1H2G

Altered substrate specificity mutant of penicillin acylase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.194 
  • R-Value Work: 0.152 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Mutations of Penicillin Acylase Residue B71 Extend Substrate Specificity by Decreasing Steric Constraints for Substrate Binding

Morillas, M.Mcvey, C.E.Brannigan, J.A.Ladurner, A.G.Forney, L.J.Virden, R.

(2003) Biochem.J. 371: 143

  • DOI: 10.1042/BJ20021383

  • PubMed Abstract: 
  • Two mutant forms of penicillin acylase from Escherichia coli strains, selected using directed evolution for the ability to use glutaryl-L-leucine for growth [Forney, Wong and Ferber (1989) Appl. Environ. Microbiol. 55, 2550-2555], are changed within ...

    Two mutant forms of penicillin acylase from Escherichia coli strains, selected using directed evolution for the ability to use glutaryl-L-leucine for growth [Forney, Wong and Ferber (1989) Appl. Environ. Microbiol. 55, 2550-2555], are changed within one codon, replacing the B-chain residue Phe(B71) with either Cys or Leu. Increases of up to a factor of ten in k (cat)/ K (m) values for substrates possessing a phenylacetyl leaving group are consistent with a decrease in K (s). Values of k (cat)/ K (m) for glutaryl-L-leucine are increased at least 100-fold. A decrease in k (cat)/ K (m) for the Cys(B71) mutant with increased pH is consistent with binding of the uncharged glutaryl group. The mutant proteins are more resistant to urea denaturation monitored by protein fluorescence, to inactivation in the presence of substrate either in the presence of urea or at high pH, and to heat inactivation. The crystal structure of the Leu(B71) mutant protein, solved to 2 A resolution, shows a flip of the side chain of Phe(B256) into the periphery of the catalytic centre, associated with loss of the pi-stacking interactions between Phe(B256) and Phe(B71). Molecular modelling demonstrates that glutaryl-L-leucine may bind with the uncharged glutaryl group in the S(1) subsite of either the wild-type or the Leu(B71) mutant but with greater potential freedom of rotation of the substrate leucine moiety in the complex with the mutant protein. This implies a smaller decrease in the conformational entropy of the substrate on binding to the mutant proteins and consequently greater catalytic activity.


    Related Citations: 
    • 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
    • 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

    School of Cell and Molecular Biosciences, University of Newcastle upon Tyne, Framlington Place, Newcastle upon Tyne NE2 4HH, UK.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PENICILLIN G ACYLASE ALPHA SUBUNIT
A
209Escherichia coliMutation(s): 0 
Gene 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 coliMutation(s): 1 
Gene Names: pac
EC: 3.5.1.11
Find proteins for P06875 (Escherichia coli)
Go to UniProtKB:  P06875
Small Molecules
Ligands 2 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
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.194 
  • R-Value Work: 0.152 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 52.020α = 70.58
b = 64.230β = 72.81
c = 70.670γ = 73.84
Software Package:
Software NamePurpose
AMoREphasing
Agrovatadata scaling
DENZOdata reduction
REFMACrefinement
ROTAVATAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2003-07-17
    Type: Initial release
  • Version 1.1: 2014-02-19
    Type: Database references, Derived calculations, Non-polymer description, Other, Structure summary, Version format compliance