PDBsum entry 1ryy

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Hydrolase PDB id
Protein chains
(+ 2 more) 612 a.a. *
Waters ×321
* Residue conservation analysis
PDB id:
Name: Hydrolase
Title: Acetobacter turbidans alpha-amino acid ester hydrolase y206a
Structure: Alpha-amino acid ester hydrolase. Chain: a, b, c, d, e, f, g, h. Fragment: alpha-amino acid ester hydrolase. Engineered: yes. Mutation: yes
Source: Acetobacter pasteurianus. Organism_taxid: 438. Gene: aeha. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Tetramer (from PQS)
2.80Å     R-factor:   0.211     R-free:   0.236
Authors: T.R.M.Barends
Key ref:
T.R.Barends et al. (2006). Acetobacter turbidans alpha-amino acid ester hydrolase: how a single mutation improves an antibiotic-producing enzyme. J Biol Chem, 281, 5804-5810. PubMed id: 16377627 DOI: 10.1074/jbc.M511187200
23-Dec-03     Release date:   22-Feb-05    
Go to PROCHECK summary

Protein chains
Pfam   ArchSchema ?
Q8VRK8  (Q8VRK8_ACEPA) -  Alpha-amino acid ester hydrolase
667 a.a.
612 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Enzyme reactions 
   Enzyme class: E.C.  - Alpha-amino-acid esterase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: An alpha-amino acid ester + H2O = an alpha-amino acid + an alcohol
alpha-amino acid ester
+ H(2)O
= alpha-amino acid
+ alcohol
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     metabolic process   2 terms 
  Biochemical function     hydrolase activity     4 terms  


DOI no: 10.1074/jbc.M511187200 J Biol Chem 281:5804-5810 (2006)
PubMed id: 16377627  
Acetobacter turbidans alpha-amino acid ester hydrolase: how a single mutation improves an antibiotic-producing enzyme.
T.R.Barends, J.J.Polderman-Tijmes, P.A.Jekel, C.Williams, G.Wybenga, D.B.Janssen, B.W.Dijkstra.
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.
  Selected figure(s)  
Figure 2.
a, stereo figure of the A. turbidans α-amino acid ester hydrolase tetramer. A surface representation is shown, in which each monomer is individually colored. b, stereo figure of the A. turbidans α-amino acid ester hydrolase monomer. The arm and α/β-hydrolase domains are shown in green, the cap domain in orange, and the jellyroll domain in blue. The side chain of the active site Ser^205 is shown in space filling representation. Helices αC-αF and strands β4-β7 are labeled. The figure was prepared using PYMOL (DeLano Scientific) and Molscript (30).
Figure 4.
Stereo picture of the 2F[o] - F[c] electron density of ampicillin in the active site of the S205A mutant, after refinement of the initial molecular replacement solution, prior to inclusion of ampicillin in the model. The density was contoured at 1.0 σ, and overlaid on the final refined structure. The figure was prepared using Xfit (22) and Raster3D (32).
  The above figures are reprinted by permission from the ASBMB: J Biol Chem (2006, 281, 5804-5810) copyright 2006.  
  Figures were selected by the author.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20436035 D.Narasimhan, M.R.Nance, D.Gao, M.C.Ko, J.Macdonald, P.Tamburi, D.Yoon, D.M.Landry, J.H.Woods, C.G.Zhan, J.J.Tesmer, and R.K.Sunahara (2010).
Structural analysis of thermostabilizing mutations of cocaine esterase.
  Protein Eng Des Sel, 23, 537-547.
PDB codes: 3i2f 3i2g 3i2h 3i2i 3i2j 3i2k
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