2FFY

AmpC beta-lactamase N289A mutant in complex with a boronic acid deacylation transition state analog compound SM3


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.07 Å
  • R-Value Free: 0.164 
  • R-Value Work: 0.133 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

The deacylation mechanism of AmpC beta-lactamase at ultrahigh resolution

Chen, Y.Minasov, G.Roth, T.A.Prati, F.Shoichet, B.K.

(2006) J.Am.Chem.Soc. 128: 2970-2976

  • DOI: 10.1021/ja056806m

  • PubMed Abstract: 
  • Beta-lactamases confer bacterial resistance to beta-lactam antibiotics, such as penicillins. The characteristic class C beta-lactamase AmpC catalyzes the reaction with several key residues including Ser64, Tyr150, and Lys67. Here, we describe a 1.07 ...

    Beta-lactamases confer bacterial resistance to beta-lactam antibiotics, such as penicillins. The characteristic class C beta-lactamase AmpC catalyzes the reaction with several key residues including Ser64, Tyr150, and Lys67. Here, we describe a 1.07 A X-ray crystallographic structure of AmpC beta-lactamase in complex with a boronic acid deacylation transition-state analogue. The high quality of the electron density map allows the determination of many proton positions. The proton on the Tyr150 hydroxyl group is clearly visible and is donated to the boronic oxygen mimicking the deacylation water. Meanwhile, Lys67 hydrogen bonds with Ser64Ogamma, Asn152Odelta1, and the backbone oxygen of Ala220. This suggests that this residue is positively charged and has relinquished the hydrogen bond with Tyr150 observed in acyl-enzyme complex structures. Together with previous biochemical and NMR studies, these observations indicate that Tyr150 is protonated throughout the reaction coordinate, disfavoring mechanisms that involve a stable tyrosinate as the general base for deacylation. Rather, the hydroxyl of Tyr150 appears to be well positioned to electrostatically stabilize the negative charge buildup in the tetrahedral high-energy intermediate. This structure, in itself, appears consistent with a mechanism involving either Tyr150 acting as a transient catalytic base in conjunction with a neutral Lys67 or the lactam nitrogen as the general base. Whereas mutagenesis studies suggest that Lys67 may be replaced by an arginine, disfavoring the conjugate base mechanism, distinguishing between these two hypotheses may ultimately depend on direct determination of the pK(a) of Lys67 along the reaction coordinate.


    Organizational Affiliation

    Department of Pharmaceutical Chemistry, University of California-San Francisco, QB3 Building Room 508D, 1700 4th Street, San Francisco, CA 94143-2550, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Beta-lactamase
A, B
358Escherichia 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 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
K
Query on K

Download SDF File 
Download CCD File 
A, B
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
PO4
Query on PO4

Download SDF File 
Download CCD File 
B
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
SM3
Query on SM3

Download SDF File 
Download CCD File 
A, B
(1R)-1-(2-THIENYLACETYLAMINO)-1-PHENYLMETHYLBORONIC ACID
C13 H14 B N O3 S
LGJCDEZMANATFA-ZDUSSCGKSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.07 Å
  • R-Value Free: 0.164 
  • R-Value Work: 0.133 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 118.840α = 90.00
b = 76.063β = 115.85
c = 97.898γ = 90.00
Software Package:
Software NamePurpose
SHELXL-97refinement
SHELXmodel building
XDSdata scaling
SHELXphasing
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-03-28
    Type: Initial release
  • Version 1.1: 2008-05-01
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance