5O3N

Crystal structure of E. cloacae 3,4-dihydroxybenzoic acid decarboxylase (AroY) reconstituted with prFMN


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.205 
  • R-Value Work: 0.184 

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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
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
3,4-dihydroxybenzoate decarboxylase
A, B
515Enterobacter 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
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
4LU
Query on 4LU

Download Ideal Coordinates CCD File 
J [auth A],
N [auth B]
1-deoxy-5-O-phosphono-1-(3,3,4,5-tetramethyl-9,11-dioxo-2,3,8,9,10,11-hexahydro-7H-quinolino[1,8-fg]pteridin-12-ium-7-y l)-D-ribitol
C22 H30 N4 O9 P
KOUJZPGFPGLHCZ-IYOUNJFTSA-O
GOL
Query on GOL

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E [auth A]
F [auth A]
G [auth A]
H [auth A]
I [auth A]
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
M [auth B]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
MN
Query on MN

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C [auth A],
K [auth B]
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
NA
Query on NA

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D [auth A],
L [auth B]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.205 
  • R-Value Work: 0.184 
  • Space Group: H 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 208.31α = 90
b = 208.31β = 90
c = 157.91γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
xia2data reduction
xia2data scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Biotechnology and Biological Sciences Research CouncilUnited KingdomBB/K017802/1

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, Structure summary
  • Version 1.2: 2017-10-25
    Changes: Database references