4U8E

Crystal structure of 4-deoxy-L-threo-5-hexosulose-uronate ketol-isomerase from Streptococcus agalactiae

Summary for 4U8E

• Entry DOI: 10.2210/pdb4u8e/pdb
• Related: 4U8F 4U8G
• Descriptor: Putative uncharacterized protein gbs1892 (2 entities in total)
• Functional Keywords: glycosaminoglycan metabolism, isomerase, rossman fold, 4-deoxy-l-threo-5-hexosulose-uronate
• Biological source: Streptococcus agalactiae NEM316
• Total number of polymer chains: 1
• Total formula weight: 24599.65

Authors

Maruyama, y.,Oiki, S.,Takase, R.,Mikami, B.,Murata, K.,Hashimoto, W. (deposition date: 2014-08-03, release date: 2015-01-21, Last modification date: 2023-11-08)

Primary citation

Maruyama, Y.,Oiki, S.,Takase, R.,Mikami, B.,Murata, K.,Hashimoto, W.
Metabolic Fate of Unsaturated Glucuronic/Iduronic Acids from Glycosaminoglycans: MOLECULAR IDENTIFICATION AND STRUCTURE DETERMINATION OF STREPTOCOCCAL ISOMERASE AND DEHYDROGENASE
J.Biol.Chem., 290:6281-6292, 2015

PubMed Abstract: 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. Genes coding for glycosaminoglycan-acting lyase, unsaturated glucuronyl hydrolase, and the 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, whereas KduI and KduD are encoded in clostridia. Tertiary and quaternary structures of DhuI and DhuD were determined by x-ray crystallography. Distinct from KduI β-barrels, DhuI adopts an α/β/α-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 glycosaminoglycan-derived unsaturated uronic acids by isomerase and dehydrogenase.

PubMed: 25605731
DOI: 10.1074/jbc.M114.604546

Experimental method

X-RAY DIFFRACTION (2 Å)