Biosynthesis of Fe–S clusters by Suf system: implications from crystal structure of SufCD complex
Bibliographic record
Abstract
IsdG and IsdI are paralogous proteins from Staphylococcus aureus that reductively degrade hemin. Final heme degradation products of IsdG and IsdI are yet to be elucidated, nor has it been determined how oxygen binds to initiate the reaction. The crystal structures of an inactive N7A variant of IsdG in complex with Fe 3+ -protoporphyrin IX (IsdG-hemin) and of IsdI in complex with cobalt protoporphyrin IX (IsdI-CoPPIX) were solved to 1.8 or better resolution. These structures show that the metalloporphyrins are buried into similar deep clefts and the propionic acids form salt bridges to two Arg residues. His77 (IsdG) or His76 (IsdI), a residue required for activity, is coordinated to Fe 3+ or Co 3+ atoms, respectively. The bound porphyrin rings form extensive steric interactions in the binding cleft such that the porphyrin rings are highly distorted from the planar. This distortion can be described as ruffled and places the b-and d-meso carbons close to the distal oxygen-binding site. In the structure of IsdI-CoPPIX, the distal side of the CoPPIX accommodates a chloride ion in a cavity formed through a conformational change in Ile55. The chloride ion participates in a hydrogen bond to the side chain amide of Asn6. We also have determined the crystal structures of IsdG-hemin and IsdI-hemin bound to cyanide to resolutions of ~1.8 . Structural information from these complexes is valuable in understanding the regiospecificity of ring cleavage. We propose a reaction mechanism in which reactive peroxide intermediate proceeds with nucleophilic oxidation at the b-or d-meso carbon of the hemin.
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How this classification was reachedexpand
Full frame distilled prediction
Teacher imitationNot calibrated prevalence, not ground truth. Human validation pending. Learned from the 10,348 direct Codex labels and 10,348 direct Gemma labels. Candidate is the union of thresholded teacher heads; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels or direct frontier model labels.
Codex and Gemma teacher scores by category
| Category | Codex | Gemma |
|---|---|---|
| Metaresearch | 0.000 | 0.000 |
| Meta-epidemiology (narrow) | 0.001 | 0.001 |
| Meta-epidemiology (broad) | 0.001 | 0.001 |
| Bibliometrics | 0.001 | 0.003 |
| Science and technology studies | 0.001 | 0.002 |
| Scholarly communication | 0.000 | 0.000 |
| Open science | 0.001 | 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 teacher head, 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".