3PNT | pdb_00003pnt

Crystal Structure of the Streptococcus pyogenes NAD+ glycohydrolase SPN in complex with IFS, the Immunity Factor for SPN


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 
    0.278 (Depositor), 0.280 (DCC) 
  • R-Value Work: 
    0.208 (Depositor), 0.216 (DCC) 
  • R-Value Observed: 
    0.212 (Depositor) 

wwPDB Validation 3D Report Full Report

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This is version 1.2 of the entry. See complete history

Literature

Structural Basis of Streptococcus pyogenes Immunity to Its NAD(+) Glycohydrolase Toxin.

Smith, C.L.Ghosh, J.Elam, J.S.Pinkner, J.S.Hultgren, S.J.Caparon, M.G.Ellenberger, T.

(2011) Structure 19: 192-202

  • DOI: https://doi.org/10.1016/j.str.2010.12.013
  • Primary Citation Related Structures: 
    3PNT, 3QB2

  • PubMed Abstract: 

    The virulence of Gram-positive bacteria is enhanced by toxins like the Streptococcus pyogenes β-NAD(+) glycohydrolase known as SPN. SPN-producing strains of S. pyogenes additionally express the protein immunity factor for SPN (IFS), which forms an inhibitory complex with SPN. We have determined crystal structures of the SPN-IFS complex and IFS alone, revealing that SPN is structurally related to ADP-ribosyl transferases but lacks the canonical binding site for protein substrates. SPN is instead a highly efficient glycohydrolase with the potential to deplete cellular levels of β-NAD(+). The protective effect of IFS involves an extensive interaction with the SPN active site that blocks access to β-NAD(+). The conformation of IFS changes upon binding to SPN, with repacking of an extended C-terminal α helix into a compact shape. IFS is an attractive target for the development of novel bacteriocidal compounds functioning by blocking the bacterium's self-immunity to the SPN toxin.


  • Organizational Affiliation
    • Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, Saint Louis, MO 63110-1093, USA.

Macromolecule Content 

  • Total Structure Weight: 100.76 kDa 
  • Atom Count: 6,793 
  • Modeled Residue Count: 821 
  • Deposited Residue Count: 858 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
NAD+-glycohydrolase
A, C
268Streptococcus pyogenesMutation(s): 0 
Gene Names: spn
EC: 3.2.2.5
UniProt
Find proteins for D7S065 (Streptococcus pyogenes)
Explore D7S065 
Go to UniProtKB:  D7S065
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupD7S065
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Immunity factor for SPN
B, D
161Streptococcus pyogenesMutation(s): 0 
Gene Names: ifs
UniProt
Find proteins for Q2VJ58 (Streptococcus pyogenes)
Explore Q2VJ58 
Go to UniProtKB:  Q2VJ58
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ2VJ58
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MSE
Query on MSE
A, C
L-PEPTIDE LINKINGC5 H11 N O2 SeMET

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free:  0.278 (Depositor), 0.280 (DCC) 
  • R-Value Work:  0.208 (Depositor), 0.216 (DCC) 
  • R-Value Observed: 0.212 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 198.817α = 90
b = 57.892β = 107.2
c = 89.699γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-03-02
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2024-11-27
    Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary