Biochemical and structural characterization of TraE from the plasmid pKM101
Bibliographic record
Abstract
In all organisms, secretion systems mediate the passage of macromolecules across cellular membranes. The bacterial type IV secretion system (T4SS) family can be divided into three functional groups. First, as typified by the Brucella suis system, T4SSs deliver effector macromolecules into eukaryotic cells during the course of infection. Second, in some Gram-negative bacteria, such as in Helicobacter pylori (ComB system), T4SSs mediate DNA uptake from and release into the extracellular environment. Thirdly, as in the IncN plasmid pKM101, T4SSs can mediate the conjugative transfer of plasmid DNA or transposons into a wide range of bacterial species. This conjugation phenomenon contributes to the spread of antibiotic resistance genes among pathogenic bacteria, leading to the emergence of multidrug-resistant pathogenic strains. TraE of the IncN plasmid pKM101 belongs to the VirB8 family of proteins, an essential component of most T4SSs that form functional dimmers in the T4SS core. Here, we present the X-ray crystallographic structure of the periplasmic domain of TraE at 2.4 Å resolution. The structure shows many similarities to the known VirB8-like protein structures from Brucella suis [1] and Agrobacterium tumefaciens [2]. However, the nature and the number of residues implicated in the dimerization interface differ considerably from those in the TraE structure [2]. Similar to other VirB8 homologs we have shown by analytical gel filtration that there is a concentration dependant equilibrium between monomeric and dimeric forms of TraE. Moreover, using a bacterial two-hybrid assay, in vivo dimerization has been demonstrated with full-length TraE and key residues for dimerization were identified by site-directed mutagenesis. Our work adds novel insights into the growing body of knowledge on VirB8-like proteins and it will inform future strategies aimed at developing inhibitors of TraE protein interactions and of plasmid transfer.
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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 | 0.000 |
| Bibliometrics | 0.001 | 0.001 |
| 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) | 0.001 | 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".