6AZP

A Structurally Dynamic N-terminal Region Drives Function of the Staphylococcal Peroxidase Inhibitor (SPIN)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.291 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.179 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history. 

Literature

A structurally dynamic N-terminal region drives function of the staphylococcal peroxidase inhibitor (SPIN).

de Jong, N.W.M., Ploscariu, N.T., Ramyar, K.X., Garcia, B.L., Herrera, A.I., Prakash, O., Katz, B.B., Leidal, K.G., Nauseef, W.M., van Kessel, K.P.M., van Strijp, J.A.G., Geisbrecht, B.V.

(2018) J. Biol. Chem. 293: 2260-2271

  • DOI: 10.1074/jbc.RA117.000134

  • PubMed Abstract: 

    • The heme-containing enzyme myeloperoxidase (MPO) is critical for optimal antimicrobial activity of human neutrophils. We recently discovered that the bacterium Staphylococcus aureus expresses a novel immune evasion protein, called SPIN, that binds ti ...

    The heme-containing enzyme myeloperoxidase (MPO) is critical for optimal antimicrobial activity of human neutrophils. We recently discovered that the bacterium Staphylococcus aureus expresses a novel immune evasion protein, called SPIN, that binds tightly to MPO, inhibits MPO activity, and contributes to bacterial survival following phagocytosis. A co-crystal structure of SPIN bound to MPO suggested that SPIN blocks substrate access to the catalytic heme by inserting an N-terminal β-hairpin into the MPO active site channel. Here, we describe a series of experiments that more completely define the structure/function relationships of SPIN. Whereas the SPIN N-terminus adopts a β-hairpin confirmation upon binding to MPO, solution NMR studies presented here are consistent with this region of SPIN being dynamically structured in the unbound state. Curiously, while the N-terminal β-hairpin of SPIN accounts for ~55% of the buried surface area in the SPIN/MPO complex, its deletion did not significantly change the affinity of SPIN for MPO but did eliminate the ability of SPIN to inhibit MPO. The flexible nature of the SPIN N-terminus rendered it susceptible to proteolytic degradation by a series of chymotrypsin-like proteases found within neutrophil granules, thereby abrogating SPIN activity. Degradation of SPIN was prevented by the S. aureus immune evasion protein Eap, which acts as a selective inhibitor of neutrophil serine proteases. Together, these studies provide insight into MPO inhibition by SPIN and suggest possible functional synergy between two distinct classes of S. aureus immune evasion proteins.

    Organizational Affiliation: 

    University Medical Center Utrecht, Netherlands.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Myeloperoxidase
A
577Homo 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
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Staphylococcal Peroxidase Inhibitor
B
60Staphylococcus aureus (strain NCTC 8325)Mutation(s): 0 
Find proteins for Q2G0X2 (Staphylococcus aureus (strain NCTC 8325))
Go to UniProtKB:  Q2G0X2
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA
Download SDF File 
Download CCD File 
A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
BMA
Query on BMA
Download SDF File 
Download CCD File 
A
BETA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-RWOPYEJCSA-N
 Ligand Interaction
NAG
Query on NAG
Download SDF File 
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: 2.291 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.179 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 128.854α = 90.00
b = 92.876β = 119.91
c = 80.460γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
PDB_EXTRACTdata extraction
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

Entry History & Funding Information

Deposition Data

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

Revision History 

  • Version 1.0: 2017-12-27
    Type: Initial release
  • Version 1.1: 2018-01-17
    Type: Database references
  • Version 1.2: 2018-02-28
    Type: Database references