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

Summary for 1I5K

• Entry DOI: 10.2210/pdb1i5k/pdb
• Descriptor: PLASMINOGEN, M PROTEIN (3 entities in total)
• Functional Keywords: human plasminogen kringle-2, kringles, vek-30, blood clotting
• Biological source: Homo sapiens (human); More
• Cellular location: Secreted: P00747; Secreted, cell wall; Peptidoglycan-anchor (Potential): P49054
• Total number of polymer chains: 4
• Total formula weight: 26819.89

Authors

Rios-Steiner, J.L.,Schenone, M.,Mochalkin, I.,Tulinsky, A.,Castellino, F.J. (deposition date: 2001-02-27, release date: 2001-08-01, Last modification date: 2024-11-13)

Primary citation

Rios-Steiner, J.L.,Schenone, M.,Mochalkin, I.,Tulinsky, A.,Castellino, F.J.
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, 2001

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-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.

PubMed: 11350170
DOI: 10.1006/jmbi.2001.4646

Experimental method

X-RAY DIFFRACTION (2.7 Å)