Structural and phylogenetic analysis of a conserved actinobacteria-specific protein (ASP1; SCO1997) from Streptomyces coelicolor
Bibliographic record
Abstract
BACKGROUND: The Actinobacteria phylum represents one of the largest and most diverse groups of bacteria, encompassing many important and well-characterized organisms including Streptomyces, Bifidobacterium, Corynebacterium and Mycobacterium. Members of this phylum are remarkably diverse in terms of life cycle, morphology, physiology and ecology. Recent comparative genomic analysis of 19 actinobacterial species determined that only 5 genes of unknown function uniquely define this large phylum 1. The cellular functions of these actinobacteria-specific proteins (ASP) are not known. RESULTS: Here we report the first characterization of one of the 5 actinobacteria-specific proteins, ASP1 (Gene ID: SCO1997) from Streptomyces coelicolor. The X-ray crystal structure of ASP1 was determined at 2.2 A. The overall structure of ASP1 retains a similar fold to the large NP-1 family of nucleoside phosphorylase enzymes; however, the function is not related. Further comparative analysis revealed two regions expected to be important for protein function: a central, divalent metal ion binding pore, and a highly conserved elbow shaped helical region at the C-terminus. Sequence analyses revealed that ASP1 is paralogous to another actinobacteria-specific protein ASP2 (SCO1662 from S. coelicolor) and that both proteins likely carry out similar function. CONCLUSION: Our structural data in combination with sequence analysis supports the idea that two of the 5 actinobacteria-specific proteins, ASP1 and ASP2, mediate similar function. This function is predicted to be novel since the structures of these proteins do not match any known protein with or without known function. Our results suggest that this function could involve divalent metal ion binding/transport.
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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 | 0.001 |
| 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".