5JOC

Crystal structure of the S61A mutant of AmpC BER


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.200 
  • R-Value Work: 0.177 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Structural basis for the extended substrate spectrum of AmpC BER and structure-guided discovery of the inhibition activity of citrate against the class C beta-lactamases AmpC BER and CMY-10.

Na, J.H.Cha, S.S.

(2016) Acta Crystallogr D Struct Biol 72: 976-985

  • DOI: 10.1107/S2059798316011311
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • AmpC BER is an extended substrate spectrum class C β-lactamase with a two-amino-acid insertion in the R2 loop compared with AmpC EC2. The crystal structures of AmpC BER (S64A mutant) and AmpC EC2 were determined. Structural comparison of the two prot ...

    AmpC BER is an extended substrate spectrum class C β-lactamase with a two-amino-acid insertion in the R2 loop compared with AmpC EC2. The crystal structures of AmpC BER (S64A mutant) and AmpC EC2 were determined. Structural comparison of the two proteins revealed that the insertion increases the conformational flexibility of the R2 loop. Two citrate molecules originating from the crystallization solution were observed in the active site of the S64A mutant. One citrate molecule makes extensive interactions with active-site residues that are highly conserved among class C β-lactamases, whereas the other one is weakly bound. Based on this structural observation, it is demonstrated that citrate, a primary metabolite that is widely used as a food additive, is a competitive inhibitor of two class C β-lactamases (AmpC BER and CMY-10). Consequently, the data indicate enhancement of the flexibility of the R2 loop as an operative strategy for molecular evolution of extended-spectrum class C β-lactamases, and also suggest that the citrate scaffold is recognized by the active sites of class C β-lactamases.


    Organizational Affiliation

    Department of Chemistry and Nano Science, Ewha Womans University, Seoul 03760, Republic of Korea.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Beta-lactamase
A, B
366Escherichia coli (strain K12)Mutation(s): 1 
Gene Names: ampC (ampA)
EC: 3.5.2.6
Find proteins for P00811 (Escherichia coli (strain K12))
Go to UniProtKB:  P00811
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CIT
Query on CIT

Download SDF File 
Download CCD File 
A, B
CITRIC ACID
C6 H8 O7
KRKNYBCHXYNGOX-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.200 
  • R-Value Work: 0.177 
  • Space Group: P 63
Unit Cell:
Length (Å)Angle (°)
a = 207.208α = 90.00
b = 207.208β = 90.00
c = 45.635γ = 120.00
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data scaling
HKL-2000data processing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Korea, Republic Of--

Revision History 

  • Version 1.0: 2017-05-03
    Type: Initial release