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 

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:  

  • 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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PENICILLIN-BINDING PROTEIN 1B
A
494Streptococcus pneumoniae (strain ATCC BAA-255 / R6)Mutation(s): 3 
Gene Names: pbp1b
EC: 2.3.2.-, 2.4.1.129
Find proteins for Q7CRA4 (Streptococcus pneumoniae (strain ATCC BAA-255 / R6))
Go to UniProtKB:  Q7CRA4
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

Download SDF File 
Download CCD File 
A
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
ZA5
Query on ZA5

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Download 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

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Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
CL
Query on CL

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Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
EDO
Query on EDO

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Download CCD File 
A
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-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 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 98.309α = 90.00
b = 149.908β = 90.00
c = 97.578γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
XSCALEdata scaling
PHASERphasing
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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