6OJT

Crystal structure of Sphingomonas paucimobilis TMY1009 LsdA phenylazophenol complex

Summary for 6OJT

• Entry DOI: 10.2210/pdb6ojt/pdb
• Descriptor: Lignostilbene-alpha,beta-dioxygenase isozyme I, 4-Hydroxyazobenzene, FE (III) ION, ... (4 entities in total)
• Functional Keywords: aromatic compound, lignostilbene, carotenoid cleavage oxygenase, lignin degradation, bacterial catabolism, oxidoreductase
• Biological source: Sphingomonas paucimobilis
• Total number of polymer chains: 2
• Total formula weight: 108757.98

Authors

Kuatsjah, E.,Verstraete, M.M.,Kobylarz, M.J.,Liu, A.K.N.,Murphy, M.E.P.,Eltis, L.D. (deposition date: 2019-04-12, release date: 2019-07-24, Last modification date: 2024-03-13)

Primary citation

Kuatsjah, E.,Verstraete, M.M.,Kobylarz, M.J.,Liu, A.K.N.,Murphy, M.E.P.,Eltis, L.D.
Identification of functionally important residues and structural features in a bacterial lignostilbene dioxygenase.
J.Biol.Chem., 294:12911-12920, 2019

PubMed Abstract: Lignostilbene-α,β-dioxygenase A (LsdA) from the bacterium TMY1009 is a nonheme iron oxygenase that catalyzes the cleavage of lignostilbene, a compound arising in lignin transformation, to two vanillin molecules. To examine LsdA's substrate specificity, we heterologously produced the dimeric enzyme with the help of chaperones. When tested on several substituted stilbenes, LsdA exhibited the greatest specificity for lignostilbene ( = 1.00 ± 0.04 × 10 m s). These experiments further indicated that the substrate's 4-hydroxy moiety is required for catalysis and that this moiety cannot be replaced with a methoxy group. Phenylazophenol inhibited the LsdA-catalyzed cleavage of lignostilbene in a reversible, mixed fashion ( = 6 ± 1 μm, = 24 ± 4 μm). An X-ray crystal structure of LsdA at 2.3 Å resolution revealed a seven-bladed β-propeller fold with an iron cofactor coordinated by four histidines, in agreement with previous observations on related carotenoid cleavage oxygenases. We noted that residues at the dimer interface are also present in LsdB, another lignostilbene dioxygenase in TMY1009, rationalizing LsdA and LsdB homo- and heterodimerization A structure of an LsdA·phenylazophenol complex identified Phe, Tyr, and Lys as contacting the 4-hydroxyphenyl moiety of the inhibitor. Phe and Tyr substitutions with His and Phe, respectively, reduced LsdA activity () ∼15- and 10-fold. The K134M variant did not detectably cleave lignostilbene, indicating that Lys plays a key catalytic role. This study expands our mechanistic understanding of LsdA and related stilbene-cleaving dioxygenases.

PubMed: 31292192
DOI: 10.1074/jbc.RA119.009428

Experimental method

X-RAY DIFFRACTION (3 Å)