7BPC

Crystal structure of 2, 3-dihydroxybenzoic acid decarboxylase from Fusarium oxysporum in complex with 2,5-DHBA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.45 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.196 

wwPDB Validation 3D Report Full Report



Literature

2,3-Dihydroxybenzoic Acid Decarboxylase from Fusarium oxysporum: Crystal Structures and Substrate Recognition Mechanism.

Song, M.Zhang, X.Liu, W.Feng, J.Cui, Y.Yao, P.Wang, M.Guo, R.T.Wu, Q.Zhu, D.

(2020) Chembiochem 

  • DOI: 10.1002/cbic.202000244
  • Primary Citation of Related Structures:  
    7BPC, 7BP1, 6M53

  • PubMed Abstract: 
  • A 2,3-dihydroxybenzoic acid decarboxylase from Fusarium oxysporum (2,3-DHBD_Fo) has a relatively high catalytic efficiency for the decarboxylation of 2,3-dihydroxybenzoic acid (DHBA) and carboxylation of catechol, thus it has a different substrate sp ...

    A 2,3-dihydroxybenzoic acid decarboxylase from Fusarium oxysporum (2,3-DHBD_Fo) has a relatively high catalytic efficiency for the decarboxylation of 2,3-dihydroxybenzoic acid (DHBA) and carboxylation of catechol, thus it has a different substrate spectrum from other benzoic acid decarboxylases. We have determined the structures of 2,3-DHBD_Fo in its apo form and complexes with catechol or 2,5-dihydroxybenzoic acid at 1.55, 1.97, and 2.45 Å resolution, respectively. The crystal structures of 2,3-DHBD_Fo show that the enzyme exists as a homotetramer, and each active center has a Zn 2+ ion coordinated by E8, H167, D291 and three water molecules. This is different from 2,6-DHBD from Rhizobium sporomusa, in which the Zn 2+ ion is also coordinated with H10. Surprisingly, mutation of A10 of 2,3-DHBD_Fo to His resulted in almost complete loss of the enzyme activity. Enzyme-substrate docking and site-directed mutation studies indicate that residue R233 Δ interacts with the 3-hydroxy group of 2,3-DHBA, and plays an important role in substrate recognition for this enzyme, thus revealing the molecular basis 2,3-dihydroxybenzoic acid decarboxylase.


    Organizational Affiliation

    National Engineering Laboratory for Industrial Enzymes, Tianjin Engineering Research Center of Biocatalytic Technology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 Xi Qi Dao, Tianjin Airport Economic Area, Tianjin, 300308, P. R. China.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
2,3-dihydroxybenzoate decarboxylaseA, B, C, D343Fusarium oxysporumMutation(s): 0 
Gene Names: BFJ70_g2310
Find proteins for A0A420U2F4 (Fusarium oxysporum)
Explore A0A420U2F4 
Go to UniProtKB:  A0A420U2F4
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GTQ
Query on GTQ

Download CCD File 
A, C
2,5-dihydroxybenzoic acid
C7 H6 O4
WXTMDXOMEHJXQO-UHFFFAOYSA-N
 Ligand Interaction
ZN
Query on ZN

Download CCD File 
A, C
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.45 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.196 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 76.769α = 90
b = 129.739β = 90
c = 140.557γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data scaling
PDB_EXTRACTdata extraction
HKL-2000data reduction
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2020-07-15
    Type: Initial release