5FCE

The crystal structure of the ligand binding region of Serine-glutamate repeat protein A (SgrA) of Enterococcus faecium


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.188 
  • R-Value Observed: 0.192 

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This is version 1.2 of the entry. See complete history


Literature

The crystal structure of the ligand-binding region of serine-glutamate repeat containing protein A (SgrA) of Enterococcus faecium reveals a new protein fold: functional characterization and insights into its adhesion function.

Nagarajan, R.Hendrickx, A.P.Ponnuraj, K.

(2016) FEBS J 283: 3039-3055

  • DOI: https://doi.org/10.1111/febs.13792
  • Primary Citation of Related Structures:  
    5FCE

  • PubMed Abstract: 

    Antimicrobial-resistant and hospital-adapted Enterococcus faecium represents a clinical problem in immunocompromised patients in hospitals worldwide. Understanding the molecular pathogenesis of E. faecium infections may provide novel therapies to treat or prevent infections. A potential target for novel treatment therapies is the serine-glutamate repeat containing protein A (SgrA), which is a cell wall-anchored LPxTG surface protein implicated in binding to fibrinogen and nidogen. Here, we report the X-ray crystal structure of the N-terminal ligand-binding domain of SgrA (rSgrA28-153 ) to a resolution of 1.79 Å. The structure revealed a new protein fold with significant differences from previously characterized DEv-IgG- and inv-IgG-like folds of adhesive proteins known as microbial surface components recognizing adhesive matrix molecules. The structure contains a Lys-Asn-Glu triad with the potential to form a Lys-Asn isopeptide bond. However, even in the absence of a stabilizing intramolecular isopeptide bond, rSgrA28-153 exhibits remarkable properties like resistance to proteases and high thermal stability. The interaction of rSgrA28-153 with fibrinogen, nidogen, laminin, and abiotic surfaces has been characterized and rSgrA28-153 binds to these molecules with high affinity. rSgrA28-153 also binds to the beta chain of fibrinogen and with high affinity and specificity. Strikingly, the presence of 29 surface-exposed hydrophobic amino acid residues likely play an important role in the selectivity of rSgrA28-153 to bind to different abiotic surfaces. The results obtained from this study have opened new avenues to explore and understand the role of this unique surface adhesin in the pathogenesis of catheter-related infections.


  • Organizational Affiliation

    Centre of Advanced Study in Crystallography and Biophysics, University of Madras, Chennai, India.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
LPXTG family cell surface protein Fms2
A, B
116Enterococcus faecium DOMutation(s): 0 
Gene Names: fms2HMPREF0351_11523
UniProt
Find proteins for Q3Y373 (Enterococcus faecium (strain ATCC BAA-472 / TX0016 / DO))
Explore Q3Y373 
Go to UniProtKB:  Q3Y373
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ3Y373
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MSE
Query on MSE
A, B
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.188 
  • R-Value Observed: 0.192 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 35.901α = 90
b = 56.722β = 107.22
c = 59.746γ = 90
Software Package:
Software NamePurpose
XSCALEdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
PHENIXphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-07-06
    Type: Initial release
  • Version 1.1: 2017-10-11
    Changes: Data collection, Derived calculations
  • Version 1.2: 2017-12-06
    Changes: Database references