Crystal structure of apo S-nitrosoglutathione reductase from Arabidopsis thalina

Experimental Data Snapshot

  • Resolution: 1.90 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.161 
  • R-Value Observed: 0.163 

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Structural and biochemical characterization of Arabidopsis alcohol dehydrogenases reveals distinct functional properties but similar redox sensitivity.

Meloni, M.Rossi, J.Fanti, S.Carloni, G.Tedesco, D.Treffon, P.Piccinini, L.Falini, G.Trost, P.Vierling, E.Licausi, F.Giuntoli, B.Musiani, F.Fermani, S.Zaffagnini, M.

(2024) Plant J 118: 1054-1070

  • DOI: https://doi.org/10.1111/tpj.16651
  • Primary Citation of Related Structures:  
    8CO4, 8CON

  • PubMed Abstract: 

    Alcohol dehydrogenases (ADHs) are a group of zinc-binding enzymes belonging to the medium-length dehydrogenase/reductase (MDR) protein superfamily. In plants, these enzymes fulfill important functions involving the reduction of toxic aldehydes to the corresponding alcohols (as well as catalyzing the reverse reaction, i.e., alcohol oxidation; ADH1) and the reduction of nitrosoglutathione (GSNO; ADH2/GSNOR). We investigated and compared the structural and biochemical properties of ADH1 and GSNOR from Arabidopsis thaliana. We expressed and purified ADH1 and GSNOR and determined two new structures, NADH-ADH1 and apo-GSNOR, thus completing the structural landscape of Arabidopsis ADHs in both apo- and holo-forms. A structural comparison of these Arabidopsis ADHs revealed a high sequence conservation (59% identity) and a similar fold. In contrast, a striking dissimilarity was observed in the catalytic cavity supporting substrate specificity and accommodation. Consistently, ADH1 and GSNOR showed strict specificity for their substrates (ethanol and GSNO, respectively), although both enzymes had the ability to oxidize long-chain alcohols, with ADH1 performing better than GSNOR. Both enzymes contain a high number of cysteines (12 and 15 out of 379 residues for ADH1 and GSNOR, respectively) and showed a significant and similar responsivity to thiol-oxidizing agents, indicating that redox modifications may constitute a mechanism for controlling enzyme activity under both optimal growth and stress conditions.

  • Organizational Affiliation

    Department of Pharmacy and Biotechnology, University of Bologna, 40126, Bologna, Italy.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Alcohol dehydrogenase class-3
A, B, C, D
379Arabidopsis thalianaMutation(s): 0 
Gene Names: ADH2ADHIIIFDH1At5g43940MRH10.4
EC: (PDB Primary Data), 1.1.1 (PDB Primary Data), (PDB Primary Data)
Find proteins for Q96533 (Arabidopsis thaliana)
Explore Q96533 
Go to UniProtKB:  Q96533
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ96533
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PG4 (Subject of Investigation/LOI)
Query on PG4

Download Ideal Coordinates CCD File 
C8 H18 O5
PGE (Subject of Investigation/LOI)
Query on PGE

Download Ideal Coordinates CCD File 
AA [auth C]
DA [auth D]
L [auth A]
M [auth A]
N [auth A]
AA [auth C],
DA [auth D],
L [auth A],
M [auth A],
N [auth A],
T [auth B],
U [auth B]
C6 H14 O4
PEG (Subject of Investigation/LOI)
Query on PEG

Download Ideal Coordinates CCD File 
H [auth A]
I [auth A]
J [auth A]
K [auth A]
R [auth B]
H [auth A],
I [auth A],
J [auth A],
K [auth A],
R [auth B],
S [auth B],
Y [auth C],
Z [auth C]
C4 H10 O3
ZN (Subject of Investigation/LOI)
Query on ZN

Download Ideal Coordinates CCD File 
BA [auth D]
CA [auth D]
E [auth A]
F [auth A]
P [auth B]
BA [auth D],
CA [auth D],
E [auth A],
F [auth A],
P [auth B],
Q [auth B],
V [auth C],
W [auth C]
EDO (Subject of Investigation/LOI)
Query on EDO

Download Ideal Coordinates CCD File 
G [auth A],
X [auth C]
C2 H6 O2
Experimental Data & Validation

Experimental Data

  • Resolution: 1.90 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.161 
  • R-Value Observed: 0.163 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 88.6α = 90
b = 93.927β = 90
c = 167.484γ = 90
Software Package:
Software NamePurpose
xia2data reduction
Aimlessdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2024-02-21
    Type: Initial release
  • Version 1.1: 2024-05-29
    Changes: Database references