Retraction Note: Endoperoxide formation by an α-ketoglutarate-dependent mononuclear non-haem iron enzyme (Nature, (2015), 527, 7579, (539-543), 10.1038/nature15519);Endoperoxide formation by an α-ketoglutarate-dependent mononuclear non-haem iron enzyme

Nature

Volumn 527, Issue 7579, 2015, Pages 539-543

  Yan, Wupeng ^a   Song, Heng ^b   Song, Fuhang ^c   Guo, Yisong ^e   Wu, Cheng Hsuan ^b   Sae Her, Ampon ^b   Pu, Yi ^b,d   Wang, Shu ^b   Naowarojna, Nathchar ^b   Weitz, Andrew ^e   Hendrich, Michael P ^e   Costello, Catherine E ^b,d   Zhang, Lixin ^c   Liu, Pinghua ^b   Jessie Zhang, Yan ^a  

^a UNIVERSITY OF TEXAS AT AUSTIN   (United States)

^b Boston University   (United States)

^c INSTITUTE OF MICROBIOLOGY   (China)

^d BOSTON UNIVERSITY SCHOOL OF MEDICINE   (United States)

^e CARNEGIE MELLON UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

2 OXOGLUTARIC ACID; ALANINE; ENDOPEROXIDE; FUMITREMORGIN B; HEME; PHENYLALANINE; PROSTAGLANDIN SYNTHASE; TYROSINE; UNCLASSIFIED DRUG; ALPHA-KETOGLUTARIC ACID; INDOLE DERIVATIVE; IRON; OXYGEN; PROSTAGLANDIN ENDOPEROXIDE;

BLOOD; CATALYSIS; CRYSTAL STRUCTURE; ENZYME ACTIVITY; FUNGUS; IRON; PUBLIC HEALTH; REACTION KINETICS; SECONDARY METABOLITE;

ABSORPTION SPECTROSCOPY; AMINO ACID SUBSTITUTION; ARTICLE; ASPERGILLUS FUMIGATUS; CATALYSIS; CONFORMATIONAL TRANSITION; CONTROLLED STUDY; CRYSTAL STRUCTURE; CRYSTALLIZATION; DEALKYLATION; DISSOCIATION CONSTANT; ELECTRON SPIN RESONANCE; HYDROPHOBICITY; HYDROXYLATION; MONONUCLEAR CELL; NONHUMAN; NUCLEOTIDE SEQUENCE; OXIDATIVE DEHYDROGENATION; OXYGEN AFFINITY; OXYGEN CONCENTRATION; PRIORITY JOURNAL; STOICHIOMETRY; X RAY CRYSTALLOGRAPHY; BINDING SITE; BIOCATALYSIS; BIOSYNTHESIS; ENZYMOLOGY; METABOLISM;

ASPERGILLUS FUMIGATUS;

ASPERGILLUS FUMIGATUS; BINDING SITES; BIOCATALYSIS; CRYSTALLOGRAPHY, X-RAY; ELECTRON SPIN RESONANCE SPECTROSCOPY; HEME; HYDROXYLATION; INDOLES; IRON; KETOGLUTARIC ACIDS; OXYGEN; PROSTAGLANDIN ENDOPEROXIDES; TYROSINE;

EID: 84948388980     PISSN: 00280836     EISSN: 14764687     Source Type: Journal    
DOI: 10.1038/s41586-021-03527-x     Document Type: Erratum

References (63)

1. Casteel, D. A. Peroxy natural products. Nat. Prod. Rep. 9, 289-312 (1992).
2. Casteel, D. A. Peroxy natural products. Nat. Prod. Rep. 16, 55-73 (1999).
3. Chaturvedi, D., Goswami, A., Saikia, P. P., Barua, N. C. & Rao, P. G. Artemisinin and its derivatives: A novel class of anti-malarial and anti-cancer agents. Chem. Soc. Rev. 39, 435-454 (2010).
4. Paddon, C. J. & Keasling, J. D. Semi-synthetic artemisinin: A model for the use of synthetic biology in pharmaceutical development. Nature Rev. Microbiol. 12, 355-367 (2014).
5. Dembitsky, V. M. Bioactive peroxides as potential therapeutic agents. Eur. J. Med. Chem. 43, 223-251 (2008).
6. Widboom, P. F., Fielding, E. N., Liu, Y. & Bruner, S. D. Structural basis for cofactor-independent dioxygenation in vancomycin biosynthesis. Nature 447, 342-345 (2007).
7. Steiner, R. A., Janssen, H. J., Roversi, P., Oakley, A. J. & Fetzner, S. Structural basis for cofactor-independent dioxygenation of N-heteroaromatic compounds at the-hydrolase fold. Proc. Natl Acad. Sci. USA 107, 657-662 (2010).
8. Thierbach, S. et al. Substrate-assisted O2 activation in a cofactor-independent dioxygenase. Chem. Biol. 21, 217-225 (2014).
9. Marnett, L. J. Cyclooxygenase mechanisms. Curr. Opin. Chem. Biol. 4, 545-552 (2000).
10. Grundmann, A. & Li, S. M. Overproduction, purification and characterization of FtmPT1, a brevianamide F prenyltransferase from Aspergillus fumigatus. Microbiology 151, 2199-2207 (2005).
11. Steffan, N., Grundmann, A., Afiyatullov, S., Ruan, H. & Li, S. M. FtmOx1, a non-heme Fe(II) and-ketoglutarate-dependent dioxygenase, catalyses the endoperoxide formation of verruculogen in Aspergillus fumigatus. Org. Biomol. Chem. 7, 4082-4087 (2009).
12. Kato, N. et al. Gene disruption and biochemical characterization of verruculogen synthase of Aspergillus fumigatus. ChemBioChem 12, 711-714 (2011).
13. Clifton, I. J. et al. Structural studies on 2-oxoglutarate oxygenases and related double-stranded-helix fold proteins. J. Inorg. Biochem. 100, 644-669 (2006).
14. Hausinger, R. P. Fe(II)/-ketoglutarate-dependent hydroxylases and related enzymes. Crit. Rev. Biochem. Mol. Biol. 39, 21-68 (2004).
15. Costas, M., Mehn, M. P., Jensen, M. P. & Que, L. Dioxygen activation at mononuclear nonheme iron active sites: Enzymes, models, and intermediates. Chem. Rev. 104, 939-986 (2004).
16. Solomon, E. I. et al. Geometric and electronic structure/function correlations in non-heme iron enzymes. Chem. Rev. 100, 235-350 (2000).
17. Kovaleva, E. G. & Lipscomb, J. D. Versatility of biological non-heme Fe(II) centers in oxygen activation reactions. Nature Chem. Biol. 4, 186-193 (2008).
18. Ryle, M. J., Padmakumar, R. & Hausinger, R. P. Stopped-flow kinetic analysis of Escherichia coli taurine/-ketoglutarate dioxygenase: Interactions with-ketoglutarate, taurine, and oxygen. Biochemistry 38, 15278-15286 (1999).
19. Liu, A., Ho, R. Y. N. & Que, L. Alternative reactivity of an-ketoglutaratedependent Iron(II) oxygenase: enzyme self-hydroxylation. J. Am. Chem. Soc. 123, 5126-5127 (2001).
20. Volkamer, A., Kuhn, D., Grombacher, T., Rippmann, F. & Rarey, M. Combining global and local measures for structure-based druggability predictions. J. Chem. Inf. Model. 52, 360-372 (2012).
21. Elkins, J. M. et al. X-ray crystal structure of Escherichia coli taurine/-ketoglutarate dioxygenase complexed to ferrous iron and substrates. Biochemistry 41, 5185-5192 (2002).
22. Liu, P. et al. Protein purification and function assignment of the epoxidase catalyzing the formation of fosfomycin. J. Am. Chem. Soc. 123, 4619-4620 (2001).
23. Vaillancourt, F. H., Yeh, E., Vosburg, D. A., O'Connor, S. E. & Walsh, C. T. Cryptic chlorination by a non-haem iron enzyme during cyclopropyl amino acid biosynthesis. Nature 436, 1191-1194 (2005).
24. Blasiak, L. C., Vaillancourt, F. H., Walsh, C. T. & Drennan, C. L. Crystal structure of the non-haem iron halogenase SyrB2 in syringomycin biosynthesis. Nature 440, 368-371 (2006).
25. Clifton, I. J. et al. Crystal structure of carbapenem synthase (CarC). J. Biol. Chem. 278, 20843-20850 (2003).
26. Chang, W. C. et al. Mechanism of the C5 stereoinversion reaction in the biosynthesis of carbapenem antibiotics. Science 343, 1140-1144 (2014).
27. Blodgett, J. A. V. et al. Unusual transformations in the biosynthesis of the antibiotic phosphinothricin tripeptide. Nature Chem. Biol. 3, 480-485 (2007).
28. Krebs, C., Galonic Fujimori, D., Walsh, C. T. & Bollinger, J. M., Jr. Non-heme Fe(IV)-oxo intermediates. Acc. Chem. Res. 40, 484-492 (2007).
29. Stubbe, J. & van der Donk, W. A. Protein radicals in enzyme catalysis. Chem. Rev. 98, 705-762 (1998).
30. Minor, W. & Otwinowski, Z. in Methods in Enzymology, Macromolecular Crystallography (Academic Press, 1997).
31. Adams, P. D. et al. PHENIX: A comprehensive Python-based system for macromolecular structure solution. Acta Crystallogr. D 66, 213-221 (2010).
32. Terwilliger, T. C. Maximum-likelihood density modification. Acta Crystallogr. D 56, 965-972 (2000).
33. Terwilliger, T. C. et al. Decision-making in structure solution using Bayesian estimates of map quality: The PHENIX AutoSol wizard. Acta Crystallogr. D 65, 582-601 (2009).
34. Baker, D., Bystroff, C., Fletterick, R. J. & Agard, D. A. PRISM: Topologically constrained phased refinement for macromolecular crystallography. Acta Crystallogr. D 49, 429-439 (1993).
35. Bricogne, G. Geometric sources of redundancy in intensity data and their use for phase determination. Acta Crystallogr. A 30, 395-405 (1974).
36. Brünger, A. T. Free R value: A novel statistical quantity for assessing the accuracy of crystal structures. Nature 355, 472-475 (1992).
37. Cowtan, K. Error estimation and bias correction in phase-improvement calculations. Acta Crystallogr. D 55, 1555-1567 (1999).
38. Cowtan, K. D. & Main, P. Improvement of macromolecular electron-density maps by the simultaneous application of real and reciprocal space constraints. Acta Crystallogr. D 49, 148-157 (1993).
39. Cowtan, K. D. & Main, P. Phase combination and cross validation in iterated density-modification calculations. Acta Crystallogr. D 52, 43-48 (1996).
40. Winn, M. D. et al. Overview of the CCP4 suite and current developments. Acta Crystallogr. D 67, 235-242 (2011).
41. Sayre, D. Least-squares phase refinement. II. High-resolution phasing of a small protein. Acta Crystallogr. A 30, 180-184 (1974).
42. Schuller, D. J. MAGICSQUASH: more versatile non-crystallographic averaging with mulitple constraints. Acta Crystallogr. D 52, 425-434 (1996).
43. Swanson, S. M. Core tracing: depicting connections between features in electron density. Acta Crystallogr. D 50, 695-708 (1994).
44. Wang, B. C. Resolution of phase ambiguity in macromolecular crystallography. Methods Enzymol. 115, 90-112 (1985).
45. Zhang, K. & Main, P. The use of Sayre's equation with solvent flattening and histogram matching for phase extension and refinement of protein structures. Acta Crystallogr. A 46, 377-381 (1990).
46. Cowtan, K. The Buccaneer software for automated model building. 1. Tracing protein chains. Acta Crystallogr. D 62, 1002-1011 (2006).
47. Cowtan, K. Fitting molecular fragments into electron density. Acta Crystallogr. D 64, 83-89 (2008).
48. Emsley, P., Lohkamp, B., Scott, W. G. & Cowtan, K. Features and development of Coot. Acta Crystallogr. D 66, 486-501 (2010).
49. Afonine, P. V. et al. Towards automated crystallographic structure refinement with phenix. refine. Acta Crystallogr. D 68, 352-367 (2012).
50. Berkholz, D. S., Shapovalov, M. V., Dunbrack, R. L., Jr & Karplus, P. A. Conformation dependence of backbone geometry in proteins. Structure 17, 1316-1325 (2009).
51. Chen, V. B. et al. MolProbity: All-atom structure validation for macromolecular crystallography. Acta Crystallogr. D 66, 12-21 (2010).
52. Headd, J. J. et al. Use of knowledge-based restraints in phenix. refine to improve macromolecular refinement at low resolution. Acta Crystallogr. D 68, 381-390 (2012).
53. Moriarty, N. W., Grosse-Kunstleve, R. W. & Adams, P. D. electronic Ligand Builder and Optimization Workbench (eLBOW): A tool for ligand coordinate and restraint generation. Acta Crystallogr. D 65, 1074-1080 (2009).
54. Tronrud, D. E., Berkholz, D. S. & Karplus, P. A. Using a conformation-dependent stereochemical library improves crystallographic refinement of proteins. Acta Crystallogr. D 66, 834-842 (2010).
55. Urzhumtseva, L., Afonine, P. V., Adams, P. D. & Urzhumtsev, A. Crystallographic model quality at a glance. Acta Crystallogr. D 65, 297-300 (2009).
56. McCoy, A. J. et al. Phaser crystallographic software. J. Appl. Crystallogr. 40, 658-674 (2007).
57. McCoy, A. J., Grosse-Kunstleve, R. W., Storoni, L. C. & Read, R. J. Likelihoodenhanced fast translation functions. Acta Crystallogr. D 61, 458-464 (2005).
58. Read, R. J. Pushing the boundaries of molecular replacement with maximum likelihood. Acta Crystallogr. D 57, 1373-1382 (2001).
59. Storoni, L. C., McCoy, A. J. & Read, R. J. Likelihood-enhanced fast rotation functions. Acta Crystallogr. D 60, 432-438 (2004).
60. Schrodinger, LLC. The PyMOL Molecular Graphics System, Version 1. 3r1 (2010).
61. Helm, I., Jalukse, L., Vilbaste, M. & Leito, I. Micro-Winkler titration method for dissolved oxygen concentration measurement. Anal. Chim. Acta 648, 167-173 (2009).
62. Ryle, M. J., Padmakumar, R. & Hausinger, R. P. Stopped-flow kinetic analysis of Escherichia coli taurine/-ketoglutarate dioxygenase: Interactions with-ketoglutarate, taurine, and oxygen. Biochemistry 38, 15278-15286 (1999).
63. Baldwin, J. et al. Mechanism of rapid electron transfer during oxygen activation in the R2 subunit of Escherichia coli ribonucleotide reductase. 1. Evidence for a transient tryptophan radical. J. Am. Chem. Soc. 122, 12195-12206 (2000).