A huge but elusive macromolecular cage in enterobacterial stress response as seen by <scp>cryoEM</scp> and <scp>X‐ray</scp> crystallography
Bibliographic record
Abstract
The E. coli inducible lysine decarboxylase LdcI is an important acid stress response enzyme, whereas the AAA+ ATPase RavA is involved in multiple stress response pathways. A complex between these two proteins is thought to counteract acid stress under starvation in E. coli . We solved the crystal structure of the RavA monomer and combined it with a negative stain EM reconstruction of the RavA‐ADP hexamer (El Bakkouri et al ., 2010). We also determined the crystal structure of the LdcI double pentamer (Kanjee et al ., 2011). While these structures provided important insights into the functions of these individual proteins, the design principles of the LdcI‐RavA complex appeared even more enigmatic because it was difficult to envision how a decamer can bind a hexamer. CryoEM analysis allowed us to fit together the pieces of the jigsaw and revealed that the LdcI‐RavA complex is a surprising macromolecular cage of the size of a ribosome formed by two LdcI decamers and five RavA hexamers (Malet et al ., 2014). We identified molecular determinants of this interaction and specific elements essential for complex formation, as well as conformational rearrangements associated with the pH‐dependent LdcI activation and with the RavA binding (Malet et al ., 2014; Kandiah et al ., 2016). Moreover, we uncovered differences between the LdcI and its close paralogue, the second E. coli lysine decarboxylase LdcC thought to play mainly a biosynthetic role, finally explaining why only the acid stress response enzyme is capable of binding RavA and forming the cage. Multiple sequence alignment coupled to a phylogenetic analysis reveals that certain enterobacteria exert evolutionary pressure on the lysine decarboxylase towards the cage‐like assembly with RavA, implying that this complex may have an important function under particular stress conditions (Kandiah et al ., 2016). Research on structure‐functional relationships of this system by a combination of cryoEM, super‐resolution fluorescence microscopy and other structural, biochemical, biophysical and cell biology techniques is on‐going.
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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 | 0.001 |
| Meta-epidemiology (broad) | 0.000 | 0.000 |
| Bibliometrics | 0.000 | 0.000 |
| Science and technology studies | 0.001 | 0.001 |
| Scholarly communication | 0.001 | 0.001 |
| Open science | 0.000 | 0.001 |
| Research integrity | 0.001 | 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".