3HHX

Crystal structure determination of Catechol 1,2-Dioxygenase from Rhodococcus opacus 1CP in complex with pyrogallol

Summary for 3HHX

• Entry DOI: 10.2210/pdb3hhx/pdb
• Related: 3HGI 3HHY
• Descriptor: Catechol 1,2-dioxygenase, FE (III) ION, (4S,7R)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-3,5,8-TRIOXA-4-PHOSPHAHEXACOSAN-1-AMINIUM 4-OXIDE, ... (5 entities in total)
• Functional Keywords: beta-sandwich, aromatic hydrocarbons catabolism, dioxygenase, iron, metal-binding, oxidoreductase
• Biological source: Rhodococcus opacus (Nocardia opaca)
• Total number of polymer chains: 1
• Total formula weight: 31670.15

Authors

Matera, I.,Ferraroni, M.,Briganti, F. (deposition date: 2009-05-18, release date: 2010-01-26, Last modification date: 2024-02-21)

Primary citation

Matera, I.,Ferraroni, M.,Kolomytseva, M.,Golovleva, L.,Scozzafava, A.,Briganti, F.
Catechol 1,2-dioxygenase from the Gram-positive Rhodococcus opacus 1CP: Quantitative structure/activity relationship and the crystal structures of native enzyme and catechols adducts.
J.Struct.Biol., 170:548-564, 2010

PubMed Abstract: The first crystallographic structures of a catechol 1,2-dioxygenase from a Gram-positive bacterium Rhodococcus opacus 1CP (Rho 1,2-CTD), a Fe(III) ion containing enzyme specialized in the aerobic biodegradation of catechols, and its adducts with catechol, 3-methylcatechol, 4-methylcatechol, pyrogallol (benzene-1,2,3-triol), 3-chlorocatechol, 4-chlorocatechol, 3,5-dichlorocatechol, 4,5-dichlorocatechol and protocatechuate (3,4-dihydroxybenzoate) have been determined and analyzed. This study represents the first extensive characterization of catechols adducts of 1,2-CTDs. The structural analyses reveal the diverse modes of binding to the active metal iron ion of the tested catechols thus allowing to identify the residues selectively involved in recognition of the diverse substrates by this class of enzymes. The comparison is further extended to the structural and functional characteristics of the other 1,2-CTDs isolated from Gram-positive and Gram-negative bacteria. Moreover the high structural homology of the present enzyme with the 3-chlorocatechol 1,2-dioxygenase from the same bacterium are discussed in terms of their different substrate specificity. The catalytic rates for Rho 1,2-CTD conversion of the tested compounds are also compared with the calculated energies of the highest occupied molecular orbital (E(HOMO)) of the substrates. A quantitative relationship (R=0.966) between the ln k(cat) and the calculated electronic parameter E(HOMO) was obtained for catechol, 3-methylcatechol, 4-methylcatechol, pyrogallol, 3-chlorocatechol, 4-chlorocatechol. This indicates that for these substrates the rate-limiting step of the reaction cycle is dependent on their nucleophilic reactivity. The discrepancies observed in the quantitative relationship for 3,5-dichlorocatechol, 4,5-dichlorocatechol and protocatechuate are ascribed to the sterical hindrances leading to the distorted binding of such catechols observed in the corresponding structures.

PubMed: 20040374
DOI: 10.1016/j.jsb.2009.12.023

Experimental method

X-RAY DIFFRACTION (2 Å)