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Cite: NAR/gkaa742 2020



PUL General Information

Literature Information

PUL ID

PUL0610

PubMed

31992772, Sci Rep. 2020 Jan 28;10(1):1329. doi: 10.1038/s41598-020-58015-5.

Characterization method

enzyme activity assay,strcutural analysis

Genomic accession number

CP001807.1

Nucelotide position range

1220087-1251526

Substrate

xylan

Loci

Rmar_1067-Rmar_1081

Species

Rhodothermus marinus/29549

Degradation or Biosynthesis

degradation

Gene Name

Locus Tag

Protein ID

Gene Position

GenBank Contig Range

EC Number

- Rmar_1067 ACY47959.1 0 - 1050 (+) CP001807.1:1220087-1221137 -
- Rmar_1068 ACY47960.1 1476 - 3870 (+) CP001807.1:1221563-1223957 -
- Rmar_1069 ACY47961.1 4025 - 7019 (+) CP001807.1:1224112-1227106 -
- Rmar_1070 ACY47962.1 7064 - 10040 (+) CP001807.1:1227151-1230127 -
- Rmar_1071 ACY47963.1 10072 - 12079 (+) CP001807.1:1230159-1232166 -
- Rmar_1072 ACY47964.1 12182 - 13955 (+) CP001807.1:1232269-1234042 -
- Rmar_1073 ACY47965.1 13977 - 15684 (+) CP001807.1:1234064-1235771 -
- Rmar_1074 ACY47966.1 15959 - 17456 (+) CP001807.1:1236046-1237543 -
- Rmar_1075 ACY47967.1 17496 - 18060 (+) CP001807.1:1237583-1238147 -
- Rmar_1076 ACY47968.1 18135 - 19179 (+) CP001807.1:1238222-1239266 -
- Rmar_1077 ACY47969.1 19250 - 22694 (+) CP001807.1:1239337-1242781 -
- Rmar_1078 ACY47970.1 22740 - 24270 (+) CP001807.1:1242827-1244357 -
- Rmar_1079 ACY47971.1 24403 - 26584 (+) CP001807.1:1244490-1246671 3.2.1.139
- Rmar_1080 ACY47972.1 26647 - 29026 (+) CP001807.1:1246734-1249113 -
- Rmar_1081 ACY47973.1 29085 - 31440 (+) CP001807.1:1249172-1251527 -

Cluster number

1

Gene name

Gene position

Gene type

Found by CGCFinder?

- 1 - 1050 (+) TF: DBD-Pfam|LacI,DBD-SUPERFAMILY|0036955 No
- 1477 - 3870 (+) CAZyme: GH43_15|CBM6 Yes
- 4026 - 7019 (+) CAZyme: GH10|CBM4|3.2.1.8 Yes
- 7065 - 10040 (+) other Yes
- 10073 - 12079 (+) other Yes
- 12183 - 13955 (+) other Yes
- 13978 - 15684 (+) other Yes
- 15960 - 17456 (+) CAZyme: GH10 Yes
- 17497 - 18060 (+) TF: DBD-Pfam|GerE Yes
- 18136 - 19179 (+) STP: STP|FecR Yes
- 19251 - 22694 (+) TC: gnl|TC-DB|Q45780|1.B.14.6.1 Yes
- 22741 - 24270 (+) TC: gnl|TC-DB|E4RVP8|8.A.46.1.5 Yes
- 24404 - 26584 (+) CAZyme: GH67 Yes
- 26648 - 29026 (+) CAZyme: GH3 Yes
- 29086 - 31440 (+) CAZyme: GH3 Yes

PUL ID

PUL0610

PubMed

31992772, Sci Rep. 2020 Jan 28;10(1):1329. doi: 10.1038/s41598-020-58015-5.

Title

Characterization and diversity of the complete set of GH family 3 enzymes from Rhodothermus marinus DSM 4253.

Author

Ara KZG, Manberger A, Gabrisko M, Linares-Pasten JA, Jasilionis A, Friethjonsson OH, Hreggviethsson GO, Janecek S, Nordberg Karlsson E

Abstract

The genome of Rhodothermus marinus DSM 4253 encodes six glycoside hydrolases (GH) classified under GH family 3 (GH3): RmBgl3A, RmBgl3B, RmBgl3C, RmXyl3A, RmXyl3B and RmNag3. The biochemical function, modelled 3D-structure, gene cluster and evolutionary relationships of each of these enzymes were studied. The six enzymes were clustered into three major evolutionary lineages of GH3: beta-N-acetyl-glucosaminidases, beta-1,4-glucosidases/beta-xylosidases and macrolide beta-glucosidases. The RmNag3 with additional beta-lactamase domain clustered with the deepest rooted GH3-lineage of beta-N-acetyl-glucosaminidases and was active on acetyl-chitooligosaccharides. RmBgl3B displayed beta-1,4-glucosidase activity and was the only representative of the lineage clustered with macrolide beta-glucosidases from Actinomycetes. The beta-xylosidases, RmXyl3A and RmXyl3B, and the beta-glucosidases RmBgl3A and RmBgl3C clustered within the major beta-glucosidases/beta-xylosidases evolutionary lineage. RmXyl3A and RmXyl3B showed beta-xylosidase activity with different specificities for para-nitrophenyl (pNP)-linked substrates and xylooligosaccharides. RmBgl3A displayed beta-1,4-glucosidase/beta-xylosidase activity while RmBgl3C was active on pNP-beta-Glc and beta-1,3-1,4-linked glucosyl disaccharides. Putative polysaccharide utilization gene clusters were also investigated for both R. marinus DSM 4253 and DSM 4252(T) (homolog strain). The analysis showed that in the homolog strain DSM 4252(T) Rmar_1080 (RmXyl3A) and Rmar_1081 (RmXyl3B) are parts of a putative polysaccharide utilization locus (PUL) for xylan utilization.