Biological Assembly 1  

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Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 55112.70 
• Atom Count: 3679 
• Residue Count: 494 
• Unique protein chains: 1

2Y2K

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

• DOI: 10.2210/pdb2Y2K/pdb

• Classification: TRANSFERASE
• Organism(s): Streptococcus pneumoniae (strain ATCC BAA-255 / R6)
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): 3 


• Deposited: 2010-12-15 Released: 2011-08-03 
• Deposition Author(s): Contreras-Martel, C., Amoroso, A., Woon, E., Zervosen, A., Inglis, S., Martins, A., Verlaine, O., Rydzik, A., Job, V., Luxen, A., Joris, B., Schofield, C., Dessen, A.

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Experimental Data Snapshot

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

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

• PubMed: 21732689 
• DOI: 10.1021/cb2001846
• Primary Citation of Related Structures:  
  2Y2Q, 2Y2P, 2Y2O, 2Y2N, 2Y2M, 2Y2L, 2Y2J, 2Y2H, 2Y2I, 2Y2G


• 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 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.

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Organizational Affiliation: 

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

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
PENICILLIN-BINDING PROTEIN 1B	A	494	Streptococcus 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
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
NA	A	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N
ZA5	A	[(2,6-DIFLUOROPHENYL)CARBONYLAMINO]METHYL-TRIHYDROXY-BORON C8 H9 B F2 N O4 WTOJBPXTZMRWEB-UHFFFAOYSA-N
SO4	A	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
CL	A	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
EDO	A	1,2-ETHANEDIOL ETHYLENE GLYCOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
ZA5	IC50: 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 = 98.309	α = 90.00
b = 149.908	β = 90.00
c = 97.578	γ = 90.00

Software Package:

Software Name	Purpose
REFMAC	refinement
XSCALE	data scaling
PHASER	phasing
XDS	data reduction

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2010-12-15 
• Released Date: 2011-08-03 
• Deposition Author(s): Contreras-Martel, C., Amoroso, A., Woon, E., Zervosen, A., Inglis, S., Martins, A., Verlaine, O., Rydzik, A., Job, V., Luxen, A., Joris, B., Schofield, C., Dessen, A.

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