5NY5

The apo structure of 3,4-dihydroxybenzoic acid decarboxylases from Enterobacter cloacae


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.203 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Regioselective para-Carboxylation of Catechols with a Prenylated Flavin Dependent Decarboxylase.

Payer, S.E.Marshall, S.A.Barland, N.Sheng, X.Reiter, T.Dordic, A.Steinkellner, G.Wuensch, C.Kaltwasser, S.Fisher, K.Rigby, S.E.J.Macheroux, P.Vonck, J.Gruber, K.Faber, K.Himo, F.Leys, D.Pavkov-Keller, T.Glueck, S.M.

(2017) Angew Chem Int Ed Engl 56: 13893-13897

  • DOI: https://doi.org/10.1002/anie.201708091
  • Primary Citation of Related Structures:  
    5NY5, 5O3M, 5O3N

  • PubMed Abstract: 

    The utilization of CO 2 as a carbon source for organic synthesis meets the urgent demand for more sustainability in the production of chemicals. Herein, we report on the enzyme-catalyzed para-carboxylation of catechols, employing 3,4-dihydroxybenzoic acid decarboxylases (AroY) that belong to the UbiD enzyme family. Crystal structures and accompanying solution data confirmed that AroY utilizes the recently discovered prenylated FMN (prFMN) cofactor, and requires oxidative maturation to form the catalytically competent prFMN iminium species. This study reports on the in vitro reconstitution and activation of a prFMN-dependent enzyme that is capable of directly carboxylating aromatic catechol substrates under ambient conditions. A reaction mechanism for the reversible decarboxylation involving an intermediate with a single covalent bond between a quinoid adduct and cofactor is proposed, which is distinct from the mechanism of prFMN-associated 1,3-dipolar cycloadditions in related enzymes.


  • Organizational Affiliation

    Department of Chemistry, Organic & Bioorganic Chemistry, University of Graz, NAWI Graz, BioTechMed Graz, Heinrichstrasse 28/2, 8010, Graz, Austria.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
3,4-dihydroxybenzoate decarboxylase
A, B
495Enterobacter cloacaeMutation(s): 0 
UniProt
Find proteins for B2DCZ6 (Enterobacter cloacae)
Explore B2DCZ6 
Go to UniProtKB:  B2DCZ6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB2DCZ6
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.203 
  • Space Group: H 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 209.907α = 90
b = 209.907β = 90
c = 162.179γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
AutoSolphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Austrian Science FundAustria--
FFGAustria--

Revision History  (Full details and data files)

  • Version 1.0: 2017-09-13
    Type: Initial release
  • Version 1.1: 2017-10-11
    Changes: Database references
  • Version 1.2: 2017-10-25
    Changes: Database references
  • Version 1.3: 2020-11-18
    Changes: Author supporting evidence