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PDBsum entry 1i5k

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protein Protein-protein interface(s) links
Blood clotting PDB id
1i5k
Jmol
Contents
Protein chains
79 a.a. *
26 a.a. *
Waters ×133
* Residue conservation analysis
PDB id:
1i5k
Name: Blood clotting
Title: Structure and binding determinants of the recombinant kringl of human plasminogen to an internal peptide from a group a streptococcal surface protein
Structure: Plasminogen. Chain: a, b. Fragment: modified recombinant kringle-2 domain. Engineered: yes. Mutation: yes. M protein. Chain: c, d. Fragment: vek-30 (30 residue internal peptide). Engineered: yes
Source: Homo sapiens. Human. Organism_taxid: 9606. Expressed in: pichia pastoris. Expression_system_taxid: 4922. Synthetic: yes. Other_details: vek-30 was synthesized by automated solid ph peptide synthesis
Biol. unit: Octamer (from PQS)
Resolution:
2.70Å     R-factor:   0.195     R-free:   0.262
Authors: J.L.Rios-Steiner,M.Schenone,I.Mochalkin,A.Tulinsky,F.J.Caste
Key ref:
J.L.Rios-Steiner et al. (2001). Structure and binding determinants of the recombinant kringle-2 domain of human plasminogen to an internal peptide from a group A Streptococcal surface protein. J Mol Biol, 308, 705-719. PubMed id: 11350170 DOI: 10.1006/jmbi.2001.4646
Date:
27-Feb-01     Release date:   01-Aug-01    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P00747  (PLMN_HUMAN) -  Plasminogen
Seq:
Struc:
 
Seq:
Struc:
810 a.a.
79 a.a.*
Protein chains
Pfam   ArchSchema ?
P49054  (PAM_STRPY) -  Plasminogen-binding group A streptococcal M-like protein PAM (Fragment)
Seq:
Struc:
388 a.a.
26 a.a.
Key:    PfamA domain  PfamB domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 3 residue positions (black crosses)

 Enzyme reactions 
   Enzyme class: Chains A, B: 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: 10.1006/jmbi.2001.4646 J Mol Biol 308:705-719 (2001)
PubMed id: 11350170  
 
 
Structure and binding determinants of the recombinant kringle-2 domain of human plasminogen to an internal peptide from a group A Streptococcal surface protein.
J.L.Rios-Steiner, M.Schenone, I.Mochalkin, A.Tulinsky, F.J.Castellino.
 
  ABSTRACT  
 
The X-ray crystal structure of a complex of a modified recombinant kringle-2 (mK2Pg), containing an upregulated lysine-binding site, bound to a functional 30 residue internal peptide (VEK-30) from an M-type protein of a group A Streptococcus surface protein, has been determined by molecular replacement methods using K4Pg as a model, and refined at 2.7 A resolution to a R-factor of 19.5 %. The X-ray crystal structure shows that VEK-30 exists as a nearly end-to-end alpha-helix in the complex with mK2Pg. The final structure also revealed that Arg17 and His18 of VEK-30 served as cationic loci for Asp54 and Asp56 of the consensus lysine-binding site of mK2Pg, while Glu20 of VEK-30 coordinates with Arg69 of the cationic binding site of mK2Pg. The hydrophobic ligand-binding pocket in mK2Pg, consisting primarily of Trp60 and Trp70, situated between the positive and negative centers of the lysine-binding site, is utilized in a novel manner in stabilizing the interaction with VEK-30 by forming a cation-pi-electron-mediated association with the positive side-chain of Arg17 of this peptide. Additional lysine-binding sites, as well as exosite electrostatic and hydrogen bonding interactions involving Glu9 and Lys14 of VEK-30, were observed in the structural model. The importance of these interactions were tested in solution by investigating the binding constants of synthetic variants of VEK-30 to mK2Pg, and it was found that, Lys14, Arg17, His18, and Glu20 of VEK-30 were the most critical amino acid binding determinants. With regard to the solution studies, circular dichroism analysis of the titration of VEK-30 with mK2Pg demonstrated that the peptidic alpha-helical structure increased substantially when bound to the kringle module, in agreement with the X-ray results.This investigation is the first to delineate structurally the mode of interaction of the lysine-binding site of a kringle with an internal pseudo-lysine residue of a peptide or protein that functionally interacts with a kringle module, and serves as a paradigm for this important class of interactions.
 
  Selected figure(s)  
 
Figure 2.
Figure 2. Ribbon drawing of the two mK2[Pg]/VEK-30 complexes in the asymmetric unit viewed approximately at right angles to the local 2-fold axis. Turquoise, m(1)K2[Pg]; white, VEK(1)-30; green, m(2)K2[Pg]; orange, VEK(2)-30. Side-chains (Lys14/114, Arg17/117, His18/118, and Glu20/120) of VEK-30 that insert in the lysine-binding site of mK2[Pg] (Asp54/154, Asp56/156, and Arg69/169) are shown as stick structures with: blue, nitrogen; red, oxygen. The lack of 2-fold symmetry of Glu20/120 between two VEK-30 helices is evident. The Figure was drawn with the program Ribbons[63].
Figure 3.
Figure 3. Ribbon and stick drawing of principal interactions of mK2[Pg]/VEK-30 complexes in the asymmetric unit viewed at right angles to the local 2-fold axis. Turquoise, m(1)K2[Pg]; white, VEK(1)-30; green, m(2)K2[Pg]; orange, VEK(2)-30. Stick structures: blue, nitrogen; red, oxygen. All residues are numbered at least once. Lack of 2-fold symmetry in inter-helical space is evident. The Figure was drawn with the program Ribbons[63].
 
  The above figures are reprinted by permission from Elsevier: J Mol Biol (2001, 308, 705-719) copyright 2001.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20199597 C.G.Earnhart, D.V.Leblanc, K.E.Alix, D.C.Desrosiers, J.D.Radolf, and R.T.Marconi (2010).
Identification of residues within ligand-binding domain 1 (LBD1) of the Borrelia burgdorferi OspC protein required for function in the mammalian environment.
  Mol Microbiol, 76, 393-408.  
20460308 C.H.Lee, K.J.Park, E.S.Sung, A.Kim, J.D.Choi, J.S.Kim, S.H.Kim, M.H.Kwon, and Y.S.Kim (2010).
Engineering of a human kringle domain into agonistic and antagonistic binding proteins functioning in vitro and in vivo.
  Proc Natl Acad Sci U S A, 107, 9567-9571.  
19800007 M.Wang, J.Zajicek, J.H.Geiger, M.Prorok, and F.J.Castellino (2010).
Solution structure of the complex of VEK-30 and plasminogen kringle 2.
  J Struct Biol, 169, 349-359.
PDB code: 2kj4
20028034 R.N.Bohnsack, M.Patel, L.J.Olson, S.S.Twining, and N.M.Dahms (2010).
Residues essential for plasminogen binding by the cation-independent mannose 6-phosphate receptor.
  Biochemistry, 49, 635-644.  
20653841 T.Iwaki, C.Malinverno, D.Smith, Z.Xu, Z.Liang, V.A.Ploplis, and F.J.Castellino (2010).
The generation and characterization of mice expressing a plasmin-inactivating active site mutation.
  J Thromb Haemost, 8, 2341-2344.  
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.  
18070889 C.Attali, C.Frolet, C.Durmort, J.Offant, T.Vernet, and A.M.Di Guilmi (2008).
Streptococcus pneumoniae choline-binding protein E interaction with plasminogen/plasmin stimulates migration across the extracellular matrix.
  Infect Immun, 76, 466-476.  
18039665 Q.Fu, M.Figuera-Losada, V.A.Ploplis, S.Cnudde, J.H.Geiger, M.Prorok, and F.J.Castellino (2008).
The lack of binding of VEK-30, an internal peptide from the group A streptococcal M-like protein, PAM, to murine plasminogen is due to two amino acid replacements in the plasminogen kringle-2 domain.
  J Biol Chem, 283, 1580-1587.  
17307854 A.Knaust, M.V.Weber, S.Hammerschmidt, S.Bergmann, M.Frosch, and O.Kurzai (2007).
Cytosolic proteins contribute to surface plasminogen recruitment of Neisseria meningitidis.
  J Bacteriol, 189, 3246-3255.  
17557824 M.Candela, S.Bergmann, M.Vici, B.Vitali, S.Turroni, B.J.Eikmanns, S.Hammerschmidt, and P.Brigidi (2007).
Binding of human plasminogen to Bifidobacterium.
  J Bacteriol, 189, 5929-5936.  
17012384 M.L.Sanderson-Smith, M.Dowton, M.Ranson, and M.J.Walker (2007).
The plasminogen-binding group A streptococcal M protein-related protein Prp binds plasminogen via arginine and histidine residues.
  J Bacteriol, 189, 1435-1440.  
16991168 F.Grandi, M.Sandal, G.Guarguaglini, E.Capriotti, R.Casadio, and B.Samorì (2006).
Hierarchical mechanochemical switches in angiostatin.
  Chembiochem, 7, 1774-1782.  
16822869 M.L.Sanderson-Smith, M.J.Walker, and M.Ranson (2006).
The maintenance of high affinity plasminogen binding by group A streptococcal plasminogen-binding M-like protein is mediated by arginine and histidine residues within the a1 and a2 repeat domains.
  J Biol Chem, 281, 25965-25971.  
16319056 M.Sanderson-Smith, M.Batzloff, K.S.Sriprakash, M.Dowton, M.Ranson, and M.J.Walker (2006).
Divergence in the plasminogen-binding group a streptococcal M protein family: functional conservation of binding site and potential role for immune selection of variants.
  J Biol Chem, 281, 3217-3226.  
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.  
  12875972 J.Sato, J.Schorey, V.A.Ploplis, E.Haalboom, L.Krahule, and F.J.Castellino (2003).
The fibrinolytic system in dissemination and matrix protein deposition during a mycobacterium infection.
  Am J Pathol, 163, 517-531.  
11856839 M.C.Abad, and J.Geiger (2002).
Crystallization and preliminary X-ray diffraction studies of human angiostatin.
  Acta Crystallogr D Biol Crystallogr, 58, 513-514.  
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
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.