8CH4

Crystal structure of the ring cleaving dioxygenase 5-nitrosalicylate 1,2-dioxygenase from Bradyrhizobium sp.

Summary for 8CH4

• Entry DOI: 10.2210/pdb8ch4/pdb
• Descriptor: 5-nitrosalicylic acid 1,2-dioxygenase, FE (III) ION (3 entities in total)
• Functional Keywords: oxidase, cupin fold, beta-barrel, oxidoreductase
• Biological source: Bradyrhizobium sp. JS329
• Total number of polymer chains: 4
• Total formula weight: 95487.45

Authors

Ferraroni, M.,Stolz, A.,Eppinger, E. (deposition date: 2023-02-07, release date: 2023-07-05, Last modification date: 2024-11-13)

Primary citation

Eppinger, E.,Stolz, A.,Ferraroni, M.
Crystal structure of the monocupin ring-cleaving dioxygenase 5-nitrosalicylate 1,2-dioxygenase from Bradyrhizobium sp.
Acta Crystallogr D Struct Biol, 79:632-640, 2023

PubMed Abstract: 5-Nitrosalicylate 1,2-dioxygenase (5NSDO) is an iron(II)-dependent dioxygenase involved in the aerobic degradation of 5-nitroanthranilic acid by the bacterium Bradyrhizobium sp. It catalyzes the opening of the 5-nitrosalicylate aromatic ring, a key step in the degradation pathway. Besides 5-nitrosalicylate, the enzyme is also active towards 5-chlorosalicylate. The X-ray crystallographic structure of the enzyme was solved at 2.1 Å resolution by molecular replacement using a model from the AI program AlphaFold. The enzyme crystallized in the monoclinic space group P2, with unit-cell parameters a = 50.42, b = 143.17, c = 60.07 Å, β = 107.3°. 5NSDO belongs to the third class of ring-cleaving dioxygenases. Members of this family convert para-diols or hydroxylated aromatic carboxylic acids and belong to the cupin superfamily, which is one of the most functionally diverse protein classes and is named on the basis of a conserved β-barrel fold. 5NSDO is a tetramer composed of four identical subunits, each folded as a monocupin domain. The iron(II) ion in the enzyme active site is coordinated by His96, His98 and His136 and three water molecules with a distorted octahedral geometry. The residues in the active site are poorly conserved compared with other dioxygenases of the third class, such as gentisate 1,2-dioxygenase and salicylate 1,2-dioxygenase. Comparison with these other representatives of the same class and docking of the substrate into the active site of 5NSDO allowed the identification of residues which are crucial for the catalytic mechanism and enzyme selectivity.

PubMed: 37326584
DOI: 10.1107/S2059798323004199

Experimental method

X-RAY DIFFRACTION (2.1 Å)