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Cite: NAR/gkaa742 2020

Because CGCFinder predicted no CGC for this PUL, the gene cluster depicted below contains dbCAN2 and CGC signature predictions for all genes in the PUL, instead of a predicted CGC.


PUL General Information

Literature Information

PUL ID

PUL0342

PubMed

19304844, J Bacteriol. 2009 May;191(10):3328-38. doi: 10.1128/JB.01628-08. Epub 2009 Mar 20.

Characterization method

enzyme activity assay,gene deletion mutant and growth assay

Genomic accession number

NC_014033.1

Nucelotide position range

3346598-3359433

Substrate

xylan

Loci

PRU_RS13995-PRU_RS14015

Species

Prevotella ruminicola/839

Degradation or Biosynthesis

degradation

Gene Name

Locus Tag

Protein ID

Gene Position

GenBank Contig Range

EC Number

- PRU_RS13995 WP_013065621.1 0 - 2181 (+) NC_014033.1:3346598-3348779 -
- PRU_RS14000 WP_013064566.1 2449 - 4915 (+) NC_014033.1:3349047-3351513 -
- PRU_RS14005 WP_013064096.1 4945 - 7531 (+) NC_014033.1:3351543-3354129 -
- PRU_RS14010 WP_080517213.1 7520 - 8927 (-) NC_014033.1:3354118-3355525 -
- PRU_RS14015 WP_013064354.1 8830 - 12835 (-) NC_014033.1:3355428-3359433 -

Cluster number

0

Gene name

Gene position

Gene type

Found by CGCFinder?

- 1 - 2181 (+) CAZyme: GH10|CE1|CBM22 No
- 2450 - 4915 (+) CAZyme: GH95 No
- 4946 - 7531 (+) CAZyme: GH3 No
- 7521 - 8927 (-) STP: STP|SBP_bac_1 No
- 8831 - 12835 (-) TF: DBD-Pfam|HTH_AraC,DBD-Pfam|HTH_AraC,DBD-SUPERFAMILY|0036286,DBD-SUPERFAMILY|0035607 No

PUL ID

PUL0342

PubMed

19304844, J Bacteriol. 2009 May;191(10):3328-38. doi: 10.1128/JB.01628-08. Epub 2009 Mar 20.

Title

Biochemical analysis of a beta-D-xylosidase and a bifunctional xylanase-ferulic acid esterase from a xylanolytic gene cluster in Prevotella ruminicola 23.

Author

Dodd D, Kocherginskaya SA, Spies MA, Beery KE, Abbas CA, Mackie RI, Cann IK

Abstract

Prevotella ruminicola 23 is an obligate anaerobic bacterium in the phylum Bacteroidetes that contributes to hemicellulose utilization within the bovine rumen. To gain insight into the cellular machinery that this organism elaborates to degrade the hemicellulosic polymer xylan, we identified and cloned a gene predicted to encode a bifunctional xylanase-ferulic acid esterase (xyn10D-fae1A) and expressed the recombinant protein in Escherichia coli. Biochemical analysis of purified Xyn10D-Fae1A revealed that this protein possesses both endo-beta-1,4-xylanase and ferulic acid esterase activities. A putative glycoside hydrolase (GH) family 3 beta-D-glucosidase gene, with a novel PA14-like insertion sequence, was identified two genes downstream of xyn10D-fae1A. Biochemical analyses of the purified recombinant protein revealed that the putative beta-D-glucosidase has activity for pNP-beta-D-xylopyranoside, pNP-alpha-L-arabinofuranoside, and xylo-oligosaccharides; thus, the gene was designated xyl3A. When incubated in combination with Xyn10D-Fae1A, Xyl3A improved the release of xylose monomers from a hemicellulosic xylan substrate, suggesting that these two enzymes function synergistically to depolymerize xylan. Directed mutagenesis studies of Xyn10D-Fae1A mapped the catalytic sites for the two enzymatic functionalities to distinct regions within the polypeptide sequence. When a mutation was introduced into the putative catalytic site for the xylanase domain (E280S), the ferulic acid esterase activity increased threefold, which suggests that the two catalytic domains for Xyn10D-Fae1A are functionally coupled. Directed mutagenesis of conserved residues for Xyl3A resulted in attenuation of activity, which supports the assignment of Xyl3A as a GH family 3 beta-D-xylosidase.