4BJZ

Crystal structure of 3-hydroxybenzoate 6-hydroxylase uncovers lipid- assisted flavoprotein strategy for regioselective aromatic hydroxylation: Native data


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.51 Å
  • R-Value Free: 0.201 
  • R-Value Work: 0.168 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal Structure of 3-Hydroxybenzoate 6-Hydroxylase Uncovers Lipid-Assisted Flavoprotein Strategy for Regioselective Aromatic Hydroxylation

Montersino, S.Orru, R.Barendregt, A.Westphal, A.H.Van Duijn, E.Mattevi, A.Van Berkel, W.J.H.

(2013) J.Biol.Chem. 288: 26235

  • DOI: 10.1074/jbc.M113.479303
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • 3-Hydroxybenzoate 6-hydroxylase (3HB6H) from Rhodococcus jostii RHA1 is a dimeric flavoprotein that catalyzes the NADH- and oxygen-dependent para-hydroxylation of 3-hydroxybenzoate to 2,5-dihydroxybenzoate. In this study, we report the crystal struct ...

    3-Hydroxybenzoate 6-hydroxylase (3HB6H) from Rhodococcus jostii RHA1 is a dimeric flavoprotein that catalyzes the NADH- and oxygen-dependent para-hydroxylation of 3-hydroxybenzoate to 2,5-dihydroxybenzoate. In this study, we report the crystal structure of 3HB6H as expressed in Escherichia coli. The overall fold of 3HB6H is similar to that of p-hydroxybenzoate hydroxylase and other flavoprotein aromatic hydroxylases. Unexpectedly, a lipid ligand is bound to each 3HB6H monomer. Mass spectral analysis identified the ligand as a mixture of phosphatidylglycerol and phosphatidylethanolamine. The fatty acid chains occupy hydrophobic channels that deeply penetrate into the interior of the substrate-binding domain of each subunit, whereas the hydrophilic part is exposed on the protein surface, connecting the dimerization domains via a few interactions. Most remarkably, the terminal part of a phospholipid acyl chain is directly involved in the substrate-binding site. Co-crystallized chloride ion and the crystal structure of the H213S variant with bound 3-hydroxybenzoate provide hints about oxygen activation and substrate hydroxylation. Essential roles are played by His-213 in catalysis and Tyr-105 in substrate binding. This phospholipid-assisted strategy to control regioselective aromatic hydroxylation is of relevance for optimization of flavin-dependent biocatalysts.


    Organizational Affiliation

    Laboratory of Biochemistry, Wageningen University, 6703 HA Wageningen, The Netherlands.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PROBABLE SALICYLATE MONOOXYGENASE
A
424Rhodococcus jostii (strain RHA1)Mutation(s): 0 
EC: 1.14.13.1
Find proteins for Q0SFK6 (Rhodococcus jostii (strain RHA1))
Go to UniProtKB:  Q0SFK6
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
P3A
Query on P3A

Download SDF File 
Download CCD File 
A
PHOSPHATIDYLGLYCEROL-PHOSPHOGLYCEROL
C41 H78 O15 P2
LXWNXFZWWXODAH-XOLIOQKMSA-L
 Ligand Interaction
CL
Query on CL

Download SDF File 
Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
FAD
Query on FAD

Download SDF File 
Download CCD File 
A
FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.51 Å
  • R-Value Free: 0.201 
  • R-Value Work: 0.168 
  • Space Group: I 41 2 2
Unit Cell:
Length (Å)Angle (°)
a = 106.790α = 90.00
b = 106.790β = 90.00
c = 142.716γ = 90.00
Software Package:
Software NamePurpose
MOSFLMdata reduction
Aimlessdata scaling
REFMACrefinement
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-07-24
    Type: Initial release
  • Version 1.1: 2013-07-31
    Type: Database references
  • Version 1.2: 2013-09-25
    Type: Database references