4XT0

Crystal Structure of Beta-etherase LigF from Sphingobium sp. strain SYK-6

Summary for 4XT0

• Entry DOI: 10.2210/pdb4xt0/pdb
• Descriptor: Protein LigF, GLUTATHIONE, 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL, ... (5 entities in total)
• Functional Keywords: beta-etherase, lignase, ligf, thioredoxin, glutathione, gst, transferase
• Biological source: Sphingobium sp. SYK-6
• Total number of polymer chains: 1
• Total formula weight: 28959.81

Authors

Helmich, K.E.,Bingman, C.A.,Donohue, T.J.,Phillips Jr., G.N. (deposition date: 2015-01-22, release date: 2016-02-03, Last modification date: 2024-02-28)

Primary citation

Helmich, K.E.,Pereira, J.H.,Gall, D.L.,Heins, R.A.,McAndrew, R.P.,Bingman, C.,Deng, K.,Holland, K.C.,Noguera, D.R.,Simmons, B.A.,Sale, K.L.,Ralph, J.,Donohue, T.J.,Adams, P.D.,Phillips, G.N.
Structural Basis of Stereospecificity in the Bacterial Enzymatic Cleavage of beta-Aryl Ether Bonds in Lignin.
J.Biol.Chem., 291:5234-5246, 2016

PubMed Abstract: Lignin is a combinatorial polymer comprising monoaromatic units that are linked via covalent bonds. Although lignin is a potential source of valuable aromatic chemicals, its recalcitrance to chemical or biological digestion presents major obstacles to both the production of second-generation biofuels and the generation of valuable coproducts from lignin's monoaromatic units. Degradation of lignin has been relatively well characterized in fungi, but it is less well understood in bacteria. A catabolic pathway for the enzymatic breakdown of aromatic oligomers linked via β-aryl ether bonds typically found in lignin has been reported in the bacterium Sphingobium sp. SYK-6. Here, we present x-ray crystal structures and biochemical characterization of the glutathione-dependent β-etherases, LigE and LigF, from this pathway. The crystal structures show that both enzymes belong to the canonical two-domain fold and glutathione binding site architecture of the glutathione S-transferase family. Mutagenesis of the conserved active site serine in both LigE and LigF shows that, whereas the enzymatic activity is reduced, this amino acid side chain is not absolutely essential for catalysis. The results include descriptions of cofactor binding sites, substrate binding sites, and catalytic mechanisms. Because β-aryl ether bonds account for 50-70% of all interunit linkages in lignin, understanding the mechanism of enzymatic β-aryl ether cleavage has significant potential for informing ongoing studies on the valorization of lignin.

PubMed: 26637355
DOI: 10.1074/jbc.M115.694307

Experimental method

X-RAY DIFFRACTION (2.07 Å)