Substrate specificity of <i>N</i>-methyltransferases in benzylisoquinoline alkaloid metabolism
Bibliographic record
Abstract
Plants such as the opium poppy have been extensively studied for their production of benzylisoquinoline alkaloids (BIAs), a class of specialized metabolites with many useful and potent pharmacological properties. Naturally occurring BIAs such as morphine and noscapine have been widely used since ancient times, but recent advances in synthetic biology and protein engineering provide exciting new opportunities for creating novel compounds with novel or improved pharmacological properties. N-methyltransferases (NMTs) play key roles in several different branches of BIA-metabolism. Hundreds of BIA NMT gene sequences from a wide variety of plants can be separated into three general groups based on function and sequence identity. Recent work from our group led to the determination of the first molecular structure of an NMT involved with BIA biosynthesis (pavine-NMT from Thalictrum flavum, M.A. Torres et al, J. Biol. Chem. 291:23403, 2016). More recently, we have determined the structures of enzymes from the two other groups of NMT's involved with BIA biosynthesis. Using pavine-NMT from T. flavum as a search model, we used molecular replacement to solve the structures of tetrahydroprotoberberine-NMT (52% sequence identity, dmin = 1.8 ) and coclaurine-NMT (63% sequence identity, dmin = 2.2 ) from Glaucium flavum. These structures reveal a high level of structural conservation in the overall protein fold, arrangement of catalytic residues at the active site and substrate-binding site for S-adenosylmethionine. A subset of residues within the binding site for the methyl-acceptor alkaloid substrate appear to define the unique substrate recognition specificities of each group of NMT's. To further explore these structure-function relationships, we have undertaken mutagenesis studies in combination with differential scanning fluorimetry, enzyme activity measurements and structure determination of enzymes with alkaloid substrates or substrate-analogs. Our presentation will discuss some of our recent progress in defining structure-function relationships in NMT enzymes and initial steps towards engineering altered substrate preferences for synthetic biology applications.
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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 | 0.000 | 0.000 |
| Open science | 0.000 | 0.000 |
| Research integrity | 0.000 | 0.000 |
| Insufficient payload (model declined to judge) | 0.001 | 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".