Promiscuous substrate catalysis in tagatose-bisphosphate aldolase.
Bibliographic record
Abstract
Tagatose-1,6-biphosphate (TBP) from Streptococcus pyogenes offers a fascinating opportunity to probe promiscuous substrate turnover in an enzyme. TBP aldolase can cleave, apart from its own substrate TBP, three other bisphosphorylated D-hexoses including fructose-1,6-bisphosphate (FBP). These four sugars are diastereoisomers and differ in stereochemistry at carbon 3 and at carbon 4 with respect to the configuration of their hydroxyl groups. We have determined high resolution structures of the native enzyme in complex with natural substrates, FBP and TBP, and two competitive inhibitors. Since the TBP aldolase crystals are catalytically active, covalent reaction intermediates of TBP aldolase in complex with substrates were trapped under acidic conditions to minimize turnover. High resolution structural analysis revealed a snapshot of both substrates covalently trapped in the active site as Schiff bases undergoing C-C bond cleavage. The structural data pointed to Glu164, by virtue of hydrogen bonding to the substrate C4-OH, as the active site residue responsible for the proton abstraction at the C4-OH that initiates substrate cleavage. The isosteric mutant enzyme Glu164Gln, virtually devoid of activity, supported this interpretation. The structures of the Glu164Gln mutant in complex with TBP, FBP and two competitive inhibitors were solved at high resolution and corroborated the expected C4-OH hydrogen bonding of ligands with the carboxyaminde amide of Gln164, indicating retention of catalytically competent active site architecture upon mutation. The structural studies were underpinned with pH-profile studies that support Glu164 as the residue responsible for nonspecific substrate cleavage catalytic mechanism. Furthermore the pH-profile of the Glu164Gln was significantly different from that of the native enzyme corroborating Glu164 acting as the conjugate base for proton abstraction. The enzyme thus uses the same catalytic mechanism to cleave both diastereoisomers FBP and TBP, while promiscuous substrate recognition appears to be a function of subtle differences in the active site architecture when compared to the active site of the highly specific FBP aldolase from rabbit muscle.
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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) | 0.000 | 0.000 |
| Meta-epidemiology (broad) | 0.000 | 0.000 |
| Bibliometrics | 0.000 | 0.000 |
| Science and technology studies | 0.000 | 0.000 |
| Scholarly communication | 0.001 | 0.000 |
| Open science | 0.001 | 0.000 |
| Research integrity | 0.000 | 0.001 |
| Insufficient payload (model declined to judge) | 0.000 | 0.000 |
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".