Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 48.64 kDa 
• Atom Count: 3448 
• Residue Count: 393 
• Unique protein chains: 1

4BJY

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

• DOI: 10.2210/pdb4BJY/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Rhodococcus jostii RHA1
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2013-04-21 Released: 2013-07-24 
• Deposition Author(s): Orru, R., Montersino, S., Barendregt, A., Westphal, A.H., van Duijn, E., Mattevi, A., van Berkel, W.J.H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.52 Å
• R-Value Free: 0.205 
• R-Value Work: 0.173 
• R-Value Observed: 0.175 

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

• PubMed: 23864660 
• DOI: 10.1074/jbc.M113.479303
• Primary Citation of Related Structures:  
  4BJY, 4BJZ, 4BK1, 4BK2, 4BK3


• 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 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.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PROBABLE SALICYLATE MONOOXYGENASE	A	424	Rhodococcus jostii RHA1	Mutation(s): 0  Gene Names: RHA1_ro01869 EC: 1.14.13.1 (PDB Primary Data), 1.14.13.24 (PDB Primary Data)
Find proteins for Q0SFK6 (Rhodococcus jostii (strain RHA1)) Explore Q0SFK6  Go to UniProtKB:  Q0SFK6

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
P3A	A	PHOSPHATIDYLGLYCEROL-PHOSPHOGLYCEROL C41 H78 O15 P2 LXWNXFZWWXODAH-XOLIOQKMSA-L
FAD	A	FLAVIN-ADENINE DINUCLEOTIDE C27 H33 N9 O15 P2 VWWQXMAJTJZDQX-UYBVJOGSSA-N
CL	A	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.52 Å
• R-Value Free: 0.205 
• R-Value Work: 0.173 
• R-Value Observed: 0.175 
• Space Group: I 4₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 106.61	α = 90
b = 106.61	β = 90
c = 142.31	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
Aimless	data scaling
SHELX	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2013-04-21 
• Released Date: 2013-07-24 
Deposition Author(s): Orru, R., Montersino, S., Barendregt, A., Westphal, A.H., van Duijn, E., Mattevi, A., van Berkel, W.J.H.

Revision History 

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