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Cite: NAR/gkaa742 2020



PUL General Information

Literature Information

PUL ID

PUL0227

PubMed

22918832, J Biol Chem. 2012 Oct 12;287(42):34946-34960. doi: 10.1074/jbc.M112.391532. Epub 2012 Aug 22.

Characterization method

enzyme activity assay,substrate binding assay

Genomic accession number

JX087428.1

Nucelotide position range

0-18201

Substrate

xylan

Loci

AFM44648.1-AFM44659.1

Species

Caldanaerobius polysaccharolyticus/44256

Degradation or Biosynthesis

degradation

Gene Name

Locus Tag

Protein ID

Gene Position

GenBank Contig Range

EC Number

- - AFM44648.1 0 - 162 (+) JX087428.1:0-162 -
agu67A - AFM44650.1 325 - 2398 (+) JX087428.1:325-2398 3.2.1.139
xyl3A - AFM44649.1 2433 - 4803 (+) JX087428.1:2433-4803 3.2.1.37
xylI - AFM44651.1 4836 - 5979 (+) JX087428.1:4836-5979 5.3.1.5
xylK - AFM44652.1 5994 - 7506 (+) JX087428.1:5994-7506 2.7.1.17
- - AFM44653.1 7539 - 8190 (+) JX087428.1:7539-8190 2.2.1.2
transketolase - AFM44655.1 8207 - 9977 (+) JX087428.1:8207-9977 2.7.13.3
- - AFM44654.1 12044 - 13529 (+) JX087428.1:12044-13529 -
xbp1 - AFM44656.1 13912 - 15232 (+) JX087428.1:13912-15232 -
- - AFM44657.1 15352 - 16237 (+) JX087428.1:15352-16237 -
- - AFM44658.1 16251 - 17112 (+) JX087428.1:16251-17112 -
- - AFM44659.1 17400 - 18201 (+) JX087428.1:17400-18201 -

Cluster number

1

Gene name

Gene position

Gene type

Found by CGCFinder?

- 1 - 162 (+) CDS No
- 326 - 2398 (+) CAZyme: GH67 Yes
- 2434 - 4803 (+) CAZyme: GH3 Yes
- 4837 - 5979 (+) other Yes
- 5995 - 7506 (+) other Yes
- 7540 - 8190 (+) other Yes
- 10727 - 11935 (+) TC: gnl|TC-DB|F4LXP4|8.A.59.2.1 Yes
- 12045 - 13529 (+) TF: DBD-Pfam|HTH_AraC,DBD-SUPERFAMILY|0036286 Yes
- 13913 - 15232 (+) other Yes
- 15353 - 16237 (+) TC: gnl|TC-DB|O51924|3.A.1.1.7 Yes
- 16252 - 17112 (+) CDS No
- 17401 - 18201 (+) CDS No

PUL ID

PUL0227

PubMed

22918832, J Biol Chem. 2012 Oct 12;287(42):34946-34960. doi: 10.1074/jbc.M112.391532. Epub 2012 Aug 22.

Title

Biochemical and structural insights into xylan utilization by the thermophilic bacterium Caldanaerobius polysaccharolyticus.

Author

Han Y, Agarwal V, Dodd D, Kim J, Bae B, Mackie RI, Nair SK, Cann IKO

Abstract

Hemicellulose is the next most abundant plant cell wall component after cellulose. The abundance of hemicellulose such as xylan suggests that their hydrolysis and conversion to biofuels can improve the economics of bioenergy production. In an effort to understand xylan hydrolysis at high temperatures, we sequenced the genome of the thermophilic bacterium Caldanaerobius polysaccharolyticus. Analysis of the partial genome sequence revealed a gene cluster that contained both hydrolytic enzymes and also enzymes key to the pentose-phosphate pathway. The hydrolytic enzymes in the gene cluster were demonstrated to convert products from a large endoxylanase (Xyn10A) predicted to anchor to the surface of the bacterium. We further use structural and calorimetric studies to demonstrate that the end products of Xyn10A hydrolysis of xylan are recognized and bound by XBP1, a putative solute-binding protein, likely for transport into the cell. The XBP1 protein showed preference for xylo-oligosaccharides as follows: xylotriose > xylobiose > xylotetraose. To elucidate the structural basis for the oligosaccharide preference, we solved the co-crystal structure of XBP1 complexed with xylotriose to a 1.8-A resolution. Analysis of the biochemical data in the context of the co-crystal structure reveals the molecular underpinnings of oligosaccharide length specificity.