WrtF from <i>Rhizobium tropici</i> CIAT 899 is a GT-A fold fucosyltransferase that binds its donor nonproductively
Bibliographic record
Abstract
CIAT 899. We show that WrtF transfers l-fucose from its donor, guanosine 5'-diphospho-β-l-fucose (GDP-Fuc), to a nonreducing end glucose, creating an α-(1→4) linkage. We determined structures of WrtF at resolutions between 1.45 and 2.3 Å in the apo state, and in complex with GDP, GDP-Fuc, nonacetylated and acetylated trisaccharide acceptors, and with a tetrasaccharide product. WrtF has an N-terminal glycosyltransferase A (GT-A) fold and a unique C-terminal α-helical bundle domain. The structures, combined with activity assays, and sequence analysis show that WrtF is unusual in using neither divalent cations nor basic residues to coordinate and stabilize the donor pyrophosphate. In contrast to almost all previously characterized GT-A glycosyltransferases that use α-linked donors that present the donor monosaccharide axially, GDP-Fuc presents its monosaccharide equatorially. GDP-Fuc binds in a compact conformation with the l-fucose endocyclic oxygen and C6 methyl packed against ribose C5 and C4, respectively. This binding mode paradoxically shields the anomeric carbon from attack; superposition of the donor and acceptor complexes suggests that these substrates would sterically hinder one another and do not appropriately orient to form a Michaelis complex. We therefore propose that the donor l-fucose must reorient in the active site prior to turnover. The preferred occluded donor binding mode may serve to "prescreen" GDP-Fuc from structurally similar candidate donors, while also minimizing counterproductive donor hydrolysis.
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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 | 0.000 |
| Meta-epidemiology (narrow) | 0.001 | 0.000 |
| Meta-epidemiology (broad) | 0.000 | 0.000 |
| Bibliometrics | 0.000 | 0.000 |
| 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".