6C39 | pdb_00006c39

Apo crystal structure of wild-type S. aureus penicillin binding protein 4 (PBP4)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.69 Å
  • R-Value Free: 
    0.196 (Depositor), 0.182 (DCC) 
  • R-Value Work: 
    0.161 (Depositor) 
  • R-Value Observed: 
    0.163 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 6C39

This is version 1.2 of the entry. See complete history

Literature

Structural and kinetic analyses of penicillin-binding protein 4 (PBP4)-mediated antibiotic resistance inStaphylococcus aureus.

Alexander, J.A.N.Chatterjee, S.S.Hamilton, S.M.Eltis, L.D.Chambers, H.F.Strynadka, N.C.J.

(2018) J Biological Chem 293: 19854-19865

  • DOI: https://doi.org/10.1074/jbc.RA118.004952
  • Primary Citation Related Structures: 
    5TW4, 5TW8, 5TX9, 5TXI, 5TY2, 5TY7, 6C39, 6C3K

  • PubMed Abstract: 

    Methicillin-resistant Staphylococcus aureus (MRSA) causes serious community-acquired and nosocomial infections worldwide. MRSA strains are resistant to a variety of antibiotics, including the classic penicillin and cephalosporin classes of β-lactams, making them intractable to treatment. Although β-lactam resistance in MRSA has been ascribed to the acquisition and activity of penicillin-binding protein 2a (PBP2a, encoded by mecA ), it has recently been observed that resistance can also be mediated by penicillin-binding protein 4 (PBP4). Previously, we have shown that broad-spectrum β-lactam resistance can arise following serial passaging of a mecA -negative COL strain of S. aureus, creating the CRB strain. This strain has two missense mutations in pbp4 and a mutation in the pbp4 promoter, both of which play an instrumental role in β-lactam resistance. To better understand PBP4's role in resistance, here we have characterized its kinetics and structure with clinically relevant β-lactam antibiotics. We present the first crystallographic PBP4 structures of apo and acyl-enzyme intermediate forms complexed with three late-generation β-lactam antibiotics: ceftobiprole, ceftaroline, and nafcillin. In parallel, we characterized the structural and kinetic effects of the PBP4 mutations present in the CRB strain. Localized within the transpeptidase active-site cleft, the two substitutions appear to have different effects depending on the drug. With ceftobiprole, the missense mutations impaired the K m value 150-fold, decreasing the proportion of inhibited PBP4. However, ceftaroline resistance appeared to be mediated by other factors, possibly including mutation of the pbp4 promoter. Our findings provide evidence that S. aureus CRB has at least two PBP4-mediated resistance mechanisms.


  • Organizational Affiliation
    • From the Department of Biochemistry and Molecular Biology.

Macromolecule Content 

  • Total Structure Weight: 82.76 kDa 
  • Atom Count: 6,356 
  • Modeled Residue Count: 718 
  • Deposited Residue Count: 734 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Serine-type D-Ala-D-Ala carboxypeptidase
A, B
367Staphylococcus aureusMutation(s): 0 
Gene Names: HMPREF3211_00659
UniProt
Find proteins for A0A0H2WY27 (Staphylococcus aureus (strain COL))
Explore A0A0H2WY27 
Go to UniProtKB:  A0A0H2WY27
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0H2WY27
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SO4

Query on SO4



Download:Ideal Coordinates CCD File
F [auth A],
K [auth B]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
ZN

Query on ZN



Download:Ideal Coordinates CCD File
C [auth A],
D [auth A],
G [auth B],
H [auth B],
I [auth B]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
NA

Query on NA



Download:Ideal Coordinates CCD File
E [auth A],
J [auth B]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.69 Å
  • R-Value Free:  0.196 (Depositor), 0.182 (DCC) 
  • R-Value Work:  0.161 (Depositor) 
  • R-Value Observed: 0.163 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 116.358α = 90
b = 92.403β = 99.23
c = 79.23γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Canadian Institutes of HealthCanada--

Revision History  (Full details and data files)

  • Version 1.0: 2018-11-07
    Type: Initial release
  • Version 1.1: 2019-01-02
    Changes: Data collection, Database references
  • Version 1.2: 2023-10-04
    Changes: Data collection, Database references, Derived calculations, Refinement description