1K5Q

PENICILLIN ACYLASE, MUTANT COMPLEXED WITH PAA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.34 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.163 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural and kinetic studies on ligand binding in wild-type and active-site mutants of penicillin acylase.

Alkema, W.B.L.Hensgens, C.M.H.Snijder, H.J.Keizer, E.Dijkstra, B.W.Janssen, D.B.

(2004) Protein Eng.Des.Sel. 17: 473-480

  • DOI: 10.1093/protein/gzh057
  • Primary Citation of Related Structures:  1JX9, 1K5S, 1K7D, 1KEC

  • PubMed Abstract: 
  • Penicillin acylase catalyses the condensation of Calpha-substituted phenylacetic acids with beta-lactam nucleophiles, producing semi-synthetic beta-lactam antibiotics. For efficient synthesis a low affinity for phenylacetic acid and a high affinity f ...

    Penicillin acylase catalyses the condensation of Calpha-substituted phenylacetic acids with beta-lactam nucleophiles, producing semi-synthetic beta-lactam antibiotics. For efficient synthesis a low affinity for phenylacetic acid and a high affinity for Calpha-substituted phenylacetic acid derivatives is desirable. We made three active site mutants, alphaF146Y, betaF24A and alphaF146Y/betaF24A, which all had a 2- to 10-fold higher affinity for Calpha-substituted compounds than wild-type enzyme. In addition, betaF24A had a 20-fold reduced affinity for phenylacetic acid. The molecular basis of the improved properties was investigated by X-ray crystallography. These studies showed that the higher affinity of alphaF146Y for (R)-alpha-methylphenylacetic acid can be explained by van der Waals interactions between alphaY146:OH and the Calpha-substituent. The betaF24A mutation causes an opening of the phenylacetic acid binding site. Only (R)-alpha-methylphenylacetic acid, but not phenylacetic acid, induces a conformation with the ligand tightly bound, explaining the weak binding of phenylacetic acid. A comparison of the betaF24A structure with other open conformations of penicillin acylase showed that betaF24 has a fixed position, whereas alphaF146 acts as a flexible lid on the binding site and reorients its position to achieve optimal substrate binding.


    Organizational Affiliation

    Department of Biochemistry, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747 AG, The Netherlands.




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 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PAC
Query on PAC

Download SDF File 
Download CCD File 
B
2-PHENYLACETIC ACID
C8 H8 O2
WLJVXDMOQOGPHL-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 %)
PACKi: 1100000 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.34 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.163 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 50.760α = 72.86
b = 63.960β = 73.91
c = 64.240γ = 73.50
Software Package:
Software NamePurpose
DENZOdata reduction
CNSphasing
REFMACrefinement
SCALEPACKdata scaling
CNSrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2003-09-02
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance