5LFD

Crystal structure of allantoin racemase from Pseudomonas fluorescens AllR


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.202 
  • R-Value Observed: 0.205 

Starting Model: experimental
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This is version 1.1 of the entry. See complete history


Literature

The Structure and Function of a Microbial Allantoin Racemase Reveal the Origin and Conservation of a Catalytic Mechanism.

Cendron, L.Ramazzina, I.Puggioni, V.Maccacaro, E.Liuzzi, A.Secchi, A.Zanotti, G.Percudani, R.

(2016) Biochemistry 55: 6421-6432

  • DOI: https://doi.org/10.1021/acs.biochem.6b00881
  • Primary Citation of Related Structures:  
    5LFD, 5LG5

  • PubMed Abstract: 

    The S enantiomer of allantoin is an intermediate of purine degradation in several organisms and the final product of uricolysis in nonhominoid mammals. Bioinformatics indicated that proteins of the Asp/Glu racemase superfamily could be responsible for the allantoin racemase (AllR) activity originally described in Pseudomonas species. In these proteins, a cysteine of the catalytic dyad is substituted with glycine, yet the recombinant enzyme displayed racemization activity with a similar efficiency (k cat /K M ≈ 5 × 10 4 M -1 s -1 ) for the R and S enantiomers of allantoin. The protein crystal structure identified a glutamate residue located three residues downstream (E78) that can functionally replace the missing cysteine; the catalytic role of E78 was confirmed by site-directed mutagenesis. Allantoin can undergo racemization through formation of a bicyclic intermediate (faster) or proton exchange at the chiral center (slower). By monitoring the two alternative mechanisms by 13 C and 1 H nuclear magnetic resonance, we found that the velocity of the faster reaction is unaffected by the enzyme, whereas the velocity of the slower reaction is increased by 7 orders of magnitude. Protein phylogenies trace the origin of the racemization mechanism in enzymes acting on glutamate, a substrate for which proton exchange is the only viable reaction mechanism. This mechanism was inherited by allantoin racemase through divergent evolution and conserved in spite of the substitution of catalytic residues.


  • Organizational Affiliation

    Department of Biomedical Sciences, University of Padova , Padova, Italy.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Allantoin racemase
A, B
242Pseudomonas fluorescensMutation(s): 0 
EC: 5.1.99.3 (PDB Primary Data), 5.1.99 (UniProt)
UniProt
Find proteins for E3SAZ9 (Pseudomonas fluorescens)
Explore E3SAZ9 
Go to UniProtKB:  E3SAZ9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupE3SAZ9
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.202 
  • R-Value Observed: 0.205 
  • Space Group: P 21 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 109.72α = 90
b = 109.72β = 90
c = 109.72γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-05-10
    Type: Initial release
  • Version 1.1: 2024-01-10
    Changes: Data collection, Database references, Refinement description