5UZU

Immune evasion by a Staphylococcal Peroxidase Inhibitor that blocks myeloperoxidase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.184 
  • R-Value Observed: 0.187 

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This is version 3.2 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: https://doi.org/10.1073/pnas.1707032114
  • Primary Citation of Related Structures:  
    5UZU

  • 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 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 H 2 O 2 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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Uncharacterised proteinA [auth B]71Staphylococcus aureusMutation(s): 0 
Gene Names: BN1321_100004ERS072738_02531ERS074020_02508ERS140147_02483HMPREF3211_00419
UniProt
Find proteins for Q2G0X2 (Staphylococcus aureus (strain NCTC 8325 / PS 47))
Explore Q2G0X2 
Go to UniProtKB:  Q2G0X2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ2G0X2
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
MyeloperoxidaseB [auth A]578Homo sapiensMutation(s): 0 
Gene Names: MPO
EC: 1.11.2.2
UniProt & NIH Common Fund Data Resources
Find proteins for P05164 (Homo sapiens)
Explore P05164 
Go to UniProtKB:  P05164
PHAROS:  P05164
GTEx:  ENSG00000005381 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP05164
Sequence Annotations
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 3
MoleculeChains Length2D Diagram Glycosylation3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
C
3N/A
Glycosylation Resources
GlyTouCan:  G15407YE
GlyCosmos:  G15407YE
GlyGen:  G15407YE
Entity ID: 4
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
D
2N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.184 
  • R-Value Observed: 0.187 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 129.034α = 90
b = 92.944β = 120.14
c = 80.394γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data collection
HKL-2000data scaling
PDB_EXTRACTdata extraction
HKL-2000data reduction
PHENIXphasing
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesAI111203
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM121511

Revision History  (Full details and data files)

  • Version 1.0: 2017-07-26
    Type: Initial release
  • Version 1.1: 2017-09-20
    Changes: Author supporting evidence, Database references, Refinement description
  • Version 2.0: 2017-12-27
    Changes: Advisory, Atomic model, Database references, Derived calculations
  • Version 2.1: 2019-12-11
    Changes: Author supporting evidence
  • Version 3.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
  • Version 3.1: 2023-10-04
    Changes: Data collection, Database references, Refinement description, Structure summary
  • Version 3.2: 2023-11-15
    Changes: Data collection