PDBsum entry 4dlb

Oxidoreductase

PDB id: 4dlb

Contents

Protein chains

379 a.a.

Ligands

NAD ×2

GOL ×5

Metals

_ZN ×4

Waters ×414

PDB id:

4dlb

Name:

Oxidoreductase

Title:

Structure of s-nitrosoglutathione reductase from tomato (solanum lycopersicum) crystallized in presence of nadh and glutathione

Structure:

Alcohol dehydrogenase class iii. Chain: a, b. Engineered: yes

Source:

Solanum lycopersicum. Tomato. Organism_taxid: 4081. Strain: cv. Amateur. Gene: adh3, gsnor. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

2.10Å R-factor: 0.184 R-free: 0.243

Authors:

D.Kopecny,M.Tylichova,P.Briozzo

Key ref:

L.Kubienová et al. (2013). Structural and functional characterization of a plant S-nitrosoglutathione reductase from Solanum lycopersicum. Biochimie, 95, 889-902. PubMed id: 23274177 DOI: 10.1016/j.biochi.2012.12.009

Date:

06-Feb-12 Release date: 26-Dec-12

Protein chains

D2Y3F4  (D2Y3F4_SOLLC) -  S-(hydroxymethyl)glutathione dehydrogenase from Solanum lycopersicum

Seq: 379 a.a.

Struc: 379 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

Enzyme reactions

• Enzyme class: E.C.1.1.1.284 - S-(hydroxymethyl)glutathione dehydrogenase.
• Reaction:
  1. S-(hydroxymethyl)glutathione + NADP⁺ = S-formylglutathione + NADPH + H⁺
  2. S-(hydroxymethyl)glutathione + NAD⁺ = S-formylglutathione + NADH + H⁺

S-(hydroxymethyl)glutathione (Bound ligand (Het Group name = NAD) matches with 91.67% similarity) + NADP(+) = S-formylglutathione + NADPH + H(+)

S-(hydroxymethyl)glutathione (Bound ligand (Het Group name = NAD) corresponds exactly) + NAD(+) = S-formylglutathione + NADH + H(+)

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

reference

DOI no: 10.1016/j.biochi.2012.12.009

Biochimie 95:889-902 (2013)

PubMed id: 23274177

Structural and functional characterization of a plant S-nitrosoglutathione reductase from Solanum lycopersicum.

L.Kubienová, D.Kopečný, M.Tylichová, P.Briozzo, J.Skopalová, M.Šebela, M.Navrátil, R.Tâche, L.Luhová, J.B.Barroso, M.Petřivalský.

ABSTRACT

S-nitrosoglutathione reductase (GSNOR), also known as S-(hydroxymethyl)glutathione (HMGSH) dehydrogenase, belongs to the large alcohol dehydrogenase superfamily, namely to the class III ADHs. GSNOR catalyses the oxidation of HMGSH to S-formylglutathione using a catalytic zinc and NAD as a coenzyme. The enzyme also catalyses the NADH-dependent reduction of S-nitrosoglutathione (GSNO). In plants, GSNO has been suggested to serve as a nitric oxide (NO) reservoir locally or possibly as NO donor in distant cells and tissues. NO and NO-related molecules such as S-nitrosothiols (S-NOs) play a central role in the regulation of normal plant physiological processes and host defence. The enzyme thus participates in the cellular homeostasis of S-NOs and in the metabolism of reactive nitrogen species. Although GSNOR has recently been characterized from several organisms, this study represents the first detailed biochemical and structural characterization of a plant GSNOR, that from tomato (Solanum lycopersicum). SlGSNOR gene expression is higher in roots and stems compared to leaves of young plants. It is highly expressed in the pistil and stamens and in fruits during ripening. The enzyme is a dimer and preferentially catalyses reduction of GSNO while glutathione and S-methylglutathione behave as non-competitive inhibitors. Using NAD, the enzyme oxidizes HMGSH and other alcohols such as cinnamylalcohol, geraniol and ω-hydroxyfatty acids. The crystal structures of the apoenzyme, of the enzyme in complex with NAD and in complex with NADH, solved up to 1.9 Å resolution, represent the first structures of a plant GSNOR. They confirm that the binding of the coenzyme is associated with the active site zinc movement and changes in its coordination. In comparison to the well characterized human GSNOR, plant GSNORs exhibit a difference in the composition of the anion-binding pocket, which negatively influences the affinity for the carboxyl group of ω-hydroxyfatty acids.