemistry, 1993; 32:10936-10944) plasminogen (PG) kringle 1 (K1) has been determined and refined at 2.48 A resolution to a crystallographic R value of 0.159. In addition, 71 water molecules and two chloride ions have been located. The folding of PGK1 is very similar to that of PGK4. The lysine/fibrin binding site, however, differs from that of both PGK4 and tissue-type PG activator (t-PA) K2 at the cationic centre. Although PGK1 can potentially have a doubly charged cationic centre utilizing Arg34 and Arg71, the side chain of Arg34 is outside of Arg71 in a solvent region and its guanidino group is flexibly disordered. Moreover, site specific mutagenesis studies show unequivocally that Arg34 can be changed to glutamine without affecting the binding ability of PGK1. Thus, PGK1 only has Arg71 at the cationic site, PGK4 has Lys35/Arg71 and t-PAK2 has only Lys33. The cationic site differences may result in subtle responses in the binding affinities of the kringles. The two chloride ions are located in the lysine binding site and effectively compensate the positive charges of the region. They also appear to be involved intermolecularly in a complex way in the crystal structure. Such intermolecular anionic interactions are also found in PGK4 and t-PAK2.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
14717962 J.H.Geiger, and S.E.Cnudde (2004).
What the structure of angiostatin may tell us about its mechanism of action.
  J Thromb Haemost, 2, 23-34.  
12646571 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.
  J Biol Chem, 278, 18199-18206.  
11928826 E.Anglés-Cano, and G.Rojas (2002).
Apolipoprotein(a): structure-function relationship at the lysine-binding site and plasminogen activator cleavage site.
  Biol Chem, 383, 93-99.  
11928808 M.Gehrmann, K.Briknarová, L.Bányai, L.Patthy, and M.Llinás (2002).
The col-1 module of human matrix metalloproteinase-2 (MMP-2): structural/functional relatedness between gelatin-binding fibronectin type II modules and lysine-binding kringle domains.
  Biol Chem, 383, 137-148.
PDB code: 1ks0
11297431 J.A.Kornblatt, I.Rajotte, and F.Heitz (2001).
Reaction of canine plasminogen with 6-aminohexanoate: a thermodynamic study combining fluorescence, circular dichroism, and isothermal titration calorimetry.
  Biochemistry, 40, 3639-3647.  
11369850 Q.Ye, M.N.Rahman, M.L.Koschinsky, and Z.Jia (2001).
High-resolution crystal structure of apolipoprotein(a) kringle IV type 7: insights into ligand binding.
  Protein Sci, 10, 1124-1129.
PDB code: 1i71
10962086 J.A.Kornblatt (2000).
Understanding the fluorescence changes of human plasminogen when it binds the ligand, 6-aminohexanoate: a synthesis.
  Biochim Biophys Acta, 1481, 1.  
8910613 Y.Cao, R.W.Ji, D.Davidson, J.Schaller, D.Marti, S.Söhndel, S.G.McCance, M.S.O'Reilly, M.Llinás, and J.Folkman (1996).
Kringle domains of human angiostatin. Characterization of the anti-proliferative activity on endothelial cells.
  J Biol Chem, 271, 29461-29467.  
7742349 A.M.Scanu, and C.Edelstein (1995).
Kringle-dependent structural and functional polymorphism of apolipoprotein (a).
  Biochim Biophys Acta, 1256, 1.  
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.