4xt0 | pdb_00004xt0

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

spinqualitylabelsall models 4xt0, resolution 2.07Å Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image   Print3D Structural highlights 4xt0 is a 1 chain structure with sequence from Sphingobium sp. SYK-6. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance. Ligands: 1PE, GSH, TRS Resources: FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT Function G2IN92_SPHSK Publication Abstract from PubMed 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 beta-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 beta-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 beta-aryl ether bonds account for 50-70% of all interunit linkages in lignin, understanding the mechanism of enzymatic beta-aryl ether cleavage has significant potential for informing ongoing studies on the valorization of lignin. Structural Basis of Stereospecificity in the Bacterial Enzymatic Cleavage of beta-Aryl Ether Bonds in Lignin.,Helmich KE, Pereira JH, Gall DL, Heins RA, McAndrew RP, Bingman C, Deng K, Holland KC, Noguera DR, Simmons BA, Sale KL, Ralph J, Donohue TJ, Adams PD, Phillips GN Jr J Biol Chem. 2016 Mar 4;291(10):5234-46. doi: 10.1074/jbc.M115.694307. Epub 2015 , Dec 4. PMID:26637355 From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

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