2Y2K

PENICILLIN-BINDING PROTEIN 1B (PBP-1B) IN COMPLEX WITH AN ALKYL BORONATE (ZA5)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.09 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.202 
  • R-Value Observed: 0.208 

wwPDB Validation   3D Report Full Report


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


Literature

Structure-Guided Design of Cell Wall Biosynthesis Inhibitors that Overcome Beta-Lactam Resistance in Staphylococcus Aureus (Mrsa).

Contreras-Martel, C., Amoroso, A., Woon, E.C., Zervosen, A., Inglis, S., Martins, A., Verlaine, O., Rydzik, A., Job, V., Luxen, A., Joris, B., Schofield, C.J., Dessen, A.

(2011) ACS Chem Biol 6: 943

  • DOI: 10.1021/cb2001846
  • Primary Citation of Related Structures:  
    2Y2G, 2Y2H, 2Y2I, 2Y2J, 2Y2K, 2Y2L, 2Y2M, 2Y2N, 2Y2O, 2Y2P

  • PubMed Abstract: 

    • β-Lactam antibiotics have long been a treatment of choice for bacterial infections since they bind irreversibly to Penicillin-Binding Proteins (PBPs), enzymes that are vital for cell wall biosynthesis. Many pathogens express drug-insensitive PBPs ren ...

    β-Lactam antibiotics have long been a treatment of choice for bacterial infections since they bind irreversibly to Penicillin-Binding Proteins (PBPs), enzymes that are vital for cell wall biosynthesis. Many pathogens express drug-insensitive PBPs rendering β-lactams ineffective, revealing a need for new types of PBP inhibitors active against resistant strains. We have identified alkyl boronic acids that are active against pathogens including methicillin-resistant S. aureus (MRSA). The crystal structures of PBP1b complexed to 11 different alkyl boronates demonstrate that in vivo efficacy correlates with the mode of inhibitor side chain binding. Staphylococcal membrane analyses reveal that the most potent alkyl boronate targets PBP1, an autolysis system regulator, and PBP2a, a low β-lactam affinity enzyme. This work demonstrates the potential of boronate-based PBP inhibitors for circumventing β-lactam resistance and opens avenues for the development of novel antibiotics that target Gram-positive pathogens.

    Organizational Affiliation: 

    Bacterial Pathogenesis Group, Institut de Biologie Structurale, Université Grenoble I, France.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
PENICILLIN-BINDING PROTEIN 1BA494Streptococcus pneumoniae R6Mutation(s): 3 
Gene Names: pbp1b, spr1909
EC: 2.4.1.129 (PDB Primary Data), 2.3.2 (PDB Primary Data), 3.4.16.4 (UniProt)
Find proteins for Q7CRA4 (Streptococcus pneumoniae (strain ATCC BAA-255 / R6))
Explore Q7CRA4 
Go to UniProtKB:  Q7CRA4
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZA5
Query on ZA5
Download Ideal Coordinates CCD File 
A
[(2,6-DIFLUOROPHENYL)CARBONYLAMINO]METHYL-TRIHYDROXY-BORON
C8 H9 B F2 N O4
WTOJBPXTZMRWEB-UHFFFAOYSA-N		 Ligand Interaction
SO4
Query on SO4
Download Ideal Coordinates CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L		 Ligand Interaction
EDO
Query on EDO
Download Ideal Coordinates CCD File 
A
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N		 Ligand Interaction
CL
Query on CL
Download Ideal Coordinates CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M		 Ligand Interaction
NA
Query on NA
Download Ideal Coordinates CCD File 
A
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N		 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
ZA5IC50 :  6900   nM  PDBBind
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.09 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.202 
  • R-Value Observed: 0.208 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 98.309α = 90
b = 149.908β = 90
c = 97.578γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

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View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-08-03
    Type: Initial release
  • Version 1.1: 2011-10-26
    Changes: Database references
  • Version 1.2: 2012-11-14
    Changes: Database references