Peroxidation and redox reactions catalyzed by truncated hemoglobins
Bibliographic record
Abstract
Roseobacter denitrificans is one member of widespread marine Rosoebacters and performs photosynthesis and denitrification aerobically. We report a native heme‐bound R. denitrificans truncated hemoglobin ( Rd . trHb) from heterologous expression in E. coli . Rd . trHb exhibits absorbance at 412, 538 and 572 nm bands with predominately alpha‐helical secondary structure. The phylogenetic classification suggests that Rd . trHb falls into group II trHbs, whereas sequence alignments indicate that it shares important heme pocket residues with both groups I and II trHbs. The resonance Raman spectra indicate that ferric Rd . trHb is mostly 6‐coordinate low‐spin and the ferrous form is a mixture of 5‐ and 6‐coordinated states. Two Fe‐His stretching modes were detected: one at 228 cm ‐1 , which represents an unconstrained neutral histidine as in other trHbs, and the other at 248 cm ‐1 , which has been reported in peroxidases and some flavohemoglobins that contain Fe‐His‐Asp (or Glu) catalytic triad, but not in trHbs. Further, Rd . trHb exhibits a significant peroxidase activity with a ( k cat / K m ) value three orders of magnitude higher than bovine Hb and only one order lower than horseradish peroxidase (HRP). The pH‐rate profiles yield a pK a value ~6.8. Homology modeling suggests that residues known to be important for interactions with heme‐bound ligands in group II trHbs from M. tuberculosis and B. subtilis are pointing toward to heme in Rd . trHb. Genomic organization and gene expression profiles imply possible functions for detoxification of reactive oxygen and nitrogen species in vivo . Altogether, Rd . trHb exhibits some distinct features and appears equipped to help Roseobacters to cope with reactive oxygen/nitrogen species and/or operate redox biochemistry.
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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 | 0.000 |
| 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) | 0.000 | 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".