7EZL | pdb_00007ezl

Rice L-galactose dehydrogenase (holo form)

• PDB DOI: https://doi.org/10.2210/pdb7EZL/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Oryza sativa Japonica Group
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2021-06-01 Released: 2021-06-23 
• Deposition Author(s): Momma, M., Fujimoto, Z.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.257 (Depositor), 0.256 (DCC) 
• R-Value Work: 
  0.209 (Depositor), 0.208 (DCC) 

Starting Model: experimental

Literature

Crystal structure of rice L-galactose dehydrogenase.

Fujimoto, Z., Momma, M., Suzuki, N.

(2026) Acta Crystallogr F Struct Biol Commun 82: 289-294

• PubMed: 42554157 
• DOI: https://doi.org/10.1107/S2053230X26007430
• Primary Citation Related Structures: 
  7EZI, 7EZL


• PubMed Abstract: 
  

  L-Galactose dehydrogenase plays a key role in the biosynthesis of L-ascorbic acid (vitamin C) in plants. Here, we report crystal structures of rice (Oryza sativa) L-galactose dehydrogenase in both apo and NAD ⁺ -bound forms at 1.2 and 1.8 Å resolution, respectively. Rice L-galactose dehydrogenase adopts a conserved (β/α) ₈ -barrel fold with a well preserved NAD ⁺ -binding cleft, as in other plant L-galactose dehydrogenases. Structural comparisons revealed conformational flexibility in the first and second loop regions, which form the lid and side wall of the NAD ⁺ -binding site. These loops undergo significant rearrangement upon NAD ⁺ binding, likely facilitating cofactor and substrate uptake. These findings suggest a flexible loop-mediated regulation of cofactor and substrate access.

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Organizational Affiliation: 
• Research Center for Advanced Analysis, National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518, Japan.

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

Macromolecule Content 

• Total Structure Weight: 35.99 kDa 
• Atom Count: 2,559 
• Modeled Residue Count: 318 
• Deposited Residue Count: 324 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
L-galactose dehydrogenase	A	324	Oryza sativa Japonica Group	Mutation(s): 0
UniProt
Find proteins for Q2QQV2 (Oryza sativa subsp. japonica) Explore Q2QQV2  Go to UniProtKB:  Q2QQV2

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAD (Subject of Investigation/LOI)	B [auth A]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C21 H27 N7 O14 P2 BAWFJGJZGIEFAR-NNYOXOHSSA-N
MG	C [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.257 (Depositor), 0.256 (DCC) 
• R-Value Work:  0.209 (Depositor), 0.208 (DCC) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 47.838	α = 90
b = 55.17	β = 101.529
c = 56.911	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2021-06-23 
Deposition Author(s): Momma, M., Fujimoto, Z.

Revision History  

• Version 1.0: 2021-06-23
  Type: Initial release
  
• Version 1.1: 2023-11-29
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.2: 2026-10-28
  Changes: Database references, Structure summary