Structural and functional characterization of ulvan lyase enzymes
Bibliographic record
Abstract
Ulvan is a complex sulfated polysaccharide biosynthesized by marine green algae and constitutes one of the two major polysaccharides of their cell wall. This water-soluble polysaccharide is composed predominantly of 3-sulfated rhamnose (R3S), glucuronic acid (GluA), iduronic acid (IdoA) and xylose. The physicochemical and biological properties of ulvan make it of interest for a variety of industrial applications. Bacteria cohabiting with the green algae contain enzymes able to degrade ulvan by a lytic -elimination mechanism. Genes coding such lyases have been discovered in the genomes of several bacteria. Pseudoalteromonas sp. strain PLSV gene PLSV_3936 encodes an ulvan lyase that cleaves the glycosidic bond between 3-sulfated rhamnose (R3S) and glucuronic acid (GluA) or iduronic acid (IdoA). Another ulvan lyase, discovered in Alteromonadales and encoded by the gene LOR_107, degrades ulvan endolyticaly cleaving the bond between the rhamnose-3-sulfate and glucuronic acid. We have characterized biochemically these two lyases and determined their three-dimensional structures. They represent the first structures of lyases capable of degrading ulvan. In spite of only 17% sequence identity, these two enzymes share the same 7-bladed propeller fold. The putative active site was identified from structure conservation and confirmed by mutagenesis and structures of these enzymes with bound tetrasaccharide substrates. The catalytic residues are histidine and tyrosine while the substrate acidic group is neutralized by an arginine. Metal ions were detected in both lyases but they play only structural roles and are not involved directly in the catalysis.
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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) | 0.001 | 0.000 |
| Meta-epidemiology (broad) | 0.000 | 0.001 |
| Bibliometrics | 0.001 | 0.001 |
| Science and technology studies | 0.000 | 0.000 |
| Scholarly communication | 0.001 | 0.000 |
| Open science | 0.000 | 0.000 |
| Research integrity | 0.000 | 0.001 |
| 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".