1E3A

A slow processing precursor penicillin acylase from Escherichia coli


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.197 
  • R-Value Work: 0.158 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structure of a Slow Processing Precursor Penicillin Acylase from Escherichia Coli Reveals the Linker Peptide Blocking the Active-Site Cleft

Hewitt, L.Kasche, V.Lummer, K.Lewis, R.J.Murshudov, G.N.Verma, C.S.Dodson, G.G.Wilson, K.S.

(2000) J.Mol.Biol. 302: 887

  • DOI: 10.1006/jmbi.2000.4105

  • PubMed Abstract: 
  • Penicillin G acylase is a periplasmic protein, cytoplasmically expressed as a precursor polypeptide comprising a signal sequence, the A and B chains of the mature enzyme (209 and 557 residues respectively) joined by a spacer peptide of 54 amino acid ...

    Penicillin G acylase is a periplasmic protein, cytoplasmically expressed as a precursor polypeptide comprising a signal sequence, the A and B chains of the mature enzyme (209 and 557 residues respectively) joined by a spacer peptide of 54 amino acid residues. The wild-type AB heterodimer is produced by proteolytic removal of this spacer in the periplasm. The first step in processing is believed to be autocatalytic hydrolysis of the peptide bond between the C-terminal residue of the spacer and the active-site serine residue at the N terminus of the B chain. We have determined the crystal structure of a slowly processing precursor mutant (Thr263Gly) of penicillin G acylase from Escherichia coli, which reveals that the spacer peptide blocks the entrance to the active-site cleft consistent with an autocatalytic mechanism of maturation. In this mutant precursor there is, however, an unexpected cleavage at a site four residues from the active-site serine residue. Analyses of the stereochemistry of the 260-261 bond seen to be cleaved in this precursor structure and of the 263-264 peptide bond have suggested factors that may govern the autocatalytic mechanism.


    Related Citations: 
    • Crystallisation of a Precursor Penicillin Acylase from Escherichia Coli
      Hewitt, L.,Kasche, V.,Lummer, K.,Rieks, A.,Wilson, K.S.
      (1999) Acta Crystallogr.,Sect.D 55: 1052


    Organizational Affiliation

    Department of Chemistry, University of York, Heslington York, YO10 5DD, UK.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PENICILLIN AMIDASE ALPHA SUBUNIT
A
260Escherichia 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 AMIDASE BETA SUBUNIT
B
560Escherichia coliMutation(s): 1 
Gene Names: pac
EC: 3.5.1.11
Find proteins for P06875 (Escherichia coli)
Go to UniProtKB:  P06875
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

Download SDF File 
Download CCD File 
B
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
CA
Query on CA

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Download CCD File 
B
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO

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Download CCD File 
B
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.197 
  • R-Value Work: 0.158 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 50.710α = 66.14
b = 64.270β = 74.18
c = 72.000γ = 74.23
Software Package:
Software NamePurpose
REFMACrefinement
SCALEPACKdata scaling
AMoREphasing
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2000-11-29
    Type: Initial release
  • Version 1.1: 2014-10-22
    Type: Data collection, Database references, Derived calculations, Other, Version format compliance