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

PUL0344

PubMed

27933102, Biotechnol Biofuels. 2016 Nov 28;9:260. doi: 10.1186/s13068-016-0674-z. eCollection 2016.
32792608, Sci Rep. 2020 Aug 13;10(1):13775. doi: 10.1038/s41598-020-70749-w.

Characterization method

gene deletion mutant and growth assay,protein structure characterization

Genomic accession number

CP000685.1

Nucelotide position range

5499208-5523115

Substrate

chitin

Loci

Fjoh_4555-Fjoh_4565

Species

Flavobacterium johnsoniae/986

Degradation or Biosynthesis

degradation

Gene Name

Locus Tag

Protein ID

Gene Position

GenBank Contig Range

EC Number

- Fjoh_4555 ABQ07554.1 0 - 4737 (-) CP000685.1:5499208-5503945 3.2.1.14
- Fjoh_4556 ABQ07555.1 5200 - 7267 (-) CP000685.1:5504408-5506475 3.2.1.52
- Fjoh_4557 ABQ07556.1 7424 - 9437 (-) CP000685.1:5506632-5508645 -
- Fjoh_4558 ABQ07557.1 9481 - 11062 (-) CP000685.1:5508689-5510270 -
- Fjoh_4559 ABQ07558.1 11072 - 14105 (-) CP000685.1:5510280-5513313 -
- Fjoh_4560 ABQ07559.1 14434 - 15457 (-) CP000685.1:5513642-5514665 -
- Fjoh_4561 ABQ07560.1 15542 - 17060 (-) CP000685.1:5514750-5516268 -
- Fjoh_4562 ABQ07561.1 17071 - 20269 (-) CP000685.1:5516279-5519477 -
- Fjoh_4563 ABQ07562.1 20530 - 21583 (+) CP000685.1:5519738-5520791 -
- Fjoh_4564 ABQ07563.1 21572 - 22274 (+) CP000685.1:5520780-5521482 -
- Fjoh_4565 ABQ07564.1 22441 - 23908 (+) CP000685.1:5521649-5523116 -

Cluster number

1

Gene name

Gene position

Gene type

Found by CGCFinder?

- 1 - 4737 (-) CAZyme: GH18 Yes
- 5201 - 7267 (-) CAZyme: GH20 Yes
- 7425 - 9437 (-) STP: STP|PIG-L Yes
- 9482 - 11062 (-) TC: gnl|TC-DB|Q8A8X0|8.A.46.2.1 Yes
- 11073 - 14105 (-) TC: gnl|TC-DB|Q8A8X1|1.B.14.6.13 Yes
- 14435 - 15457 (-) CAZyme: GH18 Yes
- 15543 - 17060 (-) TC: gnl|TC-DB|Q8A0N7|8.A.46.2.2 Yes
- 17072 - 20269 (-) TC: gnl|TC-DB|Q93TH9|1.B.14.6.2 Yes
- 20531 - 21583 (+) other Yes
- 21573 - 22274 (+) TF: DBD-Pfam|LytTR Yes
- 22442 - 23908 (+) TC: gnl|TC-DB|P0C105|2.A.1.7.2 Yes

PUL ID

PUL0344

PubMed

27933102, Biotechnol Biofuels. 2016 Nov 28;9:260. doi: 10.1186/s13068-016-0674-z. eCollection 2016.

Title

A polysaccharide utilization locus from Flavobacterium johnsoniae enables conversion of recalcitrant chitin.

Author

Larsbrink J, Zhu Y, Kharade SS, Kwiatkowski KJ, Eijsink VG, Koropatkin NM, McBride MJ, Pope PB

Abstract

BACKGROUND: Chitin is the second most abundant polysaccharide on earth and as such a great target for bioconversion applications. The phylum Bacteroidetes is one of nature's most ubiquitous bacterial lineages and is essential in the global carbon cycle with many members being highly efficient degraders of complex carbohydrates. However, despite their specialist reputation in carbohydrate conversion, mechanisms for degrading recalcitrant crystalline polysaccharides such as chitin and cellulose are hitherto unknown. RESULTS: Here we describe a complete functional analysis of a novel polysaccharide utilization locus (PUL) in the soil Bacteroidete Flavobacterium johnsoniae, tailored for conversion of chitin. The F. johnsoniae chitin utilization locus (ChiUL) consists of eleven contiguous genes encoding carbohydrate capture and transport proteins, enzymes, and a two-component sensor-regulator system. The key chitinase (ChiA) encoded by ChiUL is atypical in terms of known Bacteroidetes-affiliated PUL mechanisms as it is not anchored to the outer cell membrane and consists of multiple catalytic domains. We demonstrate how the extraordinary hydrolytic efficiency of ChiA derives from synergy between its multiple chitinolytic (endo- and exo-acting) and previously unidentified chitin-binding domains. Reverse genetics show that ChiA and PUL-encoded proteins involved in sugar binding, import, and chitin sensing are essential for efficient chitin utilization. Surprisingly, the ChiUL encodes two pairs of SusC/D-like outer membrane proteins. Ligand-binding and structural studies revealed functional differences between the two SusD-like proteins that enhance scavenging of chitin from the environment. The combined results from this study provide insight into the mechanisms employed by Bacteroidetes to degrade recalcitrant polysaccharides and reveal important novel aspects of the PUL paradigm. CONCLUSIONS: By combining reverse genetics to map essential PUL genes, structural studies on outer membrane chitin-binding proteins, and enzymology, we provide insight into the mechanisms employed by Bacteroidetes to degrade recalcitrant polysaccharides and introduce a new saccharolytic mechanism used by the phylum Bacteroidetes. The presented discovery and analysis of the ChiUL will greatly benefit future enzyme discovery efforts as well as studies regarding enzymatic intramolecular synergism.

PubMed

32792608, Sci Rep. 2020 Aug 13;10(1):13775. doi: 10.1038/s41598-020-70749-w.

Title

Structural insights of the enzymes from the chitin utilization locus of Flavobacterium johnsoniae.

Author

Mazurkewich S, Helland R, Mackenzie A, Eijsink VGH, Pope PB, Branden G, Larsbrink J

Abstract

Chitin is one of the most abundant renewable organic materials found on earth. The chitin utilization locus in Flavobacterium johnsoniae, which encodes necessary proteins for complete enzymatic depolymerization of crystalline chitin, has recently been characterized but no detailed structural information on the enzymes was provided. Here we present protein structures of the F. johnsoniae chitobiase (FjGH20) and chitinase B (FjChiB). FjGH20 is a multi-domain enzyme with a helical domain not before observed in other chitobiases and a domain organization reminiscent of GH84 (beta-N-acetylglucosaminidase) family members. The structure of FjChiB reveals that the protein lacks loops and regions associated with exo-acting activity in other chitinases and instead has a more solvent accessible substrate binding cleft, which is consistent with its endo-chitinase activity. Additionally, small angle X-ray scattering data were collected for the internal 70 kDa region that connects the N- and C-terminal chitinase domains of the unique 158 kDa multi-domain chitinase A (FjChiA). The resulting model of the molecular envelope supports bioinformatic predictions of the region comprising six domains, each with similarities to either Fn3-like or Ig-like domains. Taken together, the results provide insights into chitin utilization by F. johnsoniae and reveal structural diversity in bacterial chitin metabolism.