8CO4 | pdb_00008co4

Crystal structure of apo S-nitrosoglutathione reductase from Arabidopsis thalina


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 
    0.210 (Depositor), 0.215 (DCC) 
  • R-Value Work: 
    0.161 (Depositor), 0.168 (DCC) 
  • R-Value Observed: 
    0.163 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 8CO4

Ligand Structure Quality Assessment 


This is version 2.0 of the entry. See complete history

Literature

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 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.

Macromolecule Content 

  • Total Structure Weight: 165.73 kDa 
  • Atom Count: 12,745 
  • Modeled Residue Count: 1,514 
  • Deposited Residue Count: 1,516 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  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: 1.1.1.1 (PDB Primary Data), 1.1.1 (PDB Primary Data), 1.1.1.284 (PDB Primary Data)
UniProt
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
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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
O [auth A]TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
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]
TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
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]
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
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]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
EDO
(Subject of Investigation/LOI)

Query on EDO



Download:Ideal Coordinates CCD File
G [auth A],
X [auth C]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free:  0.210 (Depositor), 0.215 (DCC) 
  • R-Value Work:  0.161 (Depositor), 0.168 (DCC) 
  • R-Value Observed: 0.163 (Depositor) 
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
REFMACrefinement
PHENIXrefinement
xia2data reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



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
  • Version 2.0: 2025-10-01
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary