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 5CLN | pdb_00005cln

Crystal structure of a 4-oxalocrotonate tautomerase mutant at 2.7 Angstrom


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.71 Å
  • R-Value Free: 
    0.263 (Depositor), 0.254 (DCC) 
  • R-Value Work: 
    0.233 (Depositor), 0.243 (DCC) 
  • R-Value Observed: 
    0.234 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.2 of the entry. See complete history. 

Literature

Using mutability landscapes of a promiscuous tautomerase to guide the engineering of enantioselective Michaelases.

van der Meer, J.Y., Poddar, H., Baas, B.J., Miao, Y., Rahimi, M., Kunzendorf, A., van Merkerk, R., Tepper, P.G., Geertsema, E.M., Thunnissen, A.M., Quax, W.J., Poelarends, G.J.

(2016) Nat Commun 7: 10911-10911

  • DOI: https://doi.org/10.1038/ncomms10911
  • Primary Citation Related Structures: 
    5CLN, 5CLO

  • PubMed Abstract: 

    The Michael-type addition reaction is widely used in organic synthesis for carbon-carbon bond formation. However, biocatalytic methodologies for this type of reaction are scarce, which is related to the fact that enzymes naturally catalysing carbon-carbon bond-forming Michael-type additions are rare. A promising template to develop new biocatalysts for carbon-carbon bond formation is the enzyme 4-oxalocrotonate tautomerase, which exhibits promiscuous Michael-type addition activity. Here we present mutability landscapes for the expression, tautomerase and Michael-type addition activities, and enantioselectivity of 4-oxalocrotonate tautomerase. These maps of neutral, beneficial and detrimental amino acids for each residue position and enzyme property provide detailed insight into sequence-function relationships. This offers exciting opportunities for enzyme engineering, which is illustrated by the redesign of 4-oxalocrotonate tautomerase into two enantiocomplementary 'Michaelases'. These 'Michaelases' catalyse the asymmetric addition of acetaldehyde to various nitroolefins, providing access to both enantiomers of γ-nitroaldehydes, which are important precursors for pharmaceutically active γ-aminobutyric acid derivatives.


  • Organizational Affiliation: 
    • Department of Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, Antonius Deusinglaan 1, Groningen 9713 AV, The Netherlands.

Macromolecule Content 

  • Total Structure Weight: 73.78 kDa 
  • Atom Count: 5,222 
  • Modeled Residue Count: 684 
  • Deposited Residue Count: 684 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
2-hydroxymuconate tautomerase
A, B, C, D, E
A, B, C, D, E, F, G, H, I, J, K, L
57Pseudomonas putidaMutation(s): 2 
Gene Names: xylH
EC: 5.3.2.6
UniProt
Find proteins for Q01468 (Pseudomonas putida)
Explore Q01468 
Go to UniProtKB:  Q01468
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ01468
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.71 Å
  • R-Value Free:  0.263 (Depositor), 0.254 (DCC) 
  • R-Value Work:  0.233 (Depositor), 0.243 (DCC) 
  • R-Value Observed: 0.234 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 87.163α = 90
b = 87.258β = 113.73
c = 97.284γ = 90
Software Package:
Software NamePurpose
Aimlessdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European Research CouncilNetherlands242293

Revision History  (Full details and data files)

  • Version 1.0: 2016-03-09
    Type: Initial release
  • Version 1.1: 2016-03-16
    Changes: Database references
  • Version 1.2: 2024-01-10
    Changes: Data collection, Database references, Refinement description