4u8g

Crystal structure of 2-keto-3-deoxy-D-gluconate dehydrogenase from Streptococcus agalactiae

spinqualitylabelsall models 4u8g, resolution 2.90Å Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image   Print3D Structural highlights 4u8g is a 1 chain structure with sequence from Streptococcus agalactiae NEM316. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance. Resources: FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT Function Q8E370_STRA3 Publication Abstract from PubMed Glycosaminoglycans 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 From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

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