6OQ9

Solution structure of VEK50 in the bound form with plasminogen kringle 2


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 200 
  • Conformers Submitted: 15 
  • Selection Criteria: structures with the least restraint violations 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Solution structural model of the complex of the binding regions of human plasminogen with its M-protein receptor from Streptococcus pyogenes.

Yuan, Y.Ayinuola, Y.A.Singh, D.Ayinuola, O.Mayfield, J.A.Quek, A.Whisstock, J.C.Law, R.H.P.Lee, S.W.Ploplis, V.A.Castellino, F.J.

(2019) J Struct Biol 208: 18-29

  • DOI: https://doi.org/10.1016/j.jsb.2019.07.005
  • Primary Citation of Related Structures:  
    6OKW, 6OKX, 6OKY, 6OQ9, 6OQJ, 6OQK

  • PubMed Abstract: 

    VEK50 is a truncated peptide from a Streptococcal pyogenes surface human plasminogen (hPg) binding M-protein (PAM). VEK50 contains the full A-domain of PAM, which is responsible for its low nanomolar binding to hPg. The interaction of VEK50 with kringle 2, the PAM-binding domain in hPg (K2 hPg ), has been studied by high-resolution NMR spectroscopy. The data show that each VEK50 monomer in solution contains two tight binding sites for K2 hPg , one each in the a1- (RH1; R 17 H 18 ) and a2- (RH2; R 30 H 31 ) repeats within the A-domain of VEK50. Two mutant forms of VEK50, viz., VEK50[RH1/AA] (VEK50 ΔRH1 ) and VEK50[RH2/AA] (VEK50 ΔRH2 ), were designed by replacing each RH with AA, thus eliminating one of the K2 hPg binding sites within VEK50, and allowing separate study of each binding site. Using 13 C- and 15 N-labeled peptides, NMR-derived solution structures of VEK50 in its complex with K2 hPg were solved. We conclude that the A-domain of PAM can accommodate two molecules of K2 hPg docked within a short distance of each other, and the strength of the binding is slightly different for each site. The solution structure of the VEK50/K2 hPg , complex, which is a reductionist model of the PAM/hPg complex, provides insights for the binding mechanism of PAM to a host protein, a process that is critical to S. pyogenes virulence.


  • Organizational Affiliation

    W.M. Keck Center for Transgene Research, University of Notre Dame, Notre Dame, IN 46556, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Plasminogen-binding group A streptococcal M-like protein PAM52Streptococcus pyogenesMutation(s): 0 
Gene Names: pamemm
UniProt
Find proteins for P49054 (Streptococcus pyogenes)
Explore P49054 
Go to UniProtKB:  P49054
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP49054
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 200 
  • Conformers Submitted: 15 
  • Selection Criteria: structures with the least restraint violations 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)United StatesHL013423

Revision History  (Full details and data files)

  • Version 1.0: 2019-07-24
    Type: Initial release
  • Version 1.1: 2019-10-02
    Changes: Data collection, Database references
  • Version 1.2: 2019-12-18
    Changes: Author supporting evidence
  • Version 1.3: 2023-06-14
    Changes: Database references, Other
  • Version 1.4: 2024-05-15
    Changes: Data collection, Database references