25605731, J Biol Chem. 2015 Mar 6;290(10):6281-92. doi: 10.1074/jbc.M114.604546. Epub 2015 Jan 20.

Characterization method

enzyme activity assay

Genomic accession number


Nucelotide position range







Clostridium perfringens/1502

Degradation or Biosynthesis


Cluster number


Gene name

Gene position

Gene type

Found by CGCFinder?

- 1 - 3012 (+) CAZyme: PL8 Yes
kduI 3119 - 3949 (+) other Yes
kduD 3965 - 4741 (+) other Yes
eda 4738 - 5379 (+) other Yes
- 5383 - 6402 (+) STP: STP|PfkB Yes
kduI 6567 - 7397 (+) other Yes
- 7414 - 8604 (+) CAZyme: GH88 Yes
- 8621 - 9109 (+) TC: gnl|TC-DB|Q8DR76|4.A.6.1.14 Yes
- 9157 - 9948 (+) TC: gnl|TC-DB|Q8DR75|4.A.6.1.14 Yes
- 9917 - 10747 (+) TC: gnl|TC-DB|Q8DR74|4.A.6.1.14 Yes
- 10817 - 11230 (+) TC: gnl|TC-DB|Q8DR78|4.A.6.1.14 Yes
yajC 11233 - 11511 (+) other Yes
- 11651 - 13669 (+) CAZyme: PL12_1 Yes




25605731, J Biol Chem. 2015 Mar 6;290(10):6281-92. doi: 10.1074/jbc.M114.604546. Epub 2015 Jan 20.


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


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 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 glycosaminoglycan-derived unsaturated uronic acids by isomerase and dehydrogenase.