1GM7

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free: 0.173 
  • R-Value Work: 0.145 

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This is version 1.3 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, 1GM9

  • 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 this key biotechnological enzyme, mutants were made to generate inactive protein useful for producing enzyme-substrate complexes ...

    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: 
    • 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
    • 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: 265

    Organizational Affiliation

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



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
PENICILLIN G ACYLASE ALPHA SUBUNITA209Escherichia coliMutation(s): 0 
Gene Names: pac
EC: 3.5.1.11
UniProt
Find proteins for P06875 (Escherichia coli)
Explore P06875 
Go to UniProtKB:  P06875
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP06875
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
PENICILLIN G ACYLASE BETA SUBUNITB557Escherichia coliMutation(s): 1 
Gene Names: pac
EC: 3.5.1.11
UniProt
Find proteins for P06875 (Escherichia coli)
Explore P06875 
Go to UniProtKB:  P06875
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP06875
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PNN
Query on PNN

Download Ideal Coordinates CCD File 
X [auth B]PENICILLIN G
C16 H18 N2 O4 S
JGSARLDLIJGVTE-MBNYWOFBSA-N
 Ligand Interaction
EDO
Query on EDO

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A],
E [auth B],
F [auth B],
G [auth B],
C [auth A],
D [auth A],
E [auth B],
F [auth B],
G [auth B],
H [auth B],
I [auth B],
J [auth B],
K [auth B],
L [auth B],
M [auth B],
N [auth B],
O [auth B],
P [auth B],
Q [auth B],
R [auth B],
S [auth B],
T [auth B],
U [auth B],
V [auth B]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

Download Ideal Coordinates CCD File 
W [auth B]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-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: 1.45 Å
  • R-Value Free: 0.173 
  • R-Value Work: 0.145 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 51.6α = 90
b = 131.8β = 105.6
c = 63.9γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Ligand Structure Quality Assessment 



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2001-11-28
    Type: Initial release
  • Version 1.1: 2014-02-19
    Changes: Database references, Derived calculations, Non-polymer description, Other, Version format compliance
  • Version 1.2: 2016-12-07
    Changes: Database references
  • Version 1.3: 2019-07-24
    Changes: Advisory, Data collection, Derived calculations