1I5K

STRUCTURE AND BINDING DETERMINANTS OF THE RECOMBINANT KRINGLE-2 DOMAIN OF HUMAN PLASMINOGEN TO AN INTERNAL PEPTIDE FROM A GROUP A STREPTOCOCCAL SURFACE PROTEIN


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.195 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Structure and binding determinants of the recombinant kringle-2 domain of human plasminogen to an internal peptide from a group A Streptococcal surface protein.

Rios-Steiner, J.L.Schenone, M.Mochalkin, I.Tulinsky, A.Castellino, F.J.

(2001) J.Mol.Biol. 308: 705-719

  • DOI: 10.1006/jmbi.2001.4646

  • PubMed Abstract: 
  • The X-ray crystal structure of a complex of a modified recombinant kringle-2 domain of human plasminogen, K2Pg[C4G/E56D/L72Y] (mK2Pg), containing an upregulated lysine-binding site, bound to a functional 30 residue internal peptide (VEK-30) from an M ...

    The X-ray crystal structure of a complex of a modified recombinant kringle-2 domain of human plasminogen, K2Pg[C4G/E56D/L72Y] (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.


    Related Citations: 
    • The refined structure of the epsilon-aminocaproic acid complex of human plasminogen kringle 4.
      Wu, T.P.,Padmanabhan, K.,Tulinsky, A.,Mulichak, A.M.
      (1991) Biochemistry 30: 10589
    • Enhancement trough mutagenesis of the binding of the isolated kringle 2 domain of human plasminogen to omega-amino acid ligands and to an internal sequence of a Streptococcal surface protein.
      Nilsen, S.L.,Prorok, M.,Castellino, F.J.
      (1999) J.Biol.Chem. 274: 22380
    • Structure and ligand binding determinants of the recombinant kringle 5 domain of human plasminogen.
      Chang, Y.,Mochalkin, I.,McCance, S.G.,Cheng, B.,Tulinsky, A.,Castellino, F.J.
      (1998) Biochemistry 37: 3258
    • Kringle 2 mediates high affinity binding of plasminogen to an internal sequence in streptococcal surface protein PAM.
      Wistedt, A.C.,Kotarsky, H.,Marti, D.,Ringdahl, U.,Castellino, F.J.,Schaller, J.,Sjobring, U.
      (1998) J.Biol.Chem. 273: 24420


    Organizational Affiliation

    Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PLASMINOGEN
A, B
84Homo sapiensGene Names: PLG
EC: 3.4.21.7
Find proteins for P00747 (Homo sapiens)
Go to Gene View: PLG
Go to UniProtKB:  P00747
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
M PROTEIN
C, D
30Streptococcus pyogenesGene Names: pam (emm)
Find proteins for P49054 (Streptococcus pyogenes)
Go to UniProtKB:  P49054
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.195 
  • Space Group: P 61 2 2
Unit Cell:
Length (Å)Angle (°)
a = 91.980α = 90.00
b = 91.980β = 90.00
c = 151.779γ = 120.00
Software Package:
Software NamePurpose
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2001-08-01
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2011-11-16
    Type: Atomic model