Helicobacter pylori Csd4 is a peptidoglycan metallocarboxypeptidase
Bibliographic record
Abstract
The bacterial cell wall is a polymeric structure that determines the overall shape of the cell and undergoes constant remodelling during cell growth, requiring enzymes that cleave the existing peptidoglycan structure. Csd4 is an enzyme important for cell shape as deleting it in Helicobacter pylori causes the helical-shaped cells to become rod-like. Csd4 is a zinc carboxypeptidase that can cleave the tripeptide moiety found in peptidoglycan (i.e. L-Ala-γ-D-Glu-m-DAP) to release meso-diaminopimelic acid (mDAP). Structures of Csd4 were solved by X-ray crystallography up to 1.75 Å resolution in space group P212121 with zinc and substrate/product bound and contain the same unit cell dimensions. Csd4 is a monomeric enzyme with three domains: an N-terminal M14-family carboxypeptidase domain followed by two smaller domains likely important in protein-protein or protein-peptidoglycan interactions. Key interactions are observed between the protein and substrate in the active site, supporting specific substrate recognition by Csd4. A water or hydroxide molecule, which is required for catalytic activity, is also observed bound to the zinc and is poised to interact with the substrate molecule upon activation.
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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) | 0.002 | 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".