7EQH

Crystal structure of Arabidopsis GUN2/HO1 in complex with heme

• PDB DOI: https://doi.org/10.2210/pdb7EQH/pdb

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


• Deposited: 2021-05-02 Released: 2022-05-11 
• Deposition Author(s): Li, X., Wang, J., Liu, L.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.250 
• R-Value Work: 0.208 
• R-Value Observed: 0.210 

Literature

Enzymological and structural characterization of Arabidopsis thaliana heme oxygenase-1.

Wang, J., Li, X., Chang, J.W., Ye, T., Mao, Y., Wang, X., Liu, L.

(2022) FEBS Open Bio 12: 1677-1687

• PubMed: 35689519 
• DOI: https://doi.org/10.1002/2211-5463.13453
• Primary Citation of Related Structures:  
  7EQH


• PubMed Abstract: 
  

  Arabidopsis thaliana heme oxygenase-1 (AtHO-1), a metabolic enzyme in the heme degradation pathway, serves as a prototype for study of the bilin-related functions in plants. Past biological analyses revealed that AtHO-1 requires ferredoxin-NADP ⁺ reductase (FNR) and ferredoxin for its enzymatic activity. Here, we characterized the binding and degradation of heme by AtHO-1, and found that ferredoxin is a dispensable component of the reducing system that provides electrons for heme oxidation. Furthermore, we reported the crystal structure of heme-bound AtHO-1, which demonstrates both conserved and previously undescribed features of plant heme oxygenases. Finally, the electron transfer pathway from FNR to AtHO-1 is suggested based on the known structural information.

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Organizational Affiliation: 

School of Life Sciences, Anhui University, Hefei, China.

Biological Assembly 1  

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

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

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 56.71 kDa 
• Atom Count: 3,755 
• Modelled Residue Count: 424 
• Deposited Residue Count: 472 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Heme oxygenase 1, chloroplastic	A, B	236	Arabidopsis thaliana	Mutation(s): 0  Gene Names: HO1, GUN2, HY1, HY6, TED4, At2g26670, F18A8.4 EC: 1.14.14.18
UniProt
Find proteins for O48782 (Arabidopsis thaliana) Explore O48782  Go to UniProtKB:  O48782

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HEM	C [auth A], D [auth B]	PROTOPORPHYRIN IX CONTAINING FE C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.250 
• R-Value Work: 0.208 
• R-Value Observed: 0.210 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 66.622	α = 90
b = 84.759	β = 90
c = 92.87	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data scaling
PDB_EXTRACT	data extraction
HKL-2000	data reduction
PHASES	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2022-05-11 
Deposition Author(s): Li, X., Wang, J., Liu, L.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	31800251

Revision History  

• Version 1.0: 2022-05-11
  Type: Initial release
  
• Version 1.1: 2022-11-23
  Changes: Database references
• Version 1.2: 2023-11-29
  Changes: Data collection, Refinement description