1H2G

Altered substrate specificity mutant of penicillin acylase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.194 
  • R-Value Work: 0.152 

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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
  • Primary Citation of Related Structures:  
    1H2G

  • 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 one codon, replacing the B-chain residue Phe(B71) with either Cys or Leu ...

    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: 
    • 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
    • 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

    Organizational Affiliation

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



Macromolecules
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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)
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Go to UniProtKB:  P06875
Entity Groups  
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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
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  • Reference Sequence
Small Molecules
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.194 
  • R-Value Work: 0.152 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 52.02α = 70.58
b = 64.23β = 72.81
c = 70.67γ = 73.84
Software Package:
Software NamePurpose
REFMACrefinement
DENZOdata reduction
Agrovatadata scaling
ROTAVATAdata scaling
AMoREphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

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