5ZBM

Structure of glycolate oxidase containing FMN from Nicotiana benthamiana


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.188 
  • R-Value Work: 0.171 
  • R-Value Observed: 0.172 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history

Re-refinement Note

A newer entry is available that reflects an alternative modeling of the original data: 5ZBN


Literature

Structures of glycolate oxidase from Nicotiana benthamiana reveal a conserved pH sensor affecting the binding of FMN.

Liu, Y.Wu, W.Chen, Z.

(2018) Biochem Biophys Res Commun 503: 3050-3056

  • DOI: https://doi.org/10.1016/j.bbrc.2018.08.092
  • Primary Citation of Related Structures:  
    5ZBM, 5ZBN

  • PubMed Abstract: 

    Glycolate oxidase (GOX), a flavin mononucleotide (FMN)-dependent enzyme, modulates reactive oxygen species-mediated signal transduction in green plants. It has been a target protein for crop improvement because of performing a key step in photorespiration that causes the energy losses. In human, GOX is involved in the production of oxalate, which is a key metabolite in the formation of kidney stone. Here, we report the first apo-GOX structure and its complex structure with cofactor FMN from Nicotiana benthamiana by X-ray crystallography. The binding of FMN induces a pronounced conformational change of GOX tetramer. Interestingly, a conserved pH sensor found among different species might directly regulate the binding of FMN and the enzyme activity. Combined with enzymatic experiments and biophysical analyses, we provide new insights in the molecular mechanism of regulating GOX biological activity reversibly and new methods of agricultural production and clinical application.


  • Organizational Affiliation

    Beijing Advanced Innovation Center for Food Nutrition and Human Health, State Key Laboratory of Agrobiotechnology, China Agricultural University, Beijing 100193, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Glycolate oxidase
A, B
371Nicotiana benthamianaMutation(s): 0 
Gene Names: GOX
UniProt
Find proteins for E1AXT8 (Nicotiana benthamiana)
Explore E1AXT8 
Go to UniProtKB:  E1AXT8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupE1AXT8
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.188 
  • R-Value Work: 0.171 
  • R-Value Observed: 0.172 
  • Space Group: I 4
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 144.23α = 90
b = 144.23β = 90
c = 129.823γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-12-26
    Type: Initial release
  • Version 1.1: 2020-07-08
    Changes: Database references
  • Version 1.2: 2023-11-22
    Changes: Data collection, Database references, Refinement description