5HL9

E. coli PBP1b in complex with acyl-ampicillin and moenomycin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.240 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Escherichia coli Penicillin-Binding Protein 1B: Structural Insights into Inhibition.

King, D.T.Wasney, G.A.Nosella, M.Fong, A.Strynadka, N.C.

(2016) J. Biol. Chem. --: --

  • DOI: 10.1074/jbc.M116.718403
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • In Escherichia coli, the peptidoglycan cell wall is synthesized by bifunctional penicillin-binding proteins such as PBP1b that have both transpeptidase and transglycosylase activities. The PBP1b transpeptidase domain is a major target of β-lactams, a ...

    In Escherichia coli, the peptidoglycan cell wall is synthesized by bifunctional penicillin-binding proteins such as PBP1b that have both transpeptidase and transglycosylase activities. The PBP1b transpeptidase domain is a major target of β-lactams, and therefore it is important to attain a detailed understanding of its inhibition. The peptidoglycan glycosyltransferase domain of PBP1b is also considered an excellent antibiotic target yet is not exploited by any clinically approved antibacterials. Herein, we adapt a pyrophosphate sensor assay to monitor PBP1b-catalyzed glycosyltransfer and present an improved crystallographic model for inhibition of the PBP1b glycosyltransferase domain by the potent substrate analog moenomycin. We elucidate the structure of a previously disordered region in the glycosyltransferase active site and discuss its implications with regards to peptidoglycan polymerization. Furthermore, we solve the crystal structures of E. coli PBP1b bound to multiple different β-lactams in the transpeptidase active site and complement these data with gel-based competition assays to provide a detailed structural understanding of its inhibition. Taken together, these biochemical and structural data allow us to propose new insights into inhibition of both enzymatic domains in PBP1b.


    Organizational Affiliation

    From the Department of Biochemistry and Molecular Biology and Centre for Blood Research, University of British Columbia, Vancouver, British Columbia, V6T 1Z3, Canada.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Penicillin-binding protein 1B
A
747Escherichia coli (strain K12)Gene Names: mrcB (pbpF, ponB)
EC: 2.4.1.129, 3.4.16.4
Find proteins for P02919 (Escherichia coli (strain K12))
Go to UniProtKB:  P02919
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
AIX
Query on AIX

Download SDF File 
Download CCD File 
A
(2R,4S)-2-[(1R)-1-{[(2R)-2-amino-2-phenylacetyl]amino}-2-oxoethyl]-5,5-dimethyl-1,3-thiazolidine-4-carboxylic acid
AMPICILLIN (open form)
C16 H21 N3 O4 S
WHAIWIUXAXKSOT-NRWUCQMLSA-N
 Ligand Interaction
M0E
Query on M0E

Download SDF File 
Download CCD File 
A
MOENOMYCIN
MOENOMYCIN
C69 H106 N5 O34 P
NXPRJQIAIORCGO-ZLPAOQQDSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.240 
  • Space Group: P 2 21 21
Unit Cell:
Length (Å)Angle (°)
a = 62.440α = 90.00
b = 63.800β = 90.00
c = 299.350γ = 90.00
Software Package:
Software NamePurpose
Aimlessdata scaling
xia2data reduction
BUSTERrefinement
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationCountryGrant Number
Canadian Institutes of Health ResearchCanada--
Howard Hughes Medical InstituteUnited States--
Canadian Foundation for InnovationCanada--
British Columbia Knowledge Development FundCanada--
Canada Research Chair ProgramsCanada--

Revision History 

  • Version 1.0: 2016-12-14
    Type: Initial release
  • Version 1.1: 2017-09-20
    Type: Author supporting evidence