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Cite: NAR/gkaa742 2020



PUL General Information

Literature Information

PUL ID

PUL0210

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_008261.1

Nucelotide position range

473690-487358

Substrate

N-glycan

Loci

CPF_RS01980-CPF_RS02040

Species

Clostridium perfringens/1502

Degradation or Biosynthesis

degradation

Gene Name

Locus Tag

Protein ID

Gene Position

GenBank Contig Range

EC Number

- CPF_RS01980 WP_003455341.1 0 - 3012 (+) NC_008261.1:473690-476702 -
kduI CPF_RS01985 WP_003455501.1 3118 - 3949 (+) NC_008261.1:476808-477639 5.3.1.17
kduD CPF_RS01990 WP_003455308.1 3964 - 4741 (+) NC_008261.1:477654-478431 1.1.1.127
eda CPF_RS01995 WP_011590177.1 4737 - 5379 (+) NC_008261.1:478427-479069 4.1.2.14, 4.1.3.16
- CPF_RS02000 WP_003455275.1 5382 - 6402 (+) NC_008261.1:479072-480092 -
kduI CPF_RS02005 WP_003455313.1 6566 - 7397 (+) NC_008261.1:480256-481087 5.3.1.17
- CPF_RS02010 WP_003455311.1 7413 - 8604 (+) NC_008261.1:481103-482294 -
- CPF_RS02015 WP_003455664.1 8620 - 9109 (+) NC_008261.1:482310-482799 -
- CPF_RS02020 WP_003455334.1 9156 - 9948 (+) NC_008261.1:482846-483638 -
- CPF_RS02025 WP_162467389.1 9916 - 10747 (+) NC_008261.1:483606-484437 -
- CPF_RS02030 WP_003455482.1 10816 - 11230 (+) NC_008261.1:484506-484920 -
yajC CPF_RS02035 WP_003455254.1 11232 - 11511 (+) NC_008261.1:484922-485201 -
- CPF_RS02040 WP_003455377.1 11650 - 13669 (+) NC_008261.1:485340-487359 -

Cluster number

1

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

PUL ID

PUL0210

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.