4HSR

Crystal Structure of a class III engineered cephalosporin acylase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.13 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.152 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structure of a class III engineered cephalosporin acylase: comparisons with class I acylase and implications for differences in substrate specificity and catalytic activity.

Golden, E.Paterson, R.Tie, W.J.Anandan, A.Flematti, G.Molla, G.Rosini, E.Pollegioni, L.Vrielink, A.

(2013) Biochem.J. 451: 217-226

  • DOI: 10.1042/BJ20121715
  • Primary Citation of Related Structures:  4HST

  • PubMed Abstract: 
  • The crystal structure of the wild-type form of glutaryl-7-ACA (7-aminocephalosporanic acid) acylase from Pseudomonas N176 and a double mutant of the protein (H57βS/H70βS) that displays enhanced catalytic efficiency on cephalosporin C over glutaryl-7- ...

    The crystal structure of the wild-type form of glutaryl-7-ACA (7-aminocephalosporanic acid) acylase from Pseudomonas N176 and a double mutant of the protein (H57βS/H70βS) that displays enhanced catalytic efficiency on cephalosporin C over glutaryl-7-aminocephalosporanic acid has been determined. The structures show a heterodimer made up of an α-chain (229 residues) and a β-chain (543 residues) with a deep cavity, which constitutes the active site. Comparison of the wild-type and mutant structures provides insights into the molecular reasons for the observed enhanced specificity on cephalosporin C over glutaryl-7-aminocephalosporanic acid and offers the basis to evolve a further improved enzyme variant. The nucleophilic catalytic serine residue, Ser(1β), is situated at the base of the active site cavity. The electron density reveals a ligand covalently bound to the catalytic serine residue, such that a tetrahedral adduct is formed. This is proposed to mimic the transition state of the enzyme for both the maturation step and the catalysis of the substrates. A view of the transition state configuration of the enzyme provides important insights into the mechanism of substrate binding and catalysis.


    Organizational Affiliation

    School of Chemistry and Biochemistry, University of Western Australia, 35 Stirling Highway, Crawley, WA 6009, Australia.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
glutaryl-7-aminocephalosporanic acid acylase alpha chain
A
229N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
glutaryl-7-aminocephalosporanic acid acylase beta chain
B
543N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GLJ
Query on GLJ

Download SDF File 
Download CCD File 
B
5,5-dihydroxy-L-norvaline
C5 H11 N O4
FIKXYBCGRJPSSD-VKHMYHEASA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.13 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.152 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 68.161α = 90.00
b = 77.018β = 90.00
c = 192.138γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
Blu-Icedata collection
XDSdata reduction
SCALAdata scaling
SHELXSphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-02-27
    Type: Initial release
  • Version 1.1: 2013-04-10
    Type: Database references
  • Version 1.2: 2017-11-15
    Type: Refinement description