Home Repository Download Help About Statistics Taxonomy Blastx
Links
PULDB
CAZy
dbCAN2
dbCAN-seq
run_dbcan
CAZypedia
PlantCAZyme
Cite: NAR/gkaa742 2020



PUL General Information

Literature Information

PUL ID

PUL0207

PubMed

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

NC_004368.1

Nucelotide position range

1951803-1958763

Substrate

N-glycan

Loci

GBS_RS09825-GBS_RS09855

Species

Streptococcus agalactiae/1311

Degradation or Biosynthesis

degradation

Gene Name

Locus Tag

Protein ID

Gene Position

GenBank Contig Range

EC Number

- GBS_RS09825 WP_000654953.1 0 - 1905 (-) NC_004368.1:1951803-1953708 -
- GBS_RS09830 WP_000147951.1 1984 - 2800 (-) NC_004368.1:1953787-1954603 -
- GBS_RS09835 WP_000355267.1 2786 - 3653 (-) NC_004368.1:1954589-1955456 -
- GBS_RS09840 WP_000718802.1 3688 - 4183 (-) NC_004368.1:1955491-1955986 -
- GBS_RS09845 WP_000975716.1 4237 - 5434 (-) NC_004368.1:1956040-1957237 -
- GBS_RS09850 WP_000590444.1 5436 - 5871 (-) NC_004368.1:1957239-1957674 -
dhuD GBS_RS09855 WP_000139169.1 6148 - 6961 (+) NC_004368.1:1957951-1958764 1.1.1.127

Cluster number

1

Gene name

Gene position

Gene type

Found by CGCFinder?

- 1 - 1905 (-) CAZyme: PL12|PL12_1 Yes
- 1985 - 2800 (-) TC: gnl|TC-DB|Q8DR74|4.A.6.1.14 Yes
- 2787 - 3653 (-) TC: gnl|TC-DB|Q8DR75|4.A.6.1.14 Yes
- 3689 - 4183 (-) TC: gnl|TC-DB|Q8DR76|4.A.6.1.14 Yes
- 4238 - 5434 (-) CAZyme: GH88 Yes
- 5437 - 5871 (-) TC: gnl|TC-DB|Q8DR78|4.A.6.1.14 Yes
dhuD 6149 - 6961 (+) CDS No

PUL ID

PUL0207

PubMed

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

Title

Metabolic fate of unsaturated glucuronic/iduronic acids from glycosaminoglycans: molecular identification and structure determination of streptococcal isomerase and dehydrogenase.

Author

Maruyama Y, Oiki S, Takase R, Mikami B, Murata K, Hashimoto W

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 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.