1NX9

Acetobacter turbidans alpha-amino acid ester hydrolase S205A mutant complexed with ampicillin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.184 
  • R-Value Work: 0.166 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Acetobacter turbidans {alpha}-Amino Acid Ester Hydrolase: HOW A SINGLE MUTATION IMPROVES AN ANTIBIOTIC-PRODUCING ENZYME.

Barends, T.R.M.Polderman-Tijmes, J.J.Jekel, P.A.Williams, C.Wybenga, G.Janssen, D.B.Dijkstra, B.W.

(2006) J.Biol.Chem. 281: 5804-5810

  • DOI: 10.1074/jbc.M511187200
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The alpha-amino acid ester hydrolase (AEH) from Acetobacter turbidans is a bacterial enzyme catalyzing the hydrolysis and synthesis of beta-lactam antibiotics. The crystal structures of the native enzyme, both unliganded and in complex with the hydro ...

    The alpha-amino acid ester hydrolase (AEH) from Acetobacter turbidans is a bacterial enzyme catalyzing the hydrolysis and synthesis of beta-lactam antibiotics. The crystal structures of the native enzyme, both unliganded and in complex with the hydrolysis product D-phenylglycine are reported, as well as the structures of an inactive mutant (S205A) complexed with the substrate ampicillin, and an active site mutant (Y206A) with an increased tendency to catalyze antibiotic production rather than hydrolysis. The structure of the native enzyme shows an acyl binding pocket, in which D-phenylglycine binds, and an additional space that is large enough to accommodate the beta-lactam moiety of an antibiotic. In the S205A mutant, ampicillin binds in this pocket in a non-productive manner, making extensive contacts with the side chain of Tyr(112), which also participates in oxyanion hole formation. In the Y206A mutant, the Tyr(112) side chain has moved with its hydroxyl group toward the catalytic serine. Because this changes the properties of the beta-lactam binding site, this could explain the increased beta-lactam transferase activity of this mutant.


    Organizational Affiliation

    Laboratories of Biophysical Chemistry and Biochemistry, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
alpha-amino acid ester hydrolase
A, B, C, D
652Acetobacter pasteurianusMutation(s): 1 
Gene Names: aehA
EC: 3.1.1.43
Find proteins for Q8VRK8 (Acetobacter pasteurianus)
Go to UniProtKB:  Q8VRK8
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download SDF File 
Download CCD File 
A, B, C, D
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
AIC
Query on AIC

Download SDF File 
Download CCD File 
A, B, C, D
(2S,5R,6R)-6-{[(2R)-2-AMINO-2-PHENYLETHANOYL]AMINO}-3,3-DIMETHYL-7-OXO-4-THIA-1-AZABICYCLO[3.2.0]HEPTANE-2-CARBOXYLIC ACID
AMPICILLIN; D(-)-ALPHA-AMINOBENZYLPENICILLIN; 6-[D(-)-ALPHA-AMINOPHENYLLACETAMIDO]PENICILLANIC ACID
C16 H19 N3 O4 S
AVKUERGKIZMTKX-NJBDSQKTSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.184 
  • R-Value Work: 0.166 
  • Space Group: I 2 3
Unit Cell:
Length (Å)Angle (°)
a = 341.828α = 90.00
b = 341.828β = 90.00
c = 341.828γ = 90.00
Software Package:
Software NamePurpose
AMoREphasing
SCALEPACKdata scaling
REFMACrefinement
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-03-09
    Type: Initial release
  • Version 1.1: 2008-04-29
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Non-polymer description, Version format compliance