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PDBsum entry 1pmk

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protein Protein-protein interface(s) links
Hydrolase(serine protease) PDB id
1pmk
Jmol
Contents
Protein chain
78 a.a. *
Waters ×120
* Residue conservation analysis
PDB id:
1pmk
Name: Hydrolase(serine protease)
Title: Kringle-kringle interactions in multimer kringle structures
Structure: Plasminogen kringle 4. Chain: a, b. Engineered: yes
Source: Homo sapiens. Human. Organism_taxid: 9606
Resolution:
2.25Å     R-factor:   0.165    
Authors: K.Padmanabhan,A.Tulinsky
Key ref:
K.Padmanabhan et al. (1994). Kringle-kringle interactions in multimer kringle structures. Protein Sci, 3, 898-910. PubMed id: 8069221 DOI: 10.1002/pro.5560030605
Date:
25-Apr-94     Release date:   22-Jun-94    
PROCHECK
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 Headers
 References

Protein chains
Pfam   ArchSchema ?
P00747  (PLMN_HUMAN) -  Plasminogen
Seq:
Struc:
 
Seq:
Struc:
810 a.a.
78 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.

 

 
DOI no: 10.1002/pro.5560030605 Protein Sci 3:898-910 (1994)
PubMed id: 8069221  
 
 
Kringle-kringle interactions in multimer kringle structures.
K.Padmanabhan, T.P.Wu, K.G.Ravichandran, A.Tulinsky.
 
  ABSTRACT  
 
The crystal structure of a monoclinic form of human plasminogen kringle 4 (PGK4) has been solved by molecular replacement using the orthorthombic structure as a model and it has been refined by restrained least-squares methods to an R factor of 16.4% at 2.25 A resolution. The X-PLOR structure of kringle 2 of tissue plasminogen activator (t-PAK2) has been refined further using PROFFT (R = 14.5% at 2.38 A resolution). The PGK4 structure has 2 and t-PAK2 has 3 independent molecules in the asymmetric unit. There are 5 different noncrystallographic symmetry "dimers" in PGK4. Three make extensive kringle-kringle interactions related by noncrystallographic 2(1) screw axes without blocking the lysine binding site. Such associations may occur in multikringle structures such as prothrombin, hepatocyte growth factor, plasminogen (PG), and apolipoprotein [a]. The t-PAK2 structure also has noncrystallographic screw symmetry (3(1)) and mimics fibrin binding mode by having lysine of one molecule interacting electrostatically with the lysine binding site of another kringle. This ligand-like binding interaction may be important in kringle-kringle interactions involving non-lysine binding kringles with lysine or pseudo-lysine binding sites. Electrostatic intermolecular interactions involving the lysine binding site are also found in the crystal structures of PGK1 and orthorhombic PGK4. Anions associate with the cationic centers of these and t-PAK2 that appear to be more than occasional components of lysine binding site regions.
 
  Selected figure(s)  
 
Figure 4.
Fig. 4. AB' dimer of PGK4. Backboneshown thin or broken; side chains in interface and lysine binding iteshwn in heavy lines; hydrogen bonds, heavy broken lines; lysine binding site, speckled; non- crystallographic 2, screw axisshown appropriately.
Figure 8.
Fig. 8. Stereo of 3 t-PAK2mol- ecules of asymmetric nit. Molecule A shownwiththinlines, with broken lines, and C iththick lines; viewed along -axis noncrystallographic 1 screw axis.
 
  The above figures are reprinted from an Open Access publication published by the Protein Society: Protein Sci (1994, 3, 898-910) copyright 1994.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
19473980 A.C.Tharp, M.Laha, P.Panizzi, M.W.Thompson, P.Fuentes-Prior, and P.E.Bock (2009).
Plasminogen Substrate Recognition by the Streptokinase-Plasminogen Catalytic Complex Is Facilitated by Arg253, Lys256, and Lys257 in the Streptokinase {beta}-Domain and Kringle 5 of the Substrate.
  J Biol Chem, 284, 19511-19521.  
18334994 J.P.Lopez-Atalaya, B.D.Roussel, D.Levrat, J.Parcq, O.Nicole, Y.Hommet, K.Benchenane, H.Castel, J.Leprince, D.To Van, R.Bureau, S.Rault, 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.
  J Cereb Blood Flow Metab, 28, 1212-1221.  
10704226 G.M.Fless, C.J.Halfman, and E.W.Kirk (2000).
The relationship between the effect of lysine analogues and salt on the conformation of lipoprotein(a).
  Biochemistry, 39, 2740-2747.  
9521645 Y.Chang, I.Mochalkin, S.G.McCance, B.Cheng, A.Tulinsky, and F.J.Castellino (1998).
Structure and ligand binding determinants of the recombinant kringle 5 domain of human plasminogen.
  Biochemistry, 37, 3258-3271.
PDB code: 5hpg
9298949 G.M.Fless, J.Y.Santiago, J.Furbee, and S.C.Meredith (1997).
Specificity of ligand-induced conformational change of lipoprotein(a).
  Biochemistry, 36, 11304-11313.  
8611560 I.I.Mathews, P.Vanderhoff-Hanaver, F.J.Castellino, and A.Tulinsky (1996).
Crystal structures of the recombinant kringle 1 domain of human plasminogen in complexes with the ligands epsilon-aminocaproic acid and trans-4-(aminomethyl)cyclohexane-1-carboxylic Acid.
  Biochemistry, 35, 2567-2576.
PDB codes: 1cea 1ceb
  7756992 L.E.Donate, E.Gherardi, N.Srinivasan, R.Sowdhamini, S.Aparicio, and T.L.Blundell (1994).
Molecular evolution and domain structure of plasminogen-related growth factors (HGF/SF and HGF1/MSP).
  Protein Sci, 3, 2378-2394.  
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.