1AI4

PENICILLIN ACYLASE COMPLEXED WITH 3,4-DIHYDROXYPHENYLACETIC ACID


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.150 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Ligand-induced conformational change in penicillin acylase.

Done, S.H.Brannigan, J.A.Moody, P.C.E.Hubbard, R.E.

(1998) J.Mol.Biol. 284: 463-475

  • DOI: 10.1006/jmbi.1998.2180
  • Primary Citation of Related Structures:  1AI5, 1AI6, 1AI7, 1AJN, 1AJP, 1AJQ

  • PubMed Abstract: 
  • The enzyme penicillin acylase (penicillin amidohydrolase EC 3.5.1. 11) catalyses the cleavage of the amide bond in the benzylpenicillin (penicillin G) side-chain to produce phenylacetic acid and 6-aminopenicillanic acid (6-APA). The enzyme is of grea ...

    The enzyme penicillin acylase (penicillin amidohydrolase EC 3.5.1. 11) catalyses the cleavage of the amide bond in the benzylpenicillin (penicillin G) side-chain to produce phenylacetic acid and 6-aminopenicillanic acid (6-APA). The enzyme is of great pharmaceutical importance, as the product 6-APA is the starting point for the synthesis of many semi-synthetic penicillin antibiotics. Studies have shown that the enzyme is specific for hydrolysis of phenylacetamide derivatives, but is more tolerant of features in the rest of the substrate. It is this property that has led to many other applications for the enzyme, and greater knowledge of the enzyme's structure and specificity could facilitate engineering of the enzyme, enhancing its potential for chemical and industrial applications. An extensive study of the binding of a series of phenylacetic acid derivatives has been carried out. A measure of the relative degree of inhibition of the enzyme by each of the compounds has been obtained using a competitive inhibition assay, and the structures of a number of these complexes have been determined by X-ray crystallography. The structures reveal a clear rationale for the observed kinetic results, but show also that some of the ligands cause a conformational change within the binding pocket. This change can generally be understood in terms of the size and orientation of the ligand within the active site.The results reveal that ligand binding in penicillin acylase is facilitated by certain amino acid residues that can adopt two distinct, energetically favourable positions in order to accommodate a variety of compounds within the active site. The structures of these complexes provide evidence for conformational changes in the substrate-binding region that may act as a switch in the mechanism of autocatalytic processing of this enzyme.


    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.
      (1995) Nature 373: 264
    • Expression, Purification and Crystallization 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
    • Structural Studies of Penicillin Acylase
      Done, S.H.
      (1996) Thesis --: --


    Organizational Affiliation

    Department of Chemistry, University of York, Heslington, YO1 5DD, UK. done@yorvic.york.ac.uk




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PENICILLIN AMIDOHYDROLASE
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 AMIDOHYDROLASE
B
557Escherichia coliGene 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
DHY
Query on DHY

Download SDF File 
Download CCD File 
B
2-(3,4-DIHYDROXYPHENYL)ACETIC ACID
C8 H8 O4
CFFZDZCDUFSOFZ-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

Download SDF File 
Download CCD File 
B
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
DHYKi: 3130000 nM BINDINGMOAD
HAAKi: 3130000 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.150 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 52.120α = 100.20
b = 65.080β = 111.44
c = 76.300γ = 105.81
Software Package:
Software NamePurpose
AGROVATAdata scaling
REFMACrefinement
ROTAVATAdata scaling
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 1997-05-01 
  • Released Date: 1997-11-12 
  • Deposition Author(s): Done, S.H.

Revision History 

  • Version 1.0: 1997-11-12
    Type: Initial release
  • Version 1.1: 2008-03-03
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance