5X1M

Vanillate/3-O-methylgallate O-demethylase, LigM, protocatechuate-tetrahydrofolate complex form

Summary for 5X1M

• Entry DOI: 10.2210/pdb5x1m/pdb
• Related: 5X1I 5X1J 5X1K 5X1L 5X1N
• Descriptor: Vanillate/3-O-methylgallate O-demethylase, 3,4-DIHYDROXYBENZOIC ACID, 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL, ... (6 entities in total)
• Functional Keywords: lignin, sphingobium sp. syk-6, oxidoreductase
• Biological source: Sphingobium sp. SYK-6
• Total number of polymer chains: 3
• Total formula weight: 159894.41

Authors

Harada, A.,Senda, T. (deposition date: 2017-01-26, release date: 2017-05-17, Last modification date: 2023-11-22)

Primary citation

Harada, A.,Kamimura, N.,Takeuchi, K.,Yu, H.Y.,Masai, E.,Senda, T.
The crystal structure of a new O-demethylase from Sphingobium sp. strain SYK-6
FEBS J., 284:1855-1867, 2017

PubMed Abstract: In the cell, tetrahydrofolate (H folate) derivatives with a C1 unit are utilized in various ways, such as for the synthesis of amino acids and nucleic acids. While H folate derivatives with the C1 unit are typically produced in the glycine cleavage system, Sphingobium sp. strain SYK-6, which can utilize lignin-derived aromatic compounds as a sole source of carbon and energy, lacks this pathway, probably due to its unique nutrient requirements. In this bacterium, H folate-dependent O-demethylases in catabolic pathways for lignin-derived aromatic compounds seem to be involved in the C1 metabolism. LigM is one of the O-demethylases and catalyzes a C1-unit transfer from vanillate (VNL) to H folate. As the primary structure of LigM shows a similarity to T-protein in the glycine cleavage system, we hypothesized that LigM has evolved from T-protein, acquiring its unique biochemical and biological functions. To prove this hypothesis, structure-based understanding of its catalytic reaction is essential. Here, we determined the crystal structure of LigM in apo form and in complex with substrates and H folate. These crystal structures showed that the overall structure of LigM is similar to T-protein, but LigM has a few distinct characteristics, particularly in the active site. Structure-based mutational analysis revealed that His60 and Tyr247, which are not conserved in T-protein, are essential to the catalytic activity of LigM and their interactions with the oxygen atom in the methoxy group of VNL seem to facilitate a methyl moiety (C1-unit) transfer to H folate. Taken together, our structural data suggest that LigM has evolved divergently from T-protein.

PubMed: 28429420
DOI: 10.1111/febs.14085

Experimental method

X-RAY DIFFRACTION (1.9 Å)