8D7I

Bifunctional Inhibition of Neutrophil Elastase and Cathepsin G by Eap1 from S. aureus


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.63 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.188 

Starting Models: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

S. aureus Eap is a polyvalent inhibitor of neutrophil serine proteases.

Mishra, N.Gido, C.D.Herdendorf, T.J.Hammel, M.Hura, G.L.Fu, Z.Q.Geisbrecht, B.V.

(2024) J Biol Chem 300: 107627-107627

  • DOI: https://doi.org/10.1016/j.jbc.2024.107627
  • Primary Citation of Related Structures:  
    8D7I, 8D7K, 9ASS, 9ASX, 9ATK, 9ATU

  • PubMed Abstract: 

    Staphylococcus aureus expresses three high-affinity neutrophil serine protease (NSP) inhibitors known as the extracellular adherence protein domain (EAPs) proteins. Whereas EapH1 and EapH2 are comprised of a single EAP domain, the modular extracellular adherence protein (Eap) from S. aureus strain Mu50 consists of four EAP domains. We recently reported that EapH2 can simultaneously bind and inhibit cathepsin-G (CG) and neutrophil elastase (NE), which are the two most abundant NSPs. This unusual property of EapH2 arises from independent CG and NE-binding sites that lie on opposing faces of its EAP domain. Here we used X-ray crystallography and enzyme assays to show that all four individual domains of Eap (i.e. Eap1, Eap2, Eap3, and Eap4) exhibit an EapH2-like ability to form ternary complexes with CG and NE that inhibit both enzymes simultaneously. We found that Eap1, Eap2, and Eap3 have similar functional profiles insofar as NSP inhibition is concerned but that Eap4 displays an unexpected ability to inhibit two NE enzymes simultaneously. Using X-ray crystallography, we determined that this second NE-binding site in Eap4 arises through the same region of its EAP domain that also comprises its CG-binding site. Interestingly, small angle X-ray scattering data showed that stable tail-to-tail dimers of the NE/Eap4/NE ternary complex exist in solution. This arrangement is compatible with NSP-binding at all available sites in a two-domain fragment of Eap. Together, our work implies that Eap is a polyvalent inhibitor of NSPs. It also raises the possibility that higher-order structures of NSP-bound Eap may have unique functional properties.


  • Organizational Affiliation

    Department of Biochemistry & Molecular Biophysics, Kansas State University, Manhattan, Kansas, USA.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Neutrophil elastase
A, D, G, J, M
A, D, G, J, M, P
218Homo sapiensMutation(s): 0 
EC: 3.4.21.37
UniProt & NIH Common Fund Data Resources
Find proteins for P08246 (Homo sapiens)
Explore P08246 
Go to UniProtKB:  P08246
PHAROS:  P08246
GTEx:  ENSG00000197561 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP08246
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Extracellular Adherence Protein
B, E, H, K, N
B, E, H, K, N, Q
100Staphylococcus aureus subsp. aureus Mu50Mutation(s): 0 
Gene Names: mapSAV1938
UniProt
Find proteins for Q99QS1 (Staphylococcus aureus (strain Mu50 / ATCC 700699))
Explore Q99QS1 
Go to UniProtKB:  Q99QS1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ99QS1
Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Cathepsin G, C-terminal truncated form
C, F, I, L, O
C, F, I, L, O, R
223Homo sapiensMutation(s): 0 
EC: 3.4.21.20
UniProt & NIH Common Fund Data Resources
Find proteins for P08311 (Homo sapiens)
Explore P08311 
Go to UniProtKB:  P08311
PHAROS:  P08311
GTEx:  ENSG00000100448 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP08311
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.63 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.188 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 102.23α = 90
b = 152.27β = 90
c = 296.38γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
PDB_EXTRACTdata extraction

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR35GM14852

Revision History  (Full details and data files)

  • Version 1.0: 2023-06-14
    Type: Initial release
  • Version 1.1: 2023-10-25
    Changes: Data collection, Refinement description
  • Version 1.2: 2024-10-16
    Changes: Structure summary
  • Version 1.3: 2024-10-23
    Changes: Database references