4XAE | pdb_00004xae

Structure of Feruloyl-CoA 6-hydroxylase (F6H) from Arabidopsis thaliana

• PDB DOI: https://doi.org/10.2210/pdb4XAE/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Arabidopsis thaliana
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2014-12-14 Released: 2015-06-10 
• Deposition Author(s): Zhou, D., Kandavelu, P., Zhang, H., Wang, B.C., Rose, J., Yan, Y.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.77 Å
• R-Value Free: 
  0.300 (Depositor), 0.307 (DCC) 
• R-Value Work: 
  0.243 (Depositor), 0.252 (DCC) 
• R-Value Observed: 
  0.248 (Depositor) 

Starting Model: experimental

Literature

Structural Insights into Substrate Specificity of Feruloyl-CoA 6'-Hydroxylase from Arabidopsis thaliana.

Sun, X., Zhou, D., Kandavelu, P., Zhang, H., Yuan, Q., Wang, B.C., Rose, J., Yan, Y.

(2015) Sci Rep 5: 10355-10355

• PubMed: 25993561 
• DOI: https://doi.org/10.1038/srep10355


• PubMed Abstract: 
  

  Coumarins belong to an important class of plant secondary metabolites. Feruloyl-CoA 6'-hydroxylase (F6'H), a 2-oxoglutarate dependent dioxygenase (2OGD), catalyzes a pivotal step in the biosynthesis of a simple coumarin scopoletin. In this study, we determined the 3-dimensional structure of the F6'H1 apo enzyme by X-ray crystallography. It is the first reported structure of a 2OGD enzyme involved in coumarin biosynthesis and closely resembles the structure of Arabidopsis thaliana anthocyanidin synthase. To better understand the mechanism of enzyme catalysis and substrate specificity, we also generated a homology model of a related ortho-hydroxylase (C2'H) from sweet potato. By comparing these two structures, we targeted two amino acid residues and verified their roles in substrate binding and specificity by site-directed mutagenesis.

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Organizational Affiliation: 
• State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, Beijing 100029, China.
Department of Biochemistry &Molecular Biology, University of Georgia, Athens, Georgia 30602, USA.
BioChemical Engineering Program, College of Engineering, University of Georgia, Athens, Georgia 30602, USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 84.66 kDa 
• Atom Count: 5,171 
• Modeled Residue Count: 653 
• Deposited Residue Count: 746 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Feruloyl CoA ortho-hydroxylase 1	A, B	373	Arabidopsis thaliana	Mutation(s): 0  Gene Names: F6'H1, At3g13610, K20M4.5 EC: 1.14.11 (PDB Primary Data), 1.14.11.61 (UniProt)
UniProt
Find proteins for Q9LHN8 (Arabidopsis thaliana) Explore Q9LHN8  Go to UniProtKB:  Q9LHN8

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NA	C [auth A], D [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.77 Å
• R-Value Free:  0.300 (Depositor), 0.307 (DCC) 
• R-Value Work:  0.243 (Depositor), 0.252 (DCC) 
• R-Value Observed: 0.248 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 193.219	α = 90
b = 54.554	β = 111.54
c = 78.815	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-06-10 
Deposition Author(s): Zhou, D., Kandavelu, P., Zhang, H., Wang, B.C., Rose, J., Yan, Y.

Revision History  

• Version 1.0: 2015-06-10
  Type: Initial release
  
• Version 1.1: 2023-09-27
  Changes: Data collection, Database references, Derived calculations, Refinement description, Source and taxonomy
• Version 1.2: 2023-11-15
  Changes: Data collection
• Version 1.3: 2024-11-20
  Changes: Structure summary