3ZLB

Crystal structure of phosphoglycerate kinase from Streptococcus pneumoniae


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.78 Å
  • R-Value Free: 0.192 
  • R-Value Work: 0.145 
  • R-Value Observed: 0.147 

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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Pneumococcal phosphoglycerate kinase interacts with plasminogen and its tissue activator.

Fulde, M.Bernardo-Garcia, N.Rohde, M.Nachtigall, N.Frank, R.Preissner, K.T.Klett, J.Morreale, A.Chhatwal, G.S.Hermoso, J.A.Bergmann, S.

(2014) Thromb Haemost 111: 401-416

  • DOI: 10.1160/TH13-05-0421
  • Primary Citation of Related Structures:  
    3ZLB

  • PubMed Abstract: 
  • Streptococcus pneumoniae is not only a commensal of the nasopharyngeal epithelium, but may also cause life-threatening diseases. Immune-electron microscopy studies revealed that the bacterial glycolytic enzyme, phosphoglycerate kinase (PGK), is localised on the pneumococcal surface of both capsulated and non-capsulated strains and colocalises with plasminogen ...

    Streptococcus pneumoniae is not only a commensal of the nasopharyngeal epithelium, but may also cause life-threatening diseases. Immune-electron microscopy studies revealed that the bacterial glycolytic enzyme, phosphoglycerate kinase (PGK), is localised on the pneumococcal surface of both capsulated and non-capsulated strains and colocalises with plasminogen. Since pneumococci may concentrate host plasminogen (PLG) together with its activators on the bacterial cell surface to facilitate the formation of plasmin, the involvement of PGK in this process was studied. Specific binding of human or murine PLG to strain-independent PGK was documented, and surface plasmon resonance analyses indicated a high affinity interaction with the kringle domains 1-4 of PLG. Crystal structure determination of pneumococcal PGK together with peptide array analysis revealed localisation of PLG-binding site in the N-terminal region and provided structural motifs for the interaction with PLG. Based on structural analysis data, a potential interaction of PGK with tissue plasminogen activator (tPA) was proposed and experimentally confirmed by binding studies, plasmin activity assays and thrombus degradation analyses.


    Organizational Affiliation

    Simone Bergmann, PhD, Technische Universität Braunschweig, Spielmannstrasse 7, 38106 Braunschweig, Germany, Tel.: +49 531 391 5818, Fax: +49 531 391 5854, E-mail: simone.bergmann@tu-bs.de.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
PHOSPHOGLYCERATE KINASEA398Streptococcus pneumoniae D39Mutation(s): 0 
Gene Names: pgkSPD_0445
EC: 2.7.2.3
UniProt
Find proteins for Q04LZ5 (Streptococcus pneumoniae serotype 2 (strain D39 / NCTC 7466))
Explore Q04LZ5 
Go to UniProtKB:  Q04LZ5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ04LZ5
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.78 Å
  • R-Value Free: 0.192 
  • R-Value Work: 0.145 
  • R-Value Observed: 0.147 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 40.347α = 90
b = 78.227β = 96.34
c = 59.033γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-02-12
    Type: Initial release
  • Version 1.1: 2019-02-27
    Changes: Data collection, Database references, Other