6MKH

Crystal structure of pencillin binding protein 4 (PBP4) from Enterococcus faecalis in the imipenem-bound form


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.62 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.199 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history


Literature

The structures of penicillin-binding protein 4 (PBP4) and PBP5 fromEnterococciprovide structural insights into beta-lactam resistance.

Moon, T.M.D'Andrea, E.D.Lee, C.W.Soares, A.Jakoncic, J.Desbonnet, C.Garcia-Solache, M.Rice, L.B.Page, R.Peti, W.

(2018) J Biol Chem 293: 18574-18584

  • DOI: https://doi.org/10.1074/jbc.RA118.006052
  • Primary Citation of Related Structures:  
    6BSQ, 6BSR, 6MKA, 6MKF, 6MKG, 6MKH, 6MKI, 6MKJ

  • PubMed Abstract: 

    The final steps of cell-wall biosynthesis in bacteria are carried out by penicillin-binding proteins (PBPs), whose transpeptidase domains form the cross-links in peptidoglycan chains that define the bacterial cell wall. These enzymes are the targets of β-lactam antibiotics, as their inhibition reduces the structural integrity of the cell wall. Bacterial resistance to antibiotics is a rapidly growing concern; however, the structural underpinnings of PBP-derived antibiotic resistance are poorly understood. PBP4 and PBP5 are low-affinity, class B transpeptidases that confer antibiotic resistance to Enterococcus faecalis and Enterococcus faecium , respectively. Here, we report the crystal structures of PBP4 (1.8 Å) and PBP5 (2.7 Å) in their apo and acyl-enzyme complexes with the β-lactams benzylpenicillin, imipenem, and ceftaroline. We found that, although these three β-lactams adopt geometries similar to those observed in other class B PBP structures, there are small, but significant, differences that likely decrease antibiotic efficacy. Further, we also discovered that the N-terminal domain extensions in this class of PBPs undergo large rigid-body rotations without impacting the structure of the catalytic transpeptidase domain. Together, our findings are defining the subtle functional and structural differences in the Enterococcus PBPs that allow them to support transpeptidase activity while also conferring bacterial resistance to antibiotics that function as substrate mimics.


  • Organizational Affiliation

    From the Department of Chemistry and Biochemistry, College of Medicine, University of Arizona, Tucson, Arizona 85721.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
pencillin binding protein 4 (PBP4)648Enterococcus faecalisMutation(s): 0 
Gene Names: pbp4A6B47_10405DAI13_12160
UniProt
Find proteins for Q9K3C9 (Enterococcus faecalis)
Explore Q9K3C9 
Go to UniProtKB:  Q9K3C9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9K3C9
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
IM2
Query on IM2

Download Ideal Coordinates CCD File 
B [auth A](5R)-5-[(1S,2R)-1-formyl-2-hydroxypropyl]-3-[(2-{[(E)-iminomethyl]amino}ethyl)sulfanyl]-4,5-dihydro-1H-pyrrole-2-carbox ylic acid
C12 H19 N3 O4 S
UACUABDJLSUFFC-IWSPIJDZSA-N
PO4
Query on PO4

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A]
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.62 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.199 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 123.842α = 90
b = 85.401β = 110.3
c = 84.572γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

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 StatesR56 AI045626-15

Revision History  (Full details and data files)

  • Version 1.0: 2018-10-31
    Type: Initial release
  • Version 1.1: 2018-11-07
    Changes: Data collection, Database references
  • Version 1.2: 2018-12-19
    Changes: Data collection, Database references
  • Version 1.3: 2019-12-18
    Changes: Author supporting evidence
  • Version 1.4: 2024-04-03
    Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary