8ABV

Crystal structure of SpLdpA in complex with erythro-DGPD

Summary for 8ABV

• Entry DOI: 10.2210/pdb8abv/pdb
• Descriptor: SnoaL-like domain-containing protein, GLYCEROL, SULFATE ION, ... (6 entities in total)
• Functional Keywords: lignin, lyase, dehydratase
• Biological source: Sphingomonas paucimobilis
• Total number of polymer chains: 1
• Total formula weight: 31371.37

Authors

Zahn, M.,Kuatsjah, E.,Beckham, G.T.,McGeehan, J.E. (deposition date: 2022-07-04, release date: 2023-02-01, Last modification date: 2024-05-01)

Primary citation

Kuatsjah, E.,Zahn, M.,Chen, X.,Kato, R.,Hinchen, D.J.,Konev, M.O.,Katahira, R.,Orr, C.,Wagner, A.,Zou, Y.,Haugen, S.J.,Ramirez, K.J.,Michener, J.K.,Pickford, A.R.,Kamimura, N.,Masai, E.,Houk, K.N.,McGeehan, J.E.,Beckham, G.T.
Biochemical and structural characterization of a sphingomonad diarylpropane lyase for cofactorless deformylation.
Proc.Natl.Acad.Sci.USA, 120:e2212246120-e2212246120, 2023

PubMed Abstract: Lignin valorization is being intensely pursued via tandem catalytic depolymerization and biological funneling to produce single products. In many lignin depolymerization processes, aromatic dimers and oligomers linked by carbon-carbon bonds remain intact, necessitating the development of enzymes capable of cleaving these compounds to monomers. Recently, the catabolism of -1,2-diguaiacylpropane-1,3-diol (-DGPD), a ring-opened lignin-derived β-1 dimer, was reported in . The first enzyme in this pathway, LdpA (formerly LsdE), is a member of the nuclear transport factor 2 (NTF-2)-like structural superfamily that converts -DGPD to lignostilbene through a heretofore unknown mechanism. In this study, we performed biochemical, structural, and mechanistic characterization of the LdpA and another homolog identified in sp. SYK-6, for which activity was confirmed in vivo. For both enzymes, we first demonstrated that formaldehyde is the C reaction product, and we further demonstrated that both enantiomers of -DGPD were transformed simultaneously, suggesting that LdpA, while diastereomerically specific, lacks enantioselectivity. We also show that LdpA is subject to a severe competitive product inhibition by lignostilbene. Three-dimensional structures of LdpA were determined using X-ray crystallography, including substrate-bound complexes, revealing several residues that were shown to be catalytically essential. We used density functional theory to validate a proposed mechanism that proceeds via dehydroxylation and formation of a quinone methide intermediate that serves as an electron sink for the ensuing deformylation. Overall, this study expands the range of chemistry catalyzed by the NTF-2-like protein family to a prevalent lignin dimer through a cofactorless deformylation reaction.

PubMed: 36652470
DOI: 10.1073/pnas.2212246120

Experimental method

X-RAY DIFFRACTION (1.683 Å)