Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

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: 26.09 kDa 
• Atom Count: 1800 
• Modelled Residue Count: 200 
• Deposited Residue Count: 219 
• Unique protein chains: 1

3KOS

Structure of the AmpR effector binding domain from Citrobacter freundii

• PDB DOI: 10.2210/pdb3KOS/pdb

• Classification: TRANSCRIPTION
• Organism(s): Citrobacter freundii
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2009-11-13 Released: 2010-05-26 
• Deposition Author(s): Mark, B.L., Balcewich, M.D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.83 Å
• R-Value Free: 0.202 
• R-Value Work: 0.170 
• R-Value Observed: 0.173 

Literature

Crystal Structure of the AmpR Effector Binding Domain Provides Insight into the Molecular Regulation of Inducible AmpC beta-Lactamase.

Balcewich, M.D., Reeve, T.M., Orlikow, E.A., Donald, L.J., Vocadlo, D.J., Mark, B.L.

(2010) J Mol Biol 400: 998-1010

• PubMed: 20594961 
• DOI: 10.1016/j.jmb.2010.05.040
• Primary Citation of Related Structures:  
  3KOS, 3KOT


• PubMed Abstract: 
  

Hyperproduction of AmpC beta-lactamase (AmpC) is a formidable mechanism of resistance to penicillins and cephalosporins in Gram-negative bacteria such as Pseudomonas aeruginosa and Enterobacteriaceae. AmpC expression is regulated by the LysR-type transcriptional regulator AmpR. ampR and ampC genes form a divergent operon with overlapping promoters to which AmpR binds and regulates the transcription of both genes. AmpR induces ampC by binding to one member of the family of 1,6-anhydro-N-acetylmuramyl peptides, which are cytosolic catabolites of peptidoglycan that accumulate during beta-lactam challenge. To gain structural insights into AmpR regulation, we determined the crystal structure of the effector binding domain (EBD) of AmpR from Citrobacter freundii up to 1.83 A resolution. The AmpR EBD is dimeric and each monomer comprises two subdomains that adopt alpha/beta Rossmann-like folds. Located between the monomer subdomains is a pocket that was found to bind the crystallization buffer molecule 2-(N-morpholino)ethanesulfonic acid. The pocket, together with a groove along the surface of subdomain I, forms a putative effector binding site into which a molecule of 1,6-anhydro-N-acetylmuramyl pentapeptide could be modeled. Amino acid substitutions at the base of the interdomain pocket either were found to render AmpR incapable of inducing ampC (Thr103Val, Ser221Ala and Tyr264Phe) or resulted in constitutive ampC expression (Gly102Glu). While the substitutions that prevented ampC induction did not alter the overall AmpR EBD structure, circular dichroism spectroscopy revealed that the nonconservative Gly102Glu mutation affected EBD secondary structure, confirming previous work suggesting that Gly102Glu induces a conformational change to result in constitutive AmpC production.

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Organizational Affiliation: 

Department of Microbiology, University of Manitoba, 418 Buller Building, Winnipeg, Manitoba, Canada R3T 2N2.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HTH-type transcriptional activator ampR	A	219	Citrobacter freundii	Mutation(s): 3  Gene Names: ampR
UniProt
Find proteins for P12529 (Citrobacter freundii) Explore P12529  Go to UniProtKB:  P12529

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MES	B [auth A], C [auth A]	2-(N-MORPHOLINO)-ETHANESULFONIC ACID C6 H13 N O4 S SXGZJKUKBWWHRA-UHFFFAOYSA-N
GOL	D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.83 Å
• R-Value Free: 0.202 
• R-Value Work: 0.170 
• R-Value Observed: 0.173 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 125.28	α = 90
b = 34.19	β = 102.77
c = 49.98	γ = 90

Software Package:

Software Name	Purpose
MOSFLM	data reduction
SOLVE	phasing
PHENIX	refinement
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2009-11-13 
• Released Date: 2010-05-26 
Deposition Author(s): Mark, B.L., Balcewich, M.D.

Revision History  

• Version 1.0: 2010-05-26
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2018-01-24
  Changes: Structure summary