Structural and Functional Analysis of the interaction between PCNA and ATAD5
Bibliographic record
Abstract
Proliferating cell nuclear antigen (PCNA) is a DNA sliding clamp that coordinates DNA replication and repair. PCNA is loaded on and unloaded off of DNA during replication. It is loaded onto DNA by the replication factor C (RFC) complex. The mechanism of PCNA unloading is not fully understood however. ATPase family AAA domain containing protein 5 (ATAD5) interacts with subunits of RFC to form a RFC-like complex that functions in unloading PCNA. Reduced expression of ATAD5 extends the life of replication factories by retaining PCNA and other repliosome proteins on chromatin. ATAD5 also plays a role in maintaining genomic stability, as mutations to ATAD5 cause genomic instability in mice and human cells. The region of ATAD5 that interacts with PCNA had yet to be determined. Proteins interacting with PCNA usually have a PCNA-interaction protein (PIP) motif termed the PIP-box. Through sequence analysis, we identified a putative PIP-box in ATAD5. Using GST pull-down experiments, we found that the putative PIP-box bound to PCNA. Mutation of the key residues in the PIP-box abolished the binding. The interaction was also confirmed by isothermal titration calorimetry (ITC) analysis of PCNA and a synthetic peptide containing the PIP-box. The binding constant (Kd) of the PCNA-peptide interaction is 6.2μM, determined by the ITC assays. To further characterize the interaction, we co-crystallized PCNA and the ATAD5 peptide. The complex crystals diffracted to a resolution of 3.5Å. The crystals belong to the space group H3, with unit-cell parameters a = 83.6Å and c = 211.4Å. Our molecular replacement solution indicates that the peptide binds on PCNA at the conserved PIP-box binding pocket. Taken together, our work demonstrates that ATAD5 does contain a PIP motif that directly interacts with PCNA. The structure-function studies on the interaction will provide insights into the molecular mechanism of PCNA unloading and the role of ATAD5 in DNA replication and repair.
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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 | 0.001 |
| Bibliometrics | 0.000 | 0.000 |
| Science and technology studies | 0.000 | 0.000 |
| Scholarly communication | 0.000 | 0.000 |
| Open science | 0.001 | 0.000 |
| Research integrity | 0.000 | 0.001 |
| 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".