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Crystal structure of a substrate complex of myo-inositol oxygenase, a di-iron oxygenase with a key role in inositol metabolism.

Brown PM, Caradoc-Davies TT, Dickson JM, Cooper GJ, Loomes KM, Baker EN
Proc Natl Acad Sci U S A 103 15032-7 (2006)
Cited: 52 times
EuropePMC logo PMID: 17012379

Abstract

Altered metabolism of the inositol sugars myo-inositol (MI) and d-chiro-inositol is implicated in diabetic complications. In animals, catabolism of MI and D-chiro-inositol depends on the enzyme MI oxygenase (MIOX), which catalyzes the first committed step of the glucuronate-xylulose pathway, and is found almost exclusively in the kidneys. The crystal structure of MIOX, in complex with MI, has been determined by multiwavelength anomalous diffraction methods and refined at 2.0-A resolution (R=0.206, Rfree=0.253). The structure reveals a monomeric, single-domain protein with a mostly helical fold that is distantly related to the diverse HD domain superfamily. Five helices form the structural core and provide six ligands (four His and two Asp) for the di-iron center, in which the two iron atoms are bridged by a putative hydroxide ion and one of the Asp ligands, Asp-124. A key loop forms a lid over the MI substrate, which is coordinated in bidentate mode to one iron atom. It is proposed that this mode of iron coordination, and interaction with a key Lys residue, activate MI for bond cleavage. The structure also reveals the basis of substrate specificity and suggests routes for the development of specific MIOX inhibitors.

Reviews - 2huo mentioned but not cited (1)

  1. Divergence and convergence in enzyme evolution. Galperin MY, Koonin EV. J Biol Chem 287 21-28 (2012)

Articles - 2huo mentioned but not cited (8)

  1. Crystal structure of a substrate complex of myo-inositol oxygenase, a di-iron oxygenase with a key role in inositol metabolism. Brown PM, Caradoc-Davies TT, Dickson JM, Cooper GJ, Loomes KM, Baker EN. Proc Natl Acad Sci U S A 103 15032-15037 (2006)
  2. Organophosphonate-degrading PhnZ reveals an emerging family of HD domain mixed-valent diiron oxygenases. Wörsdörfer B, Lingaraju M, Yennawar NH, Boal AK, Krebs C, Bollinger JM, Pandelia ME. Proc Natl Acad Sci U S A 110 18874-18879 (2013)
  3. Crystal structure of PhnZ in complex with substrate reveals a di-iron oxygenase mechanism for catabolism of organophosphonates. van Staalduinen LM, McSorley FR, Schiessl K, Séguin J, Wyatt PB, Hammerschmidt F, Zechel DL, Jia Z. Proc Natl Acad Sci U S A 111 5171-5176 (2014)
  4. Structural and biophysical characterization of human myo-inositol oxygenase. Thorsell AG, Persson C, Voevodskaya N, Busam RD, Hammarström M, Gräslund S, Gräslund A, Hallberg BM. J Biol Chem 283 15209-15216 (2008)
  5. Lysine carboxylation: unveiling a spontaneous post-translational modification. Jimenez-Morales D, Adamian L, Shi D, Liang J. Acta Crystallogr D Biol Crystallogr 70 48-57 (2014)
  6. The HD-Domain Metalloprotein Superfamily: An Apparent Common Protein Scaffold with Diverse Chemistries. Langton M, Sun S, Ueda C, Markey M, Chen J, Paddy I, Jiang P, Chin N, Milne A, Pandelia ME. Catalysts 10 1191 (2020)
  7. Computational modeling and in silico analysis of differential regulation of myo-inositol catabolic enzymes in Cryptococcus neoformans. Mackenzie EA, Klig LS. BMC Mol Biol 9 88 (2008)
  8. Targeting the Human Influenza a Virus: The Methods, Limitations, and Pitfalls of Virtual Screening for Drug-like Candidates Including Scaffold Hopping and Compound Profiling. Scior T, Cuanalo-Contreras K, Islas AA, Martinez-Laguna Y. Viruses 15 1056 (2023)


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  2. The "Other" Inositols and Their Phosphates: Synthesis, Biology, and Medicine (with Recent Advances in myo-Inositol Chemistry). Thomas MP, Mills SJ, Potter BV. Angew Chem Int Ed Engl 55 1614-1650 (2016)
  3. myo-Inositol oxygenase: a radical new pathway for O(2) and C-H activation at a nonheme diiron cluster. Bollinger JM, Diao Y, Matthews ML, Xing G, Krebs C. Dalton Trans 905-914 (2009)
  4. Progress in Understanding the Molecular Basis Underlying Functional Diversification of Cyclic Dinucleotide Turnover Proteins. Römling U, Liang ZX, Dow JM. J Bacteriol 199 e00790-16 (2017)
  5. The enzymatic conversion of phosphonates to phosphate by bacteria. Kamat SS, Raushel FM. Curr Opin Chem Biol 17 589-596 (2013)
  6. Structure/function correlations over binuclear non-heme iron active sites. Solomon EI, Park K. J Biol Inorg Chem 21 575-588 (2016)
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  8. Advances in Novel Animal Vitamin C Biosynthesis Pathways and the Role of Prokaryote-Based Inferences to Understand Their Origin. Duque P, Vieira CP, Vieira J. Genes (Basel) 13 1917 (2022)
  9. Potential of engineering the myo-inositol oxidation pathway to increase stress resilience in plants. Alok A, Singh S, Kumar P, Bhati KK. Mol Biol Rep 49 8025-8035 (2022)
  10. [Recent progress in the theoretical studies of structure, function, and reaction of biological molecules]. Hirao H, Morokuma K. Yakugaku Zasshi 131 1151-1161 (2011)

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  2. Myoinositol oxygenase controls the level of myoinositol in Arabidopsis, but does not increase ascorbic acid. Endres S, Tenhaken R. Plant Physiol 149 1042-1049 (2009)
  3. Spectroscopic Evidence for the Two C-H-Cleaving Intermediates of Aspergillus nidulans Isopenicillin N Synthase. Tamanaha E, Zhang B, Guo Y, Chang WC, Barr EW, Xing G, St Clair J, Ye S, Neese F, Bollinger JM, Krebs C. J Am Chem Soc 138 8862-8874 (2016)
  4. Enzymatic C-H activation by metal-superoxo intermediates. Bollinger JM, Krebs C. Curr Opin Chem Biol 11 151-158 (2007)
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  6. Crystal structure of an HD-GYP domain cyclic-di-GMP phosphodiesterase reveals an enzyme with a novel trinuclear catalytic iron centre. Bellini D, Caly DL, McCarthy Y, Bumann M, An SQ, Dow JM, Ryan RP, Walsh MA. Mol Microbiol 91 26-38 (2014)
  7. Brain inositol is a novel stimulator for promoting Cryptococcus penetration of the blood-brain barrier. Liu TB, Kim JC, Wang Y, Toffaletti DL, Eugenin E, Perfect JR, Kim KJ, Xue C. PLoS Pathog 9 e1003247 (2013)
  8. Oxygen activation at mononuclear nonheme iron centers: a superoxo perspective. Mukherjee A, Cranswick MA, Chakrabarti M, Paine TK, Fujisawa K, Münck E, Que L. Inorg Chem 49 3618-3628 (2010)
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  10. Transcriptional and post-translational modulation of myo-inositol oxygenase by high glucose and related pathobiological stresses. Nayak B, Kondeti VK, Xie P, Lin S, Viswakarma N, Raparia K, Kanwar YS. J Biol Chem 286 27594-27611 (2011)
  11. Down-regulation of the myo-inositol oxygenase gene family has no effect on cell wall composition in Arabidopsis. Endres S, Tenhaken R. Planta 234 157-169 (2011)
  12. tRNA-modifying MiaE protein from Salmonella typhimurium is a nonheme diiron monooxygenase. Mathevon C, Pierrel F, Oddou JL, Garcia-Serres R, Blondin G, Latour JM, Ménage S, Gambarelli S, Fontecave M, Atta M. Proc Natl Acad Sci U S A 104 13295-13300 (2007)
  13. Contribution of myo-inositol oxygenase in AGE:RAGE-mediated renal tubulointerstitial injury in the context of diabetic nephropathy. Sharma I, Tupe RS, Wallner AK, Kanwar YS. Am J Physiol Renal Physiol 314 F107-F121 (2018)
  14. A New Microbial Pathway for Organophosphonate Degradation Catalyzed by Two Previously Misannotated Non-Heme-Iron Oxygenases. Rajakovich LJ, Pandelia ME, Mitchell AJ, Chang WC, Zhang B, Boal AK, Krebs C, Bollinger JM. Biochemistry 58 1627-1647 (2019)
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  18. Molecular-Level Insight into the Differential Oxidase and Oxygenase Reactivities of de Novo Due Ferri Proteins. Snyder RA, Butch SE, Reig AJ, DeGrado WF, Solomon EI. J Am Chem Soc 137 9302-9314 (2015)
  19. Pathobiology of renal-specific oxidoreductase/myo-inositol oxygenase in diabetic nephropathy: its implications in tubulointerstitial fibrosis. Xie P, Sun L, Oates PJ, Srivastava SK, Kanwar YS. Am J Physiol Renal Physiol 298 F1393-404 (2010)
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  21. Characterization and Crystal Structure of a Nonheme Diiron Monooxygenase Involved in Platensimycin and Platencin Biosynthesis. Dong LB, Liu YC, Cepeda AJ, Kalkreuter E, Deng MR, Rudolf JD, Chang C, Joachimiak A, Phillips GN, Shen B. J Am Chem Soc 141 12406-12412 (2019)
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  23. Systematic Perturbations of Binuclear Non-heme Iron Sites: Structure and Dioxygen Reactivity of de Novo Due Ferri Proteins. Snyder RA, Betzu J, Butch SE, Reig AJ, DeGrado WF, Solomon EI. Biochemistry 54 4637-4651 (2015)
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  25. Two duplicated genes DDI2 and DDI3 in budding yeast encode a cyanamide hydratase and are induced by cyanamide. Li J, Biss M, Fu Y, Xu X, Moore SA, Xiao W. J Biol Chem 290 12664-12675 (2015)
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  27. Artificial Self-assembling Nanocompartment for Organizing Metabolic Pathways in Yeast. Cheah LC, Stark T, Adamson LSR, Abidin RS, Lau YH, Sainsbury F, Vickers CE. ACS Synth Biol 10 3251-3263 (2021)
  28. Macrocyclization and Backbone Rearrangement During RiPP Biosynthesis by a SAM-Dependent Domain-of-Unknown-Function 692. Ayikpoe RS, Zhu L, Chen JY, Ting CP, van der Donk WA. ACS Cent Sci 9 1008-1018 (2023)
  29. C-H Bond Cleavage Is Rate-Limiting for Oxidative C-P Bond Cleavage by the Mixed Valence Diiron-Dependent Oxygenase PhnZ. Gama SR, Lo BSY, Séguin J, Pallitsch K, Hammerschmidt F, Zechel DL. Biochemistry 58 5271-5280 (2019)
  30. Circular dichroism, magnetic circular dichroism, and variable temperature variable field magnetic circular dichroism studies of biferrous and mixed-valent myo-inositol oxygenase: insights into substrate activation of O2 reactivity. Snyder RA, Bell CB, Diao Y, Krebs C, Bollinger JM, Solomon EI. J Am Chem Soc 135 15851-15863 (2013)
  31. Domain Fusion of Two Oxygenases Affords Organophosphonate Degradation in Pathogenic Fungi. Langton M, Appell M, Koob J, Pandelia ME. Biochemistry 61 956-962 (2022)
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  33. Functionally comparable but evolutionarily distinct nucleotide-targeting effectors help identify conserved paradigms across diverse immune systems. Nicastro GG, Burroughs AM, Iyer LM, Aravind L. Nucleic Acids Res 51 11479-11503 (2023)


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