4u8f | pdb_00004u8f
Crystal structure of 4-deoxy-L-threo-5-hexosulose-uronate ketol-isomerase complexed with a tartrate
Structural highlights
Publication Abstract from PubMedGlycosaminoglycans in mammalian extracellular matrices are degraded to their constituents, unsaturated uronic (glucuronic/iduronic) acids and amino sugars, through successive reactions of bacterial polysaccharide lyase and unsaturated glucuronyl hydrolase (UGL). Genes coding for glycosaminoglycans-acting lyase, UGL, and phosphotransferase system are assembled into a cluster in the genome of pathogenic bacteria, such as streptococci and clostridia. Here, we studied the streptococcal metabolic pathway of unsaturated uronic acids and the structure/function relationship of its relevant isomerase and dehydrogenase. Two proteins (gbs1892 and gbs1891) of Streptococcus agalactiae strain NEM316 were overexpressed in Escherichia coli, purified, and characterized. 4-Deoxy-L-threo-5-hexosulose-uronate (Dhu) nonenzymatically generated from unsaturated uronic acids was converted to 2-keto-3-deoxy-D-gluconate via 3-deoxy-D-glycero-2,5-hexodiulosonate through successive reactions of gbs1892 isomerase (DhuI) and gbs1891 NADH-dependent reductase/dehydrogenase (DhuD). DhuI and DhuD enzymatically corresponded to 4-deoxy-L-threo-5-hexosulose-uronate ketol-isomerase (KduI) and 2-keto-3-deoxy-D-gluconate dehydrogenase (KduD), respectively, involved in pectin metabolism, although no or low sequence identity was observed between DhuI and KduI or between DhuD and KduD, respectively. Genes for DhuI and DhuD were found to be included in the streptococcal genetic cluster, while KduI and KduD are encoded in clostridia. Tertiary and quaternary structures of DhuI and DhuD were determined by X-ray crystallography. Distinct from KduI beta-barrels, DhuI adopts an alpha/beta/alpha-barrel structure as a basic scaffold similar to that of ribose 5-phosphate isomerase. The structure of DhuD is unable to accommodate the substrate/cofactor, suggesting that conformational changes are essential to trigger enzyme catalysis. This is the first report on the bacterial metabolism of glycosaminoglycans-derived unsaturated uronic acids by isomerase and dehydrogenase. Metabolic fate of unsaturated glucuronic/iduronic acids from glycosaminoglycans: molecular identification and structure determination of Streptococcal isomerase and dehydrogenase.,Maruyama Y, Oiki S, Takase R, Mikami B, Murata K, Hashimoto W J Biol Chem. 2015 Jan 20. pii: jbc.M114.604546. PMID:25605731[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. References
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