1GM9

Crystal structures of penicillin acylase enzyme-substrate complexes: Structural insights into the catalytic mechanism


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.190 
  • R-Value Work: 0.153 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal Structures of Penicillin Acylase Enzyme- Substrate Complexes: Structural Insights Into the Catalytic Mechanism

Mcvey, C.E.Walsh, M.A.Dodson, G.G.Wilson, K.S.Brannigan, J.A.

(2001) J.Mol.Biol. 313: 139

  • DOI: 10.1006/jmbi.2001.5043
  • Primary Citation of Related Structures:  1GK9, 1GKF, 1GM7, 1GM8
  • Also Cited By: 1H2G

  • PubMed Abstract: 
  • The crystal structure of penicillin G acylase from Escherichia coli has been determined to a resolution of 1.3 A from a crystal form grown in the presence of ethylene glycol. To study aspects of the substrate specificity and catalytic mechanism of th ...

    The crystal structure of penicillin G acylase from Escherichia coli has been determined to a resolution of 1.3 A from a crystal form grown in the presence of ethylene glycol. To study aspects of the substrate specificity and catalytic mechanism of this key biotechnological enzyme, mutants were made to generate inactive protein useful for producing enzyme-substrate complexes. Owing to the intimate association of enzyme activity and precursor processing in this protein family (the Ntn hydrolases), most attempts to alter active-site residues lead to processing defects. Mutation of the invariant residue Arg B263 results in the accumulation of a protein precursor form. However, the mutation of Asn B241, a residue implicated in stabilisation of the tetrahedral intermediate during catalysis, inactivates the enzyme but does not prevent autocatalytic processing or the ability to bind substrates. The crystal structure of the Asn B241 Ala oxyanion hole mutant enzyme has been determined in its native form and in complex with penicillin G and penicillin G sulphoxide. We show that Asn B241 has an important role in maintaining the active site geometry and in productive substrate binding, hence the structure of the mutant protein is a poor model for the Michaelis complex. For this reason, we subsequently solved the structure of the wild-type protein in complex with the slowly processed substrate penicillin G sulphoxide. Analysis of this structure suggests that the reaction mechanism proceeds via direct nucleophilic attack of Ser B1 on the scissile amide and not as previously proposed via a tightly H-bonded water molecule acting as a "virtual" base.


    Related Citations: 
    • Penicillin Acylase Has a Single-Amino-Acid Catalytic Centre
      Duggleby, H.J.,Tolley, S.P.,Hill, C.P.,Dodson, E.J.,Dodson, G.,Moody, P.C.E.
      (1995) Nature 373: 264
    • Expression, Purification and Crystallisation of Penicillin G Acylase from Escherichia Coli Atcc 11105
      Hunt, P.D.,Tolley, S.P.,Ward, R.J.,Hill, C.P.,Dodson, G.G.
      (1990) Protein Eng. 3: 635


    Organizational Affiliation

    Structural Biology Laboratory Chemistry Department, University of York, York YO10 5DD, UK.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PENICILLIN G ACYLASE ALPHA SUBUNIT
A
209Escherichia coliGene Names: pac
EC: 3.5.1.11
Find proteins for P06875 (Escherichia coli)
Go to UniProtKB:  P06875
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
PENICILLIN G ACYLASE BETA SUBUNIT
B
557Escherichia coliGene Names: pac
EC: 3.5.1.11
Find proteins for P06875 (Escherichia coli)
Go to UniProtKB:  P06875
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

Download SDF File 
Download CCD File 
B
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO

Download SDF File 
Download CCD File 
A, B
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
SOX
Query on SOX

Download SDF File 
Download CCD File 
B
N-[(2S,4S,6R)-2-(DIHYDROXYMETHYL)-4-HYDROXY-3,3-DIMETHYL-7-OXO-4LAMBDA~4~-THIA-1-AZABICYCLO[3.2.0]HEPT-6-YL]-2-PHENYLACETAMIDE
OXIDISED PENICILLIN G
C16 H20 N2 O5 S
WMPGEOZLAYOFHH-MBNYWOFBSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
SME
Query on SME
A
L-PEPTIDE LINKINGC5 H11 N O3 SMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.190 
  • R-Value Work: 0.153 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 51.200α = 90.00
b = 131.700β = 105.90
c = 64.000γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
REFMACrefinement
AMoREphasing
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2001-11-28
    Type: Initial release
  • Version 1.1: 2013-06-12
    Type: Data collection, Database references, Derived calculations, Non-polymer description, Other, Structure summary, Version format compliance
  • Version 1.2: 2016-12-07
    Type: Database references