Structural And Functional Characterization Of Ulvan Degrading Polysaccharide Lyase Enzymes
Bibliographic record
Abstract
Ulvans are the sulfated cell wall polysaccharide present in marine green algae. Ulvan polysaccharides are composed mainly of 3‐sulfated rhamnose, glucuronic acid, iduronic acid and xylose. The sulfation pattern in ulvan resemble glycosaminoglycans in vertebrates. The structural features of ulvan make it a good candidate for variety of industrial applications in agriculture, food, pharmaceutical, chemical, and biomaterials industries. Identification of ulvan‐degrading microorganism and the corresponding enzymes will increase the potential application of this highly abundant naturally occurring polysaccharide. Bacterial microbiomes associated with the green algae contain enzymes to degrade ulvan by a lytic β‐elimination mechanism. Genome sequencing projects lead to the identification of many such ulvan degrading enzymes from several bacteria Nonlabens ulvanivorans, Pseudoalteromonas sp. strain PLSV, Alteromonas sp . strain LOR and LTR. Using X‐ray crystallography and enzyme activity assays, we solved the structure and biochemically characterized three ulvan lyases, PLSV3936 , LOR107 and NLR48 . All three enzymes share very low sequence identity and act differentially on substrate. Despite their low sequence identity, PLSV3936 and LOR107 share the same 7‐bladed β propeller fold. However, the complex structure with the bound tetrasaccharide substrate reveals the difference in the active site and mode of cleavage. Whereas, NLR48 has a β jelly roll scaffold. Complex structure of NLR48 with tetrasaccharide substrate suggest that NLR48 appears to utilize lysine and tyrosine as catalytic residues and the substrate acidic group is neutralized by a glutamine residue. Our results expand the information about ulvan degrading enzymes to potentiate the use of ulvan polysaccharide. Support or Funding Information The financial support was provided by a grant from the Natural Science and Engineering Research Council of Canada This abstract is from the Experimental Biology 2018 Meeting. There is no full text article associated with this abstract published in The FASEB Journal .
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How this classification was reachedexpand
Full frame machine prediction
Teacher imitationNot calibrated prevalence, not ground truth. Human validation pending. The Gemma side is a direct model label for every work in the frame, read from the title-only record. The Codex side is a classifier learned from the 10,348 direct Codex labels and calibrated to design-weighted sample rates; fields without enough sample support carry no Codex call. Candidate is the union of the two sides; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels.
Distilled classifier scores by category (both heads)
| Category | Codex | Gemma |
|---|---|---|
| Metaresearch | 0.000 | 0.001 |
| Meta-epidemiology (narrow) | 0.000 | 0.000 |
| Meta-epidemiology (broad) | 0.000 | 0.001 |
| Bibliometrics | 0.000 | 0.001 |
| Science and technology studies | 0.000 | 0.000 |
| Scholarly communication | 0.000 | 0.000 |
| Open science | 0.000 | 0.000 |
| Research integrity | 0.000 | 0.000 |
| Insufficient payload (model declined to judge) | 0.001 | 0.001 |
Machine scores (provisional)
The two teacher heads of the student model, read on this work. A score orders the frame for review; it never asserts a category, and the validation status ships verbatim with every row.
Baseline scores from an immature model (maturity gate not passed, 7 training rounds). Scores rank; they never assert a category.
score_only:v0-immature-baseline · verbatim from the scoring run: score_only means the number may rank works, and no category label ships from itClassification
machine, unvalidatedMachine predicted; a candidate call from one source (direct Gemma or distilled Codex), not a consensus.
How this classification was reached, model by model and score by score, is at the end of the page under "How this classification was reached".