5UZU

Immune evasion by a Staphylococcal Peroxidase Inhibitor that blocks myeloperoxidase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.403 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.184 

wwPDB Validation 3D Report Full Report


This is version 2.0 of the entry. See complete history

Literature

Immune evasion by a staphylococcal inhibitor of myeloperoxidase.

de Jong, N.W.M.Ramyar, K.X.Guerra, F.E.Nijland, R.Fevre, C.Voyich, J.M.McCarthy, A.J.Garcia, B.L.van Kessel, K.P.M.van Strijp, J.A.G.Geisbrecht, B.V.Haas, P.A.

(2017) Proc. Natl. Acad. Sci. U.S.A. 114: 9439-9444

  • DOI: 10.1073/pnas.1707032114

  • PubMed Abstract: 
  • Staphylococcus aureus is highly adapted to its host and has evolved many strategies to resist opsonization and phagocytosis. Even after uptake by neutrophils, S. aureus shows resistance to killing, which suggests the presence of phagosomal immune eva ...

    Staphylococcus aureus is highly adapted to its host and has evolved many strategies to resist opsonization and phagocytosis. Even after uptake by neutrophils, S. aureus shows resistance to killing, which suggests the presence of phagosomal immune evasion molecules. With the aid of secretome phage display, we identified a highly conserved protein that specifically binds and inhibits human myeloperoxidase (MPO), a major player in the oxidative defense of neutrophils. We have named this protein "staphylococcal peroxidase inhibitor" (SPIN). To gain insight into inhibition of MPO by SPIN, we solved the cocrystal structure of SPIN bound to a recombinant form of human MPO at 2.4-Å resolution. This structure reveals that SPIN acts as a molecular plug that prevents H2O2 substrate access to the MPO active site. In subsequent experiments, we observed that SPIN expression increases inside the neutrophil phagosome, where MPO is located, compared with outside the neutrophil. Moreover, bacteria with a deleted gene encoding SPIN showed decreased survival compared with WT bacteria after phagocytosis by neutrophils. Taken together, our results demonstrate that S. aureus secretes a unique proteinaceous MPO inhibitor to enhance survival by interfering with MPO-mediated killing.


    Organizational Affiliation

    Medical Microbiology, University Medical Center Utrecht, 3584 CX Utrecht, The Netherlands.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Uncharacterised protein
B
71Staphylococcus aureus (strain NCTC 8325)Mutation(s): 0 
Find proteins for Q2G0X2 (Staphylococcus aureus (strain NCTC 8325))
Go to UniProtKB:  Q2G0X2
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Myeloperoxidase
A
578Homo sapiensMutation(s): 0 
Gene Names: MPO
EC: 1.11.2.2
Find proteins for P05164 (Homo sapiens)
Go to Gene View: MPO
Go to UniProtKB:  P05164
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

Download SDF File 
Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
CA
Query on CA

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Download CCD File 
A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
BMA
Query on BMA

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Download CCD File 
A
BETA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-RWOPYEJCSA-N
 Ligand Interaction
NAG
Query on NAG

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Download CCD File 
A
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
CSO
Query on CSO
A
L-PEPTIDE LINKINGC3 H7 N O3 SCYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.403 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.184 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 129.034α = 90.00
b = 92.944β = 120.14
c = 80.394γ = 90.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
HKL-2000data scaling
DENZOdata reduction
PHENIXphasing
SCALEPACKdata scaling
HKL-2000data reduction
PHENIXrefinement
HKL-2000data collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious DiseasesUnited StatesAI111203
National Institutes of Health/National Institute of General Medical SciencesUnited StatesGM121511

Revision History 

  • Version 1.0: 2017-07-26
    Type: Initial release
  • Version 1.1: 2017-09-20
    Type: Author supporting evidence, Database references, Refinement description
  • Version 2.0: 2017-12-27
    Type: Advisory, Atomic model, Database references, Derived calculations