4OQG

Crystal structure of TEM-1 beta-lactamase in complex with boron-based inhibitor EC25


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.203 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Negative Epistasis and Evolvability in TEM-1 beta-Lactamase--The Thin Line between an Enzyme's Conformational Freedom and Disorder.

Dellus-Gur, E.Elias, M.Caselli, E.Prati, F.Salverda, M.L.de Visser, J.A.Fraser, J.S.Tawfik, D.S.

(2015) J. Mol. Biol. 427: 2396-2409

  • DOI: 10.1016/j.jmb.2015.05.011
  • Primary Citation of Related Structures:  4OP5, 4OP8, 4OPQ, 4OPR, 4OPY, 4OPZ, 4OQ0, 4OQH, 4OQI

  • PubMed Abstract: 
  • Epistasis is a key factor in evolution since it determines which combinations of mutations provide adaptive solutions and which mutational pathways toward these solutions are accessible by natural selection. There is growing evidence for the pervasiv ...

    Epistasis is a key factor in evolution since it determines which combinations of mutations provide adaptive solutions and which mutational pathways toward these solutions are accessible by natural selection. There is growing evidence for the pervasiveness of sign epistasis--a complete reversion of mutational effects, particularly in protein evolution--yet its molecular basis remains poorly understood. We describe the structural basis of sign epistasis between G238S and R164S, two adaptive mutations in TEM-1 β-lactamase--an enzyme that endows antibiotics resistance. Separated by 10 Å, these mutations initiate two separate trajectories toward increased hydrolysis rates and resistance toward second and third-generation cephalosporins antibiotics. Both mutations allow the enzyme's active site to adopt alternative conformations and accommodate the new antibiotics. By solving the corresponding set of crystal structures, we found that R164S causes local disorder whereas G238S induces discrete conformations. When combined, the mutations in 238 and 164 induce local disorder whereby nonproductive conformations that perturb the enzyme's catalytic preorganization dominate. Specifically, Asn170 that coordinates the deacylating water molecule is misaligned, in both the free form and the inhibitor-bound double mutant. This local disorder is not restored by stabilizing global suppressor mutations and thus leads to an evolutionary cul-de-sac. Conformational dynamism therefore underlines the reshaping potential of protein's structures and functions but also limits protein evolvability because of the fragility of the interactions networks that maintain protein structures.


    Organizational Affiliation

    Department of Biological Chemistry, Weizmann Institute of Science, Rehovot 76100, Israel.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Ampicillin resistance protein
A, B, C, D, E, F
263Escherichia coliGene Names: blaTEM-116 (bla)
EC: 3.5.2.6
Find proteins for Q79DR3 (Escherichia coli)
Go to UniProtKB:  Q79DR3
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
2UL
Query on 2UL

Download SDF File 
Download CCD File 
A, B, C, D, F
3-[(2R)-2-{[(2R)-2-amino-2-phenylacetyl]amino}-2-(dihydroxyboranyl)ethyl]benzoic acid
C17 H19 B N2 O5
WMZXFYUXEUIIHA-LSDHHAIUSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.203 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 81.690α = 90.00
b = 81.690β = 90.00
c = 497.920γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
StructureStudiodata collection
XDSdata reduction
MOLREPphasing
XSCALEdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-05-20
    Type: Initial release
  • Version 1.1: 2016-02-24
    Type: Other
  • Version 1.2: 2018-01-17
    Type: Database references