1ERM

X-RAY CRYSTAL STRUCTURE OF TEM-1 BETA LACTAMASE IN COMPLEX WITH A DESIGNED BORONIC ACID INHIBITOR (1R)-1-ACETAMIDO-2-(3-CARBOXYPHENYL)ETHANE BORONIC ACID


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Work: 0.177 
  • R-Value Observed: 0.177 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structure-based design guides the improved efficacy of deacylation transition state analogue inhibitors of TEM-1 beta-Lactamase(,).

Ness, S.Martin, R.Kindler, A.M.Paetzel, M.Gold, M.Jensen, S.E.Jones, J.B.Strynadka, N.C.

(2000) Biochemistry 39: 5312-5321

  • DOI: 10.1021/bi992505b
  • Primary Citation of Related Structures:  
    1ERQ, 1ERO, 1ERM

  • PubMed Abstract: 
  • Transition state analogue boronic acid inhibitors mimicking the structures and interactions of good penicillin substrates for the TEM-1 beta-lactamase of Escherchia coli were designed using graphic analyses based on the enzyme's 1.7 A crystallographic structure ...

    Transition state analogue boronic acid inhibitors mimicking the structures and interactions of good penicillin substrates for the TEM-1 beta-lactamase of Escherchia coli were designed using graphic analyses based on the enzyme's 1.7 A crystallographic structure. The synthesis of two of these transition state analogues, (1R)-1-phenylacetamido-2-(3-carboxyphenyl)ethylboronic acid (1) and (1R)-1-acetamido-2-(3-carboxy-2-hydroxyphenyl)ethylboronic acid (2), is reported. Kinetic measurements show that, as designed, compounds 1 and 2 are highly effective deacylation transition state analogue inhibitors of TEM-1 beta-lactamase, with inhibition constants of 5.9 and 13 nM, respectively. These values identify them as among the most potent competitive inhibitors yet reported for a beta-lactamase. The best inhibitor of the current series was (1R)-1-phenylacetamido-2-(3-carboxyphenyl)ethylboronic acid (1, K(I) = 5.9 nM), which resembles most closely the best known substrate of TEM-1, benzylpenicillin (penicillin G). The high-resolution crystallographic structures of these two inhibitors covalently bound to TEM-1 are also described. In addition to verifying the design features, these two structures show interesting and unanticipated changes in the active site area, including strong hydrogen bond formation, water displacement, and rearrangement of side chains. The structures provide new insights into the further design of this potent class of beta-lactamase inhibitors.


    Related Citations: 
    • Structure-based design of a potent transition state analogue for TEM-1 beta-lactamase
      Strynadka, N.C.J., Martin, R., Jensen, S.E., Gold, M., Jones, J.B.
      (1996) Nat Struct Biol 3: 688

    Organizational Affiliation

    Department of Biochemistry and Molecular Biology, University of British Columbia, 2146 Health Sciences Mall, Vancouver, British Columbia, Canada.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
TEM-1 BETA-LACTAMASEA263Escherichia coliMutation(s): 0 
Gene Names: blablaT-3blaT-4blaT-5blaT-6
EC: 3.5.2.6
Find proteins for P62593 (Escherichia coli)
Explore P62593 
Go to UniProtKB:  P62593
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
BJI
Query on BJI

Download CCD File 
A
1(R)-1-ACETAMIDO-2-(3-CARBOXYPHENYL)ETHYL BORONIC ACID
C11 H14 B N O5
OBZSRKUYUGJGIM-JTQLQIEISA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
BHD
Query on BHD
AL-PEPTIDE LINKINGC4 H7 N O5ASP
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Work: 0.177 
  • R-Value Observed: 0.177 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 63.03α = 90
b = 89.06β = 90
c = 42.16γ = 90
Software Package:
Software NamePurpose
SDMSdata collection
SDMSdata reduction
MLPHAREphasing
TNTrefinement
SDMSdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2000-05-10
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2012-06-20
    Changes: Non-polymer description