101
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Integrative view of 2-oxoglutarate/Fe(II)-dependent oxygenase diversity and functions in bacteria. Biochim Biophys Acta Gen Subj 2017; 1861:323-334. [DOI: 10.1016/j.bbagen.2016.12.001] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2016] [Revised: 11/09/2016] [Accepted: 12/01/2016] [Indexed: 12/11/2022]
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102
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Wang Y, Li J, Liu A. Oxygen activation by mononuclear nonheme iron dioxygenases involved in the degradation of aromatics. J Biol Inorg Chem 2017; 22:395-405. [PMID: 28084551 DOI: 10.1007/s00775-017-1436-5] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Accepted: 01/03/2017] [Indexed: 11/25/2022]
Abstract
Molecular oxygen is utilized in numerous metabolic pathways fundamental for life. Mononuclear nonheme iron-dependent oxygenase enzymes are well known for their involvement in some of these pathways, activating O2 so that oxygen atoms can be incorporated into their primary substrates. These reactions often initiate pathways that allow organisms to use stable organic molecules as sources of carbon and energy for growth. From the myriad of reactions in which these enzymes are involved, this perspective recounts the general mechanisms of aromatic dihydroxylation and oxidative ring cleavage, both of which are ubiquitous chemical reactions found in life-sustaining processes. The organic substrate provides all four electrons required for oxygen activation and insertion in the reactions mediated by extradiol and intradiol ring-cleaving catechol dioxygenases. In contrast, two of the electrons are provided by NADH in the cis-dihydroxylation mechanism of Rieske dioxygenases. The catalytic nonheme Fe center, with the aid of active site residues, facilitates these electron transfers to O2 as key elements of the activation processes. This review discusses some general questions for the catalytic strategies of oxygen activation and insertion into aromatic compounds employed by mononuclear nonheme iron-dependent dioxygenases. These include: (1) how oxygen is activated, (2) whether there are common intermediates before oxygen transfer to the aromatic substrate, and (3) are these key intermediates unique to mononuclear nonheme iron dioxygenases?
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Affiliation(s)
- Yifan Wang
- Department of Chemistry, University of Texas at San Antonio, San Antonio, TX, 78249, USA
| | - Jiasong Li
- Department of Chemistry, University of Texas at San Antonio, San Antonio, TX, 78249, USA
| | - Aimin Liu
- Department of Chemistry, University of Texas at San Antonio, San Antonio, TX, 78249, USA.
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103
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Kal S, Que L. Dioxygen activation by nonheme iron enzymes with the 2-His-1-carboxylate facial triad that generate high-valent oxoiron oxidants. J Biol Inorg Chem 2017; 22:339-365. [PMID: 28074299 DOI: 10.1007/s00775-016-1431-2] [Citation(s) in RCA: 166] [Impact Index Per Article: 23.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2016] [Accepted: 12/13/2016] [Indexed: 11/24/2022]
Abstract
The 2-His-1-carboxylate facial triad is a widely used scaffold to bind the iron center in mononuclear nonheme iron enzymes for activating dioxygen in a variety of oxidative transformations of metabolic significance. Since the 1990s, over a hundred different iron enzymes have been identified to use this platform. This structural motif consists of two histidines and the side chain carboxylate of an aspartate or a glutamate arranged in a facial array that binds iron(II) at the active site. This triad occupies one face of an iron-centered octahedron and makes the opposite face available for the coordination of O2 and, in many cases, substrate, allowing the tailoring of the iron-dioxygen chemistry to carry out a plethora of diverse reactions. Activated dioxygen-derived species involved in the enzyme mechanisms include iron(III)-superoxo, iron(III)-peroxo, and high-valent iron(IV)-oxo intermediates. In this article, we highlight the major crystallographic, spectroscopic, and mechanistic advances of the past 20 years that have significantly enhanced our understanding of the mechanisms of O2 activation and the key roles played by iron-based oxidants.
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Affiliation(s)
- Subhasree Kal
- Department of Chemistry, Center for Metals in Biocatalysis, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Lawrence Que
- Department of Chemistry, Center for Metals in Biocatalysis, University of Minnesota, Minneapolis, MN, 55455, USA.
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104
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Fischer AA, Lindeman SV, Fiedler AT. Spectroscopic and computational studies of reversible O2 binding by a cobalt complex of relevance to cysteine dioxygenase. Dalton Trans 2017; 46:13229-13241. [DOI: 10.1039/c7dt01600j] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Spectroscopic and computational studies of reversible O2 binding by a cobalt active-site mimic shed light on the catalytic mechanism of cysteine dioxygenases.
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105
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Basu Mallik S, Pai A, Shenoy RR, Jayashree BS. Novel flavonol analogues as potential inhibitors of JMJD3 histone demethylase-A study based on molecular modelling. J Mol Graph Model 2016; 72:81-87. [PMID: 28064082 DOI: 10.1016/j.jmgm.2016.12.002] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2016] [Revised: 10/21/2016] [Accepted: 12/01/2016] [Indexed: 12/12/2022]
Abstract
Epigenetic modulation of gene expression has drawn enormous attention among researchers globally in the present scenario. Since their discovery, Jmj-C histone demethylases were identified as useful markers in understanding the role of epigenetics in inflammatory conditions and in cancer as well. This has created arousal of interest in search of suitable candidates. Potential inhibitors from various other scaffolds such as hydroxyquinolines, hydroxamic acids and triazolopyridines have already been identified and reported. In this direction, our present study attempts to target one of the important members of the family- namely JMJD3 (also known as KDM6B), that plays a pivotal role in inflammatory and immune reactions. Using molecular modeling approaches, myricetin analogues were identified as promising inhibitors of JMJD3. Extensive literature review showed myricetin as the most promising flavonol inhibitor for this enzyme. It served as a prototype for our study and modification of it's scaffold led to generation of analogues. The ZINC database was used as a repository for natural compounds and their analogues. Using similarity search options, 65 analogues of myricetin were identified and screened against JMJD3 (PDB ID: 4ASK), using the high throughput virtual screening and ligand docking tools in Maestro Molecular Modeling platform (version 10.5) from Schrödinger, LLC. 8 analogues out of 65 were identified as the most appropriate candidates which gave the best pose in ligand docking. Their binding mode and energy calculations were analysed using induced fit docking (IFD) and prime-MMGBSA tool, respectively. Thus, our findings highlight the most promising analogues of myricetin with comparable binding affinity as well as binding energy than their counterparts that could be taken for further optimisation as inhibitors of JMJD3 in both in vitro and in vivo screening studies.
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Affiliation(s)
- Sanchari Basu Mallik
- Department of Pharmacology, Manipal College of Pharmaceutical Sciences, Manipal University, Manipal, 576104, India
| | - Aravinda Pai
- Department of Pharmaceutical Chemistry, Manipal College of Pharmaceutical Sciences, Manipal University, Manipal, 576104, India
| | - Rekha R Shenoy
- Department of Pharmacology, Manipal College of Pharmaceutical Sciences, Manipal University, Manipal, 576104, India
| | - B S Jayashree
- Department of Pharmaceutical Chemistry, Manipal College of Pharmaceutical Sciences, Manipal University, Manipal, 576104, India.
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106
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Zhu Y, Ksibe AZ, Schäfer H, Blindauer CA, Bugg TDH, Chen Y. O2-independent demethylation of trimethylamineN-oxide by Tdm ofMethylocella silvestris. FEBS J 2016; 283:3979-3993. [DOI: 10.1111/febs.13902] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2016] [Revised: 09/09/2016] [Accepted: 09/15/2016] [Indexed: 12/11/2022]
Affiliation(s)
- Yijun Zhu
- School of Life Sciences; University of Warwick; Coventry UK
| | - Amira Z. Ksibe
- Department of Chemistry; University of Warwick; Coventry UK
| | | | | | | | - Yin Chen
- School of Life Sciences; University of Warwick; Coventry UK
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107
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Lakk-Bogáth D, Csonka R, Speier G, Réglier M, Simaan AJ, Naubron JV, Giorgi M, Lázár K, Kaizer J. Formation, Characterization, and Reactivity of a Nonheme Oxoiron(IV) Complex Derived from the Chiral Pentadentate Ligand asN4Py. Inorg Chem 2016; 55:10090-10093. [PMID: 27690396 DOI: 10.1021/acs.inorgchem.6b01089] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The chiral pentadentate low-spin (S = 1) oxoiron(IV) complex [FeIV(O)(asN4Py)]2+ (2) was synthesized and spectroscopically characterized. Its formation kinetics, reactivity, and (enantio)selectivity in an oxygen-atom-transfer reaction was investigated in detail and compared to a similar pentadentate ligand-containing system.
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Affiliation(s)
- Dóra Lakk-Bogáth
- Department of Chemistry, University of Pannonia , 8201 Veszprém, Hungary
| | - Róbert Csonka
- Department of Chemistry, University of Pannonia , 8201 Veszprém, Hungary
| | - Gábor Speier
- Department of Chemistry, University of Pannonia , 8201 Veszprém, Hungary
| | - Marius Réglier
- Aix Marseille Université, CNRS, Centrale Marseille, iSm2 UMR 7313 , 13397 Marseille, France
| | - A Jalila Simaan
- Aix Marseille Université, CNRS, Centrale Marseille, iSm2 UMR 7313 , 13397 Marseille, France
| | - Jean-Valère Naubron
- Aix Marseille Université, CNRS, Centrale Marseille, Spectropole FR1739 , 13397 Marseille, France
| | - Michel Giorgi
- Aix Marseille Université, CNRS, Centrale Marseille, Spectropole FR1739 , 13397 Marseille, France
| | - Károly Lázár
- Research Centre for Energy, Hungarian Academy of Sciences , H-1525 Budapest, Hungary
| | - József Kaizer
- Department of Chemistry, University of Pannonia , 8201 Veszprém, Hungary
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108
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Abstract
Regulated covalent modifications of lipid A are implicated in virulence of pathogenic Gram-negative bacteria. The Salmonella PhoP/PhoQ-activated gene pagP is required for resistance to cationic antimicrobial peptides and for biosynthesis of hepta-acylated lipid A species containing palmitate. Interestingly, pagP encodes an unusual enzyme of lipid A biosynthesis localized in the outer membrane, whereas all previously characterized lipid A enzymes are cytoplasmic or associated with the inner membrane. PagP is not unique, however, as pagL encodes another outer membrane enzyme in Salmonella that deacylates the 3 position of lipid A.S. typhimurium also synthesizes S-2-hydroxymyristate modified lipid A in a PhoP/PhoQ-dependent manner. We postulated that 2-hydroxylation might be catalyzed by a novel dioxygenase. Using well-characterized dioxygenase sequences as probes, tBLASTn searches revealed unassigned open reading frame(s) with similarity to mammalian aspartyl β-hydroxylases in bacteria known to make 2-hydroxyacylated lipid A. The S. typhimurium aspartyl β-hydroxylase homologue ( lpxO) was cloned and expressed in Escherichia coli K-12, which does not contain lpxO. Analysis of the resulting construct revealed that lpxO expression induces O2-dependent formation of 2-hydroxymyristate-modified lipid A in E. coli. LpxO may be an inner membrane enzyme that catalyzes Fe2+/ascorbate/α-ketoglutarate dependent hydroxylation of lipid A. We propose that 2-hydroxymyristate released from LPS inside infected animal cells might be converted to 2-hydroxymyristoyl coenzyme A, a potent inhibitor of protein N-myristoyl transferase.
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Affiliation(s)
- Christian R.H. Raetz
- Department of Biochemistry, Duke University Medical Center, Durham, North Carolina, USA,
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109
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De A, Garai M, Yadav HR, Choudhury AR, Biswas B. Catalytic promiscuity of an iron(II)-phenanthroline complex. Appl Organomet Chem 2016. [DOI: 10.1002/aoc.3551] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Abhranil De
- Department of Chemistry; Raghunathpur College; Purulia 723133 India
| | - Mamoni Garai
- Department of Chemistry; Raghunathpur College; Purulia 723133 India
| | - Hare Ram Yadav
- Department of Chemical Sciences; Indian Institute of Science Education and Research Mohali; Sector 81, S. A. S. Nagar, Manauli PO Mohali 140306 India
| | - Angshuman Roy Choudhury
- Department of Chemical Sciences; Indian Institute of Science Education and Research Mohali; Sector 81, S. A. S. Nagar, Manauli PO Mohali 140306 India
| | - Bhaskar Biswas
- Department of Chemistry; Raghunathpur College; Purulia 723133 India
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110
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Dey D, De A, Yadav HR, Guin PS, Choudhury AR, Kole N, Biswas B. An Oxido-Bridged Diiron(II) Complex as Functional Model of Catechol Dioxygenase. ChemistrySelect 2016. [DOI: 10.1002/slct.201600575] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Dhananjay Dey
- Department of Chemistry; Raghunathpur College; Purulia 723 133,West Bengal India
| | - Abhranil De
- Department of Chemistry; Raghunathpur College; Purulia 723 133,West Bengal India
| | - Hare Ram Yadav
- Department of Chemical Sciences; Indian Institute of Science Education and Research Mohali; S.A.S. Nagar, Manauli PO Mohali 140 306 India
| | | | - Angshuman Roy Choudhury
- Department of Chemical Sciences; Indian Institute of Science Education and Research Mohali; S.A.S. Nagar, Manauli PO Mohali 140 306 India
| | - Niranjan Kole
- Department of Chemistry; Raghunathpur College; Purulia 723 133,West Bengal India
| | - Bhaskar Biswas
- Department of Chemistry; Raghunathpur College; Purulia 723 133,West Bengal India
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111
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Lakshman TR, Chatterjee S, Chakraborty B, Paine TK. Substrate-dependent aromatic ring fission of catechol and 2-aminophenol with O2 catalyzed by a nonheme iron complex of a tripodal N4 ligand. Dalton Trans 2016; 45:8835-44. [PMID: 27148606 DOI: 10.1039/c5dt04541j] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The catalytic reactivity of an iron(ii) complex [(TPA)Fe(II)(CH3CN)2](2+) (1) (TPA = tris(2-pyridylmethyl)amine) towards oxygenative aromatic C-C bond cleavage of catechol and 2-aminophenol is presented. Complex 1 exhibits catalytic and regioselective C-C bond cleavage of 3,5-di-tert-butylcatechol (H2DBC) to form intradiol products, whereas it catalyzes extradiol-type C-C bond cleavage of 2-amino-4,6-di-tert-butylphenol (H2AP). The catalytic reactions are found to be pH-dependent and the complex exhibits maximum turnovers at pH 5 in acetonitrile-phthalate buffer. An iron(iii)-catecholate complex [(TPA)Fe(III)(DBC)](+) (2) is formed in the ring cleavage of catechol. In the extradiol-type cleavage of H2AP, an iron(iii)-2-iminobenzosemiquinonate complex [(TPA)Fe(III)(ISQ)](2+) (3) (ISQ = 4,6-di-tert-butyl-2-iminobenzosemiquinonate radical anion) is observed in the reaction pathway. This work shows the importance of the nature of 'redox non-innocent' substrates in governing the mode of ring fission reactivity.
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Affiliation(s)
- Triloke Ranjan Lakshman
- Department of Inorganic Chemistry, Indian Association for the Cultivation of Science, 2A&2B Raja S. C. Mullick Road, Jadavpur, Kolkata-700032, India.
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112
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Thermodynamics of substrate binding to the metal site in homoprotocatechuate 2,3-dioxygenase: Using ITC under anaerobic conditions to study enzyme–substrate interactions. Biochim Biophys Acta Gen Subj 2016; 1860:910-916. [DOI: 10.1016/j.bbagen.2015.07.013] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2015] [Revised: 07/17/2015] [Accepted: 07/24/2015] [Indexed: 11/24/2022]
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113
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Abstract
Nogalamycin, an aromatic polyketide displaying high cytotoxicity, has a unique structure, with one of the carbohydrate units covalently attached to the aglycone via an additional carbon-carbon bond. The underlying chemistry, which implies a particularly challenging reaction requiring activation of an aliphatic carbon atom, has remained enigmatic. Here, we show that the unusual C5''-C2 carbocyclization is catalyzed by the non-heme iron α-ketoglutarate (α-KG)-dependent SnoK in the biosynthesis of the anthracycline nogalamycin. The data are consistent with a mechanistic proposal whereby the Fe(IV) = O center abstracts the H5'' atom from the amino sugar of the substrate, with subsequent attack of the aromatic C2 carbon on the radical center. We further show that, in the same metabolic pathway, the homologous SnoN (38% sequence identity) catalyzes an epimerization step at the adjacent C4'' carbon, most likely via a radical mechanism involving the Fe(IV) = O center. SnoK and SnoN have surprisingly similar active site architectures considering the markedly different chemistries catalyzed by the enzymes. Structural studies reveal that the differences are achieved by minor changes in the alignment of the substrates in front of the reactive ferryl-oxo species. Our findings significantly expand the repertoire of reactions reported for this important protein family and provide an illustrative example of enzyme evolution.
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114
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Weichold V, Milbredt D, van Pée KH. Die spezifische enzymatische Halogenierung - von der Entdeckung halogenierender Enzyme bis zu deren Anwendung in vitro und in vivo. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201509573] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Veit Weichold
- Fachrichtung Chemie und Lebensmittelchemie, Allgemeine Biochemie; TU Dresden; 01062 Dresden Deutschland
| | - Daniela Milbredt
- Fachrichtung Chemie und Lebensmittelchemie, Allgemeine Biochemie; TU Dresden; 01062 Dresden Deutschland
| | - Karl-Heinz van Pée
- Fachrichtung Chemie und Lebensmittelchemie, Allgemeine Biochemie; TU Dresden; 01062 Dresden Deutschland
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115
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Weichold V, Milbredt D, van Pée KH. Specific Enzymatic Halogenation-From the Discovery of Halogenated Enzymes to Their Applications In Vitro and In Vivo. Angew Chem Int Ed Engl 2016; 55:6374-89. [DOI: 10.1002/anie.201509573] [Citation(s) in RCA: 85] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2015] [Revised: 12/02/2015] [Indexed: 01/22/2023]
Affiliation(s)
- Veit Weichold
- Fachrichtung Chemie und Lebensmittelchemie, Allgemeine Biochemie; TU Dresden; 01062 Dresden Germany
| | - Daniela Milbredt
- Fachrichtung Chemie und Lebensmittelchemie, Allgemeine Biochemie; TU Dresden; 01062 Dresden Germany
| | - Karl-Heinz van Pée
- Fachrichtung Chemie und Lebensmittelchemie, Allgemeine Biochemie; TU Dresden; 01062 Dresden Germany
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116
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The different catalytic roles of the metal-binding ligands in human 4-hydroxyphenylpyruvate dioxygenase. Biochem J 2016; 473:1179-89. [PMID: 26936969 DOI: 10.1042/bcj20160146] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Accepted: 03/02/2016] [Indexed: 11/17/2022]
Abstract
4-Hydroxyphenylpyruvate dioxygenase (HPPD) is a non-haem iron(II)-dependent oxygenase that catalyses the conversion of 4-hydroxyphenylpyruvate (HPP) to homogentisate (HG). In the active site, a strictly conserved 2-His-1-Glu facial triad co-ordinates the iron ready for catalysis. Substitution of these residues resulted in about a 10-fold decrease in the metal binding affinity, as measured by isothermal titration calorimetry, and a large reduction in enzyme catalytic efficiencies. The present study revealed the vital role of the ligand Glu(349) in enzyme function. Replacing this residue with alanine resulted in loss of activity. The E349G variant retained 5% activity for the coupled reaction, suggesting that co-ordinating water may be able to support activation of the trans-bound dioxygen upon substrate binding. The reaction catalysed by the H183A variant was fully uncoupled. H183A variant catalytic activity resulted in protein cleavage between Ile(267) and Ala(268) and the production of an N-terminal fragment. The H266A variant was able to produce 4-hydroxyphenylacetate (HPA), demonstrating that decarboxylation had occurred but that there was no subsequent product formation. Structural modelling of the variant enzyme with bound dioxygen revealed the rearrangement of the co-ordination environment and the dynamic behaviour of bound dioxygen in the H266A and H183A variants respectively. These models suggest that the residues regulate the geometry of the reactive oxygen intermediate during the oxidation reaction. The mutagenesis and structural simulation studies demonstrate the critical and unique role of each ligand in the function of HPPD, and which correlates with their respective co-ordination position.
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117
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Wójcik A, Radoń M, Borowski T. Mechanism of O2 Activation by α-Ketoglutarate Dependent Oxygenases Revisited. A Quantum Chemical Study. J Phys Chem A 2016; 120:1261-74. [PMID: 26859709 DOI: 10.1021/acs.jpca.5b12311] [Citation(s) in RCA: 61] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Four mechanisms previously proposed for dioxygen activation catalyzed by α-keto acid dependent oxygenases (α-KAO) were studied with dispersion-corrected DFT methods employing B3LYP and TPSSh functionals in combination with triple-ζ basis set (cc-pVTZ). The aim of this study was to revisit mechanisms suggested in the past decade and resolve remaining issues related to dioxygen activation. Mechanism A, which runs on the quintet potential energy surface (PES) and includes formation of an Fe(III)-superoxide radical anion complex, subsequent oxidative decarboxylation, and O-O bond cleavage, was found to be most likely. However, mechanism B taking place on the septet PES involves a rate limiting barrier comparable to the one found for mechanism A, and thus it cannot be excluded, though two other mechanisms (C and D) were ruled out. Mechanism C is a minor variation of mechanism A, whereas mechanism D proceeds through formation of a triplet Fe(IV)-alkyl peroxo bridged intermediate. The study covered also full optimization of relevant minimum energy crossing points (MECPs). The relative energy of critical intermediates was also studied with the CCSD(T) method in order to benchmark TPSSh and B3LYP functionals with respect to their credibility in predicting relative energies of septet and triplet spin states of the ternary enzyme-Fe-α-keto glutarate (α-KG)-O2 complex.
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Affiliation(s)
- Anna Wójcik
- Department of Computational Biophysics and Bioinformatics, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University , ul. Gronostajowa 7, 30-387 Cracow, Poland
| | - Mariusz Radoń
- Department of Chemistry, Jagiellonian University , ul. Ingardena 3, 30-060 Cracow, Poland
| | - Tomasz Borowski
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences , ul. Niezapominajek 8, 30-239 Cracow, Poland
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118
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Folkertsma E, de Waard EF, Korpershoek G, van Schaik AJ, Solozabal Mirón N, Borrmann M, Nijsse S, Moelands MAH, Lutz M, Otte M, Moret M, Klein Gebbink RJM. Mimicry of the 2‐His‐1‐Carboxylate Facial Triad Using Bulky N,N,O‐Ligands: Non‐Heme Iron Complexes Featuring a Single Facial Ligand and Easily Exchangeable Co‐Ligands. Eur J Inorg Chem 2016. [DOI: 10.1002/ejic.201501406] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Emma Folkertsma
- Organic Chemistry and Catalysis, Debye Institute for Nanomaterials Science, Faculty of Science, Utrecht University, Universiteitsweg 99, 3584 CG Utrecht, The Netherlands, http://www.uu.nl/en/research/organic‐chemistry‐catalysis
| | - Esther F. de Waard
- Organic Chemistry and Catalysis, Debye Institute for Nanomaterials Science, Faculty of Science, Utrecht University, Universiteitsweg 99, 3584 CG Utrecht, The Netherlands, http://www.uu.nl/en/research/organic‐chemistry‐catalysis
| | - Gerda Korpershoek
- Organic Chemistry and Catalysis, Debye Institute for Nanomaterials Science, Faculty of Science, Utrecht University, Universiteitsweg 99, 3584 CG Utrecht, The Netherlands, http://www.uu.nl/en/research/organic‐chemistry‐catalysis
| | - Arnoldus J. van Schaik
- Organic Chemistry and Catalysis, Debye Institute for Nanomaterials Science, Faculty of Science, Utrecht University, Universiteitsweg 99, 3584 CG Utrecht, The Netherlands, http://www.uu.nl/en/research/organic‐chemistry‐catalysis
| | - Naiara Solozabal Mirón
- Organic Chemistry and Catalysis, Debye Institute for Nanomaterials Science, Faculty of Science, Utrecht University, Universiteitsweg 99, 3584 CG Utrecht, The Netherlands, http://www.uu.nl/en/research/organic‐chemistry‐catalysis
| | - Mandy Borrmann
- Organic Chemistry and Catalysis, Debye Institute for Nanomaterials Science, Faculty of Science, Utrecht University, Universiteitsweg 99, 3584 CG Utrecht, The Netherlands, http://www.uu.nl/en/research/organic‐chemistry‐catalysis
| | - Sjoerd Nijsse
- Organic Chemistry and Catalysis, Debye Institute for Nanomaterials Science, Faculty of Science, Utrecht University, Universiteitsweg 99, 3584 CG Utrecht, The Netherlands, http://www.uu.nl/en/research/organic‐chemistry‐catalysis
| | - Marcel A. H. Moelands
- Organic Chemistry and Catalysis, Debye Institute for Nanomaterials Science, Faculty of Science, Utrecht University, Universiteitsweg 99, 3584 CG Utrecht, The Netherlands, http://www.uu.nl/en/research/organic‐chemistry‐catalysis
| | - Martin Lutz
- Crystal and Structural Chemistry, Bijvoet Center for Biomolecular Research, Faculty of Science, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Matthias Otte
- Organic Chemistry and Catalysis, Debye Institute for Nanomaterials Science, Faculty of Science, Utrecht University, Universiteitsweg 99, 3584 CG Utrecht, The Netherlands, http://www.uu.nl/en/research/organic‐chemistry‐catalysis
| | - Marc‐Etienne Moret
- Organic Chemistry and Catalysis, Debye Institute for Nanomaterials Science, Faculty of Science, Utrecht University, Universiteitsweg 99, 3584 CG Utrecht, The Netherlands, http://www.uu.nl/en/research/organic‐chemistry‐catalysis
| | - Robertus J. M. Klein Gebbink
- Organic Chemistry and Catalysis, Debye Institute for Nanomaterials Science, Faculty of Science, Utrecht University, Universiteitsweg 99, 3584 CG Utrecht, The Netherlands, http://www.uu.nl/en/research/organic‐chemistry‐catalysis
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Henderson KL, Boyles DK, Le VH, Lewis EA, Emerson JP. ITC Methods for Assessing Buffer/Protein Interactions from the Perturbation of Steady-State Kinetics. Methods Enzymol 2016; 567:257-78. [DOI: 10.1016/bs.mie.2015.08.034] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
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120
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Zhang J, Liu Z, Liang J, Wu J, Cheng F, Wang X. Three genes encoding AOP2, a protein involved in aliphatic glucosinolate biosynthesis, are differentially expressed in Brassica rapa. JOURNAL OF EXPERIMENTAL BOTANY 2015; 66:6205-18. [PMID: 26188204 PMCID: PMC4588880 DOI: 10.1093/jxb/erv331] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
The glucosinolate biosynthetic gene AOP2 encodes an enzyme that plays a crucial role in catalysing the conversion of beneficial glucosinolates into anti-nutritional ones. In Brassica rapa, three copies of BrAOP2 have been identified, but their function in establishing the glucosinolate content of B. rapa is poorly understood. Here, we used phylogenetic and gene structure analyses to show that BrAOP2 proteins have evolved via a duplication process retaining two highly conserved domains at the N-terminal and C-terminal regions, while the middle part has experienced structural divergence. Heterologous expression and in vitro enzyme assays and Arabidopsis mutant complementation studies showed that all three BrAOP2 genes encode functional BrAOP2 proteins that convert the precursor methylsulfinyl alkyl glucosinolate to the alkenyl form. Site-directed mutagenesis showed that His356, Asp310, and Arg376 residues are required for the catalytic activity of one of the BrAOP2 proteins (BrAOP2.1). Promoter-β-glucuronidase lines revealed that the BrAOP2.3 gene displayed an overlapping but distinct tissue- and cell-specific expression profile compared with that of the BrAOP2.1 and BrAOP2.2 genes. Quantitative real-time reverse transcription-PCR assays demonstrated that BrAOP2.1 showed a slightly different pattern of expression in below-ground tissue at the seedling stage and in the silique at the reproductive stage compared with BrAOP2.2 and BrAOP2.3 genes in B. rapa. Taken together, our results revealed that all three BrAOP2 paralogues are active in B. rapa but have functionally diverged.
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Affiliation(s)
- Jifang Zhang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Zhongguancun Nandajie No. 12, Haidian District, Beijing 100081, PR China
| | - Zhiyuan Liu
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Zhongguancun Nandajie No. 12, Haidian District, Beijing 100081, PR China
| | - Jianli Liang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Zhongguancun Nandajie No. 12, Haidian District, Beijing 100081, PR China
| | - Jian Wu
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Zhongguancun Nandajie No. 12, Haidian District, Beijing 100081, PR China
| | - Feng Cheng
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Zhongguancun Nandajie No. 12, Haidian District, Beijing 100081, PR China
| | - Xiaowu Wang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Zhongguancun Nandajie No. 12, Haidian District, Beijing 100081, PR China
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121
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Abstract
Hypoxia inducible factors (HIFs) play vital roles in cellular maintenance of oxygen homeostasis. These transcription factors are responsible for the expression of genes involved in angiogenesis, metabolism, and cell proliferation. Here, we generate a detailed mathematical model for the enzyme kinetics of α-ketoglutarate-dependent HIF prolyl 4-hydroxylase domain (PHD) dioxygenases to simulate our in vitro data showing synergistic PHD inhibition by succinate and hypoxia in experimental models of succinate dehydrogenase loss, which phenocopy familial paraganglioma. Our mathematical model confirms the inhibitory synergy of succinate and hypoxia under physiologically-relevant conditions. In agreement with our experimental data, the model predicts that HIF1α is not stabilized under atmospheric oxygen concentrations, as observed. Further, the model confirms that addition of α-ketoglutarate can reverse PHD inhibition by succinate and hypoxia in SDH-deficient cells.
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Affiliation(s)
- Justin P Peters
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine, 200 First St. SW, Rochester, MN 55905, USA
| | - Yeng F Her
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine, 200 First St. SW, Rochester, MN 55905, USA
| | - L James Maher
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine, 200 First St. SW, Rochester, MN 55905, USA
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Yi W, Yuan L, Kun Y, Zhengwen H, Jing T, Xu F, Hong G, Yong W. What factors influence the reactivity of C-H hydroxylation and C=C epoxidation by [Fe(IV)(L(ax))(1,4,8,11-tetramethyl-1,4,8,11-tetraazacyclotetradecane)(O)](n+). J Biol Inorg Chem 2015; 20:1123-34. [PMID: 26345158 DOI: 10.1007/s00775-015-1294-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2014] [Accepted: 08/26/2015] [Indexed: 11/26/2022]
Abstract
Density functional theory is used to investigate geometric structures and mechanisms for hydroxylation and epoxidation from propene for four non-heme iron complexes, [Fe(IV)(L(ax))(TMC)(O)](n+), which are the inverted isomers of [Fe(IV)(O)(TMC)(Lax)](n+) (Lax = acetonitrile (AN), monoanionic trifluoroacetate (TF), azide (N3), thiolate (SR)). The Fe(IV)O unit is found to be sterically less hindered in [Fe(IV)(L(ax))(TMC)(O)](n+) than that in [Fe(IV)(O)(TMC)(L(ax))](n+). Becke, three-parameter, Lee-Yang-Parr (B3LYP) calculations show that hydroxylation and epoxidation proceed via a two-state-reactivity on competing triplet and quintet spin surfaces; and the reactions have been invariably mediated by the S = 2 state. The reaction pathways computed reveal that 2-AN is the most reactive in the four [Fe(IV)(L(ax))(TMC)(O)](n+) complexes; along the reaction pathway, the axial ligand moves away from the iron center, and thus, the energy of the LUMO decreases. The anionic axial ligand, which is more electron releasing than neutral AN, shows a strong overlap of iron orbitals. Thus, the anionic ligand does not move away from the iron center. The H-abstraction is affected by the tunneling contribution, the more electron donation power of the axial ligand, the more effect of the tunneling contribution. Adding the tunneling correction, the relative reactivity of the hydroxylation follows the trend: 2-AN > 2-SR ≈ 2-N3 > 2-TF. However, for the epoxidation, the reactivity is in the following order of 2-AN > 2-TF > 2-N3 > 2-SR. Except for 2-AN, 2-X (L(ax) = TF, N3, SR) complexes chemoselectively hydroxylate even in the presence of a C=C double bond.
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Affiliation(s)
- Wang Yi
- School of Biological Engineering, Dalian Polytechnic University, Dalian, 116034, China.
| | - Liu Yuan
- School of Biological Engineering, Dalian Polytechnic University, Dalian, 116034, China
| | - Yang Kun
- Department of Physics, Dalian Maritime University, 1 Linghai Road, Dalian, 116026, China
| | - He Zhengwen
- School of Biological Engineering, Dalian Polytechnic University, Dalian, 116034, China
| | - Tian Jing
- School of Biological Engineering, Dalian Polytechnic University, Dalian, 116034, China
| | - Fei Xu
- School of Biological Engineering, Dalian Polytechnic University, Dalian, 116034, China
| | - Guo Hong
- School of Biological Engineering, Dalian Polytechnic University, Dalian, 116034, China
| | - Wang Yong
- State Key Laboratory for Oxo Synthesis and Selective Oxidation, Lanzhou Institute of Chemical Physics, Chinese Academy of Sciences, Lanzhou, 730000, China.
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Arraes FBM, Beneventi MA, Lisei de Sa ME, Paixao JFR, Albuquerque EVS, Marin SRR, Purgatto E, Nepomuceno AL, Grossi-de-Sa MF. Implications of ethylene biosynthesis and signaling in soybean drought stress tolerance. BMC PLANT BIOLOGY 2015; 15:213. [PMID: 26335593 PMCID: PMC4557918 DOI: 10.1186/s12870-015-0597-z] [Citation(s) in RCA: 65] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2015] [Accepted: 08/20/2015] [Indexed: 05/20/2023]
Abstract
BACKGROUND Ethylene is a phytohormone known for inducing a triple response in seedlings, leaf abscission and other responses to various stresses. Several studies in model plants have evaluated the importance of this hormone in crosstalk signaling with different metabolic pathways, in addition to responses to biotic stresses. However, the mechanism of action in plants of agricultural interest, such as soybean, and its participation in abiotic stresses remain unclear. RESULTS The studies presented in this work allowed for the identification of 176 soybean genes described elsewhere for ethylene biosynthesis (108 genes) and signal transduction (68 genes). A model to predict these routes in soybean was proposed, and it had great representability compared to those described for Arabidopsis thaliana and Oryza sativa. Furthermore, analysis of putative gene promoters from soybean gene orthologs permitted the identification of 29 families of cis-acting elements. These elements are essential for ethylene-mediated regulation and its possible crosstalk with other signaling pathways mediated by other plant hormones. From genes that are differentially expressed in the transcriptome database, we analyzed the relative expression of some selected genes in resistant and tolerant soybean plants subjected to water deficit. The differential expression of a set of five soybean ethylene-related genes (MAT, ACS, ACO, ETR and CTR) was validated with RT-qPCR experiments, which confirmed variations in the expression of these soybean target genes, as identified in the transcriptome database. In particular, two families of ethylene biosynthesis genes (ACS and ACO) were upregulated under these experimental conditions, whereas CTR (involved in ethylene signal transduction) was downregulated. In the same samples, high levels of ethylene production were detected and were directly correlated with the free fraction levels of ethylene's precursor. Thus, the combination of these data indicated the involvement of ethylene biosynthesis and signaling in soybean responses to water stress. CONCLUSIONS The in silico analysis, combined with the quantification of ethylene production (and its precursor) and RT-qPCR experiments, allowed for a better understanding of the importance of ethylene at a molecular level in this crop as well as its role in the response to abiotic stresses. In summary, all of the data presented here suggested that soybean responses to water stress could be regulated by a crosstalk network among different signaling pathways, which might involve various phytohormones, such as auxins, ABA and jasmonic acid. The integration of in silico and physiological data could also contribute to the application of biotechnological strategies to the development of improved cultivars with regard to different stresses, such as the isolation of stress-specific plant promoters.
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Affiliation(s)
- Fabricio Barbosa Monteiro Arraes
- Federal University of Rio Grande do Sul, Campus do Vale, Av. Bento Gonçalves 9500, Postal Code 15005, CEP 91501-970, Porto Alegre, RS, Brazil.
- Embrapa Genetic Resources and Biotechnology, PqEB, Av. W5-Norte, Postal Code 02372, CEP 70770-910, Brasilia, DF, Brazil.
| | - Magda Aparecida Beneventi
- Federal University of Rio Grande do Sul, Campus do Vale, Av. Bento Gonçalves 9500, Postal Code 15005, CEP 91501-970, Porto Alegre, RS, Brazil.
- Embrapa Genetic Resources and Biotechnology, PqEB, Av. W5-Norte, Postal Code 02372, CEP 70770-910, Brasilia, DF, Brazil.
| | - Maria Eugenia Lisei de Sa
- Embrapa Genetic Resources and Biotechnology, PqEB, Av. W5-Norte, Postal Code 02372, CEP 70770-910, Brasilia, DF, Brazil.
- Agricultural Research Company of Minas Gerais State, Rua Afonso Rato 1301, Postal Code 311, CEP 38001-970, Uberaba, MG, Brazil.
| | - Joaquin Felipe Roca Paixao
- Embrapa Genetic Resources and Biotechnology, PqEB, Av. W5-Norte, Postal Code 02372, CEP 70770-910, Brasilia, DF, Brazil.
- Brasilia University - Biology Institute, Brasilia, DF, Brazil.
| | | | - Silvana Regina Rockenbach Marin
- Embrapa Soybean, Rodovia Carlos João Strass, SN, Acesso Orlando Amaral, Distrito de Warta, Postal Code 231, CEP 86001-970, Londrina, PR, Brazil.
| | - Eduardo Purgatto
- Food Chemistry and Biochemistry Laboratory, Sao Paulo University, Av. Lineu Prestes 580, Bloco 14, Cidade Universitaria, CEP 05508-000, Sao Paulo, SP, Brazil.
| | - Alexandre Lima Nepomuceno
- Embrapa Soybean, Rodovia Carlos João Strass, SN, Acesso Orlando Amaral, Distrito de Warta, Postal Code 231, CEP 86001-970, Londrina, PR, Brazil.
| | - Maria Fatima Grossi-de-Sa
- Embrapa Genetic Resources and Biotechnology, PqEB, Av. W5-Norte, Postal Code 02372, CEP 70770-910, Brasilia, DF, Brazil.
- Catholic University of Brasilia, SGAN 916, Modulo B, Av. W5, Asa Norte, CEP 70790-160, Brasilia, DF, Brazil.
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124
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Abstract
Mononuclear non-heme Fe(II)- and 2-oxoglutarate (2OG)-dependent oxygenases comprise a large family of enzymes that utilize an Fe(IV)-oxo intermediate to initiate diverse oxidative transformations with important biological roles. Here, four of the major types of Fe(II)/2OG-dependent reactions are detailed: hydroxylation, halogenation, ring formation, and desaturation. In addition, an atypical epimerization reaction is described. Studies identifying several key intermediates in catalysis are concisely summarized, and the proposed mechanisms are explained. In addition, a variety of other transformations catalyzed by selected family members are briefly described to further highlight the chemical versatility of these enzymes.
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Affiliation(s)
- Salette Martinez
- Departments of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan 48824
| | - Robert P Hausinger
- Departments of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan 48824; Departments of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824.
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125
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Abstract
Aromatic amino acid hydroxylases are members of a larger group of enzymes that use a mononuclear nonheme Fe center to catalyze a variety of thermodynamically challenging reactions in which O2 is used in the oxidative transformation of substrates. The hydroxylase enzymes are catalytically active in the ferrous oxidation state and are high-spin. To render the catalytic site EPR-active, we have used nitric oxide (NO) as a surrogate for substrate O2 to form an S=3/2 paramagnetic center. While the continuous-wave (cw)-EPR spectra of NO-enzyme adducts are rather generic, they provide electron spin echo envelope modulation (ESEEM) data that are rich with structural information derived from ligand hyperfine couplings. This chapter will focus on (2)H-ESEEM spectroscopy, an approach that we have taken for assigning these spectra and harvesting the unique information on Fe(II) coordination chemistry that they provide. While these spectroscopic measurements are routine, an emphasis will be placed on the analysis of cw-EPR and (2)H-ESEEM data using an unconstrained nonlinear optimization approach. These analysis methods are based on simple custom "scripts" that run in the MATLAB environment and that use EasySpin, a public-domain EPR simulation package, as their calculation engine. The examples provided here use a strategy that can be adapted for the treatment of most EPR measurements.
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126
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Kozlevčar B, Jakomin K, Počkaj M, Jagličić Z, Beyer A, Burzlaff N, Kitanovski N. Dinuclear Nitrato Coordination Compounds with Bis(3,5-tert-butylpyrazol-1-yl)acetate. Eur J Inorg Chem 2015. [DOI: 10.1002/ejic.201500368] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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127
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McCracken J, Cappillino PJ, McNally JS, Krzyaniak MD, Howart M, Tarves PC, Caradonna JP. Characterization of Water Coordination to Ferrous Nitrosyl Complexes with fac-N2O, cis-N2O2, and N2O3 Donor Ligands. Inorg Chem 2015; 54:6486-97. [DOI: 10.1021/acs.inorgchem.5b00788] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- John McCracken
- Department of Chemistry, Michigan State University, East
Lansing, Michigan 48824, United States
| | - Patrick J. Cappillino
- Department of Chemistry, Boston University, Boston, Massachusetts 02215, United States
- Department of Chemistry and Biochemistry, University of Massachusetts at Dartmouth, North Dartmouth, Massachusetts 02347, United States
| | - Joshua S. McNally
- Department of Chemistry, Boston University, Boston, Massachusetts 02215, United States
| | - Matthew D. Krzyaniak
- Department of Chemistry, Michigan State University, East
Lansing, Michigan 48824, United States
| | - Michael Howart
- Department of Chemistry, Michigan State University, East
Lansing, Michigan 48824, United States
| | - Paul C. Tarves
- Department of Chemistry, Boston University, Boston, Massachusetts 02215, United States
| | - John P. Caradonna
- Department of Chemistry, Boston University, Boston, Massachusetts 02215, United States
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128
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Sattler SA, Wang X, Lewis KM, DeHan PJ, Park CM, Xin Y, Liu H, Xian M, Xun L, Kang C. Characterizations of Two Bacterial Persulfide Dioxygenases of the Metallo-β-lactamase Superfamily. J Biol Chem 2015; 290:18914-23. [PMID: 26082492 DOI: 10.1074/jbc.m115.652537] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2015] [Indexed: 12/21/2022] Open
Abstract
Persulfide dioxygenases (PDOs), also known as sulfur dioxygenases (SDOs), oxidize glutathione persulfide (GSSH) to sulfite and GSH. PDOs belong to the metallo-β-lactamase superfamily and play critical roles in animals, plants, and microorganisms, including sulfide detoxification. The structures of two PDOs from human and Arabidopsis thaliana have been reported; however, little is known about the substrate binding and catalytic mechanism. The crystal structures of two bacterial PDOs from Pseudomonas putida and Myxococcus xanthus were determined at 1.5- and 2.5-Å resolution, respectively. The structures of both PDOs were homodimers, and their metal centers and β-lactamase folds were superimposable with those of related enzymes, especially the glyoxalases II. The PDOs share similar Fe(II) coordination and a secondary coordination sphere-based hydrogen bond network that is absent in glyoxalases II, in which the corresponding residues are involved instead in coordinating a second metal ion. The crystal structure of the complex between the Pseudomonas PDO and GSH also reveals the similarity of substrate binding between it and glyoxalases II. Further analysis implicates an identical mode of substrate binding by known PDOs. Thus, the data not only reveal the differences in metal binding and coordination between the dioxygenases and the hydrolytic enzymes in the metallo-β-lactamase superfamily, but also provide detailed information on substrate binding by PDOs.
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Affiliation(s)
- Steven A Sattler
- From the School of Molecular Biosciences, Washington State University, Pullman, Washington 99164-4660
| | - Xia Wang
- From the School of Molecular Biosciences, Washington State University, Pullman, Washington 99164-4660, the State Key Laboratory of Microbial Technology, Shandong University, Jinan, Shandong, China, and
| | - Kevin M Lewis
- the Department of Chemistry, Washington State University, Pullman, Washington 99164-4630
| | - Preston J DeHan
- From the School of Molecular Biosciences, Washington State University, Pullman, Washington 99164-4660
| | - Chung-Min Park
- the Department of Chemistry, Washington State University, Pullman, Washington 99164-4630
| | - Yufeng Xin
- the State Key Laboratory of Microbial Technology, Shandong University, Jinan, Shandong, China, and
| | - Honglei Liu
- the State Key Laboratory of Microbial Technology, Shandong University, Jinan, Shandong, China, and
| | - Ming Xian
- the Department of Chemistry, Washington State University, Pullman, Washington 99164-4630
| | - Luying Xun
- From the School of Molecular Biosciences, Washington State University, Pullman, Washington 99164-4660, the State Key Laboratory of Microbial Technology, Shandong University, Jinan, Shandong, China, and
| | - ChulHee Kang
- From the School of Molecular Biosciences, Washington State University, Pullman, Washington 99164-4660, the Department of Chemistry, Washington State University, Pullman, Washington 99164-4630
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129
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McCracken J, Eser BE, Mannikko D, Krzyaniak MD, Fitzpatrick PF. HYSCORE Analysis of the Effects of Substrates on Coordination of Water to the Active Site Iron in Tyrosine Hydroxylase. Biochemistry 2015; 54:3759-71. [DOI: 10.1021/acs.biochem.5b00363] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- John McCracken
- Department
of Chemistry, Michigan State University, East Lansing, Michigan 48824, United States
| | - Bekir E. Eser
- Department
of Biochemistry, University of Texas Health Science Center, San Antonio, Texas 78229, United States
| | - Donald Mannikko
- Department
of Chemistry, Michigan State University, East Lansing, Michigan 48824, United States
| | - Matthew D. Krzyaniak
- Department
of Chemistry, Michigan State University, East Lansing, Michigan 48824, United States
| | - Paul F. Fitzpatrick
- Department
of Biochemistry, University of Texas Health Science Center, San Antonio, Texas 78229, United States
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130
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Andersson I, Valegård K. 2-Oxoglutarate-Dependent Oxygenases of Cephalosporin Synthesis. 2-OXOGLUTARATE-DEPENDENT OXYGENASES 2015. [DOI: 10.1039/9781782621959-00385] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Central steps in the biosynthetic pathways of some of the most commonly used antibiotics, the cephalosporins, are catalysed by 2-oxoglutarate (2OG)-dependent oxygenases. Deacetoxycephalosporin C synthase (DAOCS) catalyses the 2OG-dependent oxidative expansion of the five-membered thiazolidine ring of the penicillin nucleus into the six-membered dihydrothiazine ring of the cephalosporin nucleus. DAOCS uses dioxygen to create a reactive iron–oxygen intermediate from ferrous ion to drive the reaction. In prokaryotic cephalosporin producers, the cephalosporin product, DAOC, is hydroxylated at the 3′-position to form deacetylcephalosporin C (DAC) as catalysed by a second 2OG-dependent enzyme, DAC synthase (DACS). In eukaryotic cephalosporin producers, the reaction is catalysed by a bifunctional enzyme, DAOC/DACS, that catalyses both the ring expansion and the 3′-hydroxylation reactions. The prokaryotic and eukaryotic enzymes are closely related to DAOCS by sequence, suggesting these enzymes may have evolved by gene duplication. Cephamycin C-producing microorganisms use two enzymes, encoded by the genes cmcI/J, to convert cephalosporins to their 7α-methoxy derivatives that are less vulnerable to β-lactam hydrolysing enzymes. The methoxylation reaction is dependent on Fe(ii), 2OG and S-adenosylmethionine, suggesting the involvement of another 2OG-dependent oxygenase. Herein, structural and mechanistic features are summarized for these 2OG enzymes that utilize this common and flexible mode of dioxygen activation.
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Affiliation(s)
- Inger Andersson
- Department of Cell and Molecular Biology, Uppsala University Box 596, S-751 24 Uppsala Sweden
| | - Karin Valegård
- Department of Cell and Molecular Biology, Uppsala University Box 596, S-751 24 Uppsala Sweden
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131
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Shah DD, Moran GR. 4-Hydroxyphenylpyruvate Dioxygenase and Hydroxymandelate Synthase: 2-Oxo Acid-Dependent Oxygenases of Importance to Agriculture and Medicine. 2-OXOGLUTARATE-DEPENDENT OXYGENASES 2015. [DOI: 10.1039/9781782621959-00438] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Despite a separate evolutionary lineage, 4-hydroxyphenylpyruvate dioxygenase (HPPD) and hydroxymandelate synthase (HMS) are appropriately grouped with the 2-oxo acid-dependent oxygenase (2OADO) family of enzymes. HPPD and HMS accomplish highly similar overall chemistry to that observed in the majority of 2OADOs but require only two substrates rather than three. 2OADOs typically use the 2-oxo acid of 2-oxoglutarate (2OG) as a source of electrons to reduce and activate dioxygen in order to oxidize a third specific substrate. HPPD and HMS use instead the pyruvate substituent of 4-hydroxyphenylpyruvate to activate dioxygen and then proceed to also hydroxylate this substrate, each yielding a distinctly different aromatic product. HPPD catalyses the second and committed step of tyrosine catabolism, a pathway common to nearly all aerobes. Plants require the HPPD reaction to biosynthesize plastoquinones and therefore HPPD inhibitors can have potent herbicidal activity. The ubiquity of the HPPD reaction, however, has meant that HPPD-specific molecules developed as herbicides have other uses in different forms of life. In humans herbicidal HPPD inhibitors can be used therapeutically to alleviate specific inborn defects and also to retard the progress of certain bacterial and fungal infections. This review is intended as a concise overview of the contextual and catalytic chemistries of HPPD and HMS.
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Affiliation(s)
- Dhara D. Shah
- Department of Chemistry and Biochemistry, University of Wisconsin-Milwaukee 3210 N. Cramer St Milwaukee WI 53211-3209 USA
| | - Graham R. Moran
- Department of Chemistry and Biochemistry, University of Wisconsin-Milwaukee 3210 N. Cramer St Milwaukee WI 53211-3209 USA
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132
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Liu F, Geng J, Gumpper RH, Barman A, Davis I, Ozarowski A, Hamelberg D, Liu A. An Iron Reservoir to the Catalytic Metal: THE RUBREDOXIN IRON IN AN EXTRADIOL DIOXYGENASE. J Biol Chem 2015; 290:15621-15634. [PMID: 25918158 DOI: 10.1074/jbc.m115.650259] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2015] [Indexed: 01/06/2023] Open
Abstract
The rubredoxin motif is present in over 74,000 protein sequences and 2,000 structures, but few have known functions. A secondary, non-catalytic, rubredoxin-like iron site is conserved in 3-hydroxyanthranilate 3,4-dioxygenase (HAO), from single cellular sources but not multicellular sources. Through the population of the two metal binding sites with various metals in bacterial HAO, the structural and functional relationship of the rubredoxin-like site was investigated using kinetic, spectroscopic, crystallographic, and computational approaches. It is shown that the first metal presented preferentially binds to the catalytic site rather than the rubredoxin-like site, which selectively binds iron when the catalytic site is occupied. Furthermore, an iron ion bound to the rubredoxin-like site is readily delivered to an empty catalytic site of metal-free HAO via an intermolecular transfer mechanism. Through the use of metal analysis and catalytic activity measurements, we show that a downstream metabolic intermediate can selectively remove the catalytic iron. As the prokaryotic HAO is often crucial for cell survival, there is a need for ensuring its activity. These results suggest that the rubredoxin-like site is a possible auxiliary iron source to the catalytic center when it is lost during catalysis in a pathway with metabolic intermediates of metal-chelating properties. A spare tire concept is proposed based on this biochemical study, and this concept opens up a potentially new functional paradigm for iron-sulfur centers in iron-dependent enzymes as transient iron binding and shuttling sites to ensure full metal loading of the catalytic site.
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Affiliation(s)
- Fange Liu
- Department of Chemistry, Georgia State University, Atlanta, Georgia 30303; Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, Georgia 30303.
| | - Jiafeng Geng
- Department of Chemistry, Georgia State University, Atlanta, Georgia 30303; Molecular Basis of Disease Program, Georgia State University, Atlanta, Georgia 30303.
| | - Ryan H Gumpper
- Department of Chemistry, Georgia State University, Atlanta, Georgia 30303
| | - Arghya Barman
- Department of Chemistry, Georgia State University, Atlanta, Georgia 30303
| | - Ian Davis
- Department of Chemistry, Georgia State University, Atlanta, Georgia 30303; Molecular Basis of Disease Program, Georgia State University, Atlanta, Georgia 30303
| | - Andrew Ozarowski
- National High Magnetic Field Laboratory, Florida State University, Tallahassee, Florida 32310
| | - Donald Hamelberg
- Department of Chemistry, Georgia State University, Atlanta, Georgia 30303; Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, Georgia 30303; Molecular Basis of Disease Program, Georgia State University, Atlanta, Georgia 30303
| | - Aimin Liu
- Department of Chemistry, Georgia State University, Atlanta, Georgia 30303; Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, Georgia 30303; Molecular Basis of Disease Program, Georgia State University, Atlanta, Georgia 30303.
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133
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Kundu S. Unity in diversity, a systems approach to regulating plant cell physiology by 2-oxoglutarate-dependent dioxygenases. FRONTIERS IN PLANT SCIENCE 2015; 6:98. [PMID: 25814993 PMCID: PMC4356072 DOI: 10.3389/fpls.2015.00098] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2014] [Accepted: 02/06/2015] [Indexed: 05/24/2023]
Abstract
Could a disjoint group of enzymes synchronize their activities and execute a complex multi-step, measurable, and reproducible response? Here, I surmise that the alpha-ketoglutarate dependent superfamily of non-haem iron (II) dioxygenases could influence cell physiology as a cohesive unit, and that the broad spectra of substrates transformed is an absolute necessity to this portrayal. This eclectic group comprises members from all major taxa, and participates in pesticide breakdown, hypoxia signaling, and osmotic stress neutralization. The oxidative decarboxylation of 2-oxoglutarate to succinate is coupled with a concomitant substrate hydroxylation and, in most cases, is followed by an additional specialized conversion. The domain profile of a protein sequence was used as an index of miscellaneous reaction chemistry and interpreted alongside existent kinetic data in a linear model of integrated function. Statistical parameters were inferred by the creation of a novel, empirically motivated flat-file database of over 3800 sequences (DB2OG) with putative 2-oxoglutarate dependent activity. The collated information was categorized on the basis of existing annotation schema. The data suggests that 2OG-dependent enzymes incorporate several desirable features of a systems level player. DB2OG, is free, accessible without a login to all users, and available at the following URL (http://comp-biol.theacms.in/DB2OG.html).
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Affiliation(s)
- Siddhartha Kundu
- *Correspondence: Siddhartha Kundu, School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Mehrauli Road, New Delhi, Delhi 110067, India e-mail: ;
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134
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Henderson KL, Müller TA, Hausinger RP, Emerson JP. Calorimetric assessment of Fe(2+) binding to α-ketoglutarate/taurine dioxygenase: ironing out the energetics of metal coordination by the 2-His-1-carboxylate facial triad. Inorg Chem 2015; 54:2278-83. [PMID: 25668068 DOI: 10.1021/ic502881q] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
The thermodynamic properties of Fe(2+) binding to the 2-His-1-carboxylate facial triad in α-ketoglutarate/taurine dioxygenase (TauD) were explored using isothermal titration calorimetry. Direct titrations of Fe(2+) into TauD and chelation experiments involving the titration of ethylenediaminetetraacetic acid into Fe(2+)-TauD were performed under an anaerobic environment to yield a binding equilibrium of 2.4 (±0.1) × 10(7) (Kd = 43 nM) and a ΔG° value of -10.1 (±0.03) kcal/mol. Further analysis of the enthalpy/entropy contributions indicates a highly enthalpic binding event, where ΔH = -11.6 (±0.3) kcal/mol. Investigations into the unfavorable entropy term led to the observation of water molecules becoming organized within the Fe(2+)-TauD structure.
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Affiliation(s)
- Kate L Henderson
- Department of Chemistry, Mississippi State University , Mississippi State, Mississippi 39762, United States
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135
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Faponle AS, Quesne MG, Sastri CV, Banse F, de Visser SP. Differences and comparisons of the properties and reactivities of iron(III)-hydroperoxo complexes with saturated coordination sphere. Chemistry 2015; 21:1221-36. [PMID: 25399782 PMCID: PMC4316188 DOI: 10.1002/chem.201404918] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2014] [Indexed: 11/06/2022]
Abstract
Heme and nonheme monoxygenases and dioxygenases catalyze important oxygen atom transfer reactions to substrates in the body. It is now well established that the cytochrome P450 enzymes react through the formation of a high-valent iron(IV)-oxo heme cation radical. Its precursor in the catalytic cycle, the iron(III)-hydroperoxo complex, was tested for catalytic activity and found to be a sluggish oxidant of hydroxylation, epoxidation and sulfoxidation reactions. In a recent twist of events, evidence has emerged of several nonheme iron(III)-hydroperoxo complexes that appear to react with substrates via oxygen atom transfer processes. Although it was not clear from these studies whether the iron(III)-hydroperoxo reacted directly with substrates or that an initial O-O bond cleavage preceded the reaction. Clearly, the catalytic activity of heme and nonheme iron(III)-hydroperoxo complexes is substantially different, but the origins of this are still poorly understood and warrant a detailed analysis. In this work, an extensive computational analysis of aromatic hydroxylation by biomimetic nonheme and heme iron systems is presented, starting from an iron(III)-hydroperoxo complex with pentadentate ligand system (L5(2)). Direct C-O bond formation by an iron(III)-hydroperoxo complex is investigated, as well as the initial heterolytic and homolytic bond cleavage of the hydroperoxo group. The calculations show that [(L5(2))Fe(III)(OOH)](2+) should be able to initiate an aromatic hydroxylation process, although a low-energy homolytic cleavage pathway is only slightly higher in energy. A detailed valence bond and thermochemical analysis rationalizes the differences in chemical reactivity of heme and nonheme iron(III)-hydroperoxo and show that the main reason for this particular nonheme complex to be reactive comes from the fact that they homolytically split the O-O bond, whereas a heterolytic O-O bond breaking in heme iron(III)-hydroperoxo is found.
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Affiliation(s)
- Abayomi S Faponle
- Manchester Institute of Biotechnology and School of Chemical Engineering and Analytical Science, The University of Manchester131 Princess Street, Manchester M1 7DN (UK) E-mail:
| | - Matthew G Quesne
- Manchester Institute of Biotechnology and School of Chemical Engineering and Analytical Science, The University of Manchester131 Princess Street, Manchester M1 7DN (UK) E-mail:
| | - Chivukula V Sastri
- Department of Chemistry, Indian Institute of Technology Guwahati781039, Assam (India)
| | - Frédéric Banse
- Institut de Chimie Moleculaire et des Materiaux d'Orsay, Laboratoire de Chimie Inorganique, Université Paris-Sud11 91405 Orsay Cedex (France) E-mail:
| | - Sam P de Visser
- Manchester Institute of Biotechnology and School of Chemical Engineering and Analytical Science, The University of Manchester131 Princess Street, Manchester M1 7DN (UK) E-mail:
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136
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Štefane B, Perdih F, Višnjevac A, Požgan F. Novel triazole-based ligands and their zinc(ii) and nickel(ii) complexes with a nitrogen donor environment as potential structural models for mononuclear active sites. NEW J CHEM 2015. [DOI: 10.1039/c4nj01642d] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A tridentate N,N,N-1,2,3-triazole-based ligand successfully coordinated to nickel ions through the less Lewis basic N2 atom of the triazole ring.
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Affiliation(s)
- Bogdan Štefane
- Faculty of Chemistry and Chemical Technology
- University of Ljubljana
- 1000 Ljubljana
- Slovenia
- EN-FIST Centre of Excellence
| | - Franc Perdih
- Faculty of Chemistry and Chemical Technology
- University of Ljubljana
- 1000 Ljubljana
- Slovenia
- EN-FIST Centre of Excellence
| | | | - Franc Požgan
- Faculty of Chemistry and Chemical Technology
- University of Ljubljana
- 1000 Ljubljana
- Slovenia
- EN-FIST Centre of Excellence
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137
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138
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Canta M, Rodríguez M, Costas M. Recent Advances in the Selective Oxidation of Alkyl C-H Bonds Catalyzed by Iron Coordination Complexes. Top Curr Chem (Cham) 2015; 372:27-54. [PMID: 26318344 DOI: 10.1007/128_2015_659] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Selective and stereoretentive oxidation of alkyl C-H bonds has been described over the last decade by employing biologically inspired iron coordination complexes as catalysts and hydrogen peroxide as oxidant. Examples of catalyst dependent C-H site selectivity have started to appear. The current paper describes an account of these findings.
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Affiliation(s)
- Mercè Canta
- Departament de Química i Institut de Química Computacional i Catàlisi, Universitat de Girona, Facultat de Ciències, Campus de Montilivi, 17071, Girona, Catalonia, Spain
| | - Mònica Rodríguez
- Departament de Química i Institut de Química Computacional i Catàlisi, Universitat de Girona, Facultat de Ciències, Campus de Montilivi, 17071, Girona, Catalonia, Spain
| | - Miquel Costas
- Departament de Química i Institut de Química Computacional i Catàlisi, Universitat de Girona, Facultat de Ciències, Campus de Montilivi, 17071, Girona, Catalonia, Spain.
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139
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Roux Y, Ghattas W, Avenier F, Guillot R, Simaan AJ, Mahy JP. Synthesis and characterization of [Fe(BPMEN)ACC]SbF6: a structural and functional mimic of ACC-oxidase. Dalton Trans 2015; 44:5966-8. [DOI: 10.1039/c5dt00347d] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Miming plants: an original synthesis led to the preparation of the first model of the active site of the ethylene-forming enzyme ACC-oxidase. The prepared complex is a structural and a functional model as it reacts with hydrogen peroxide to produce the phytohormone ethylene.
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Affiliation(s)
- Y. Roux
- Institut de Chimie Moléculaire et des Matériaux d'Orsay
- Université Paris Sud
- Orsay 91405 CEDEX
- France
| | - W. Ghattas
- Institut de Chimie Moléculaire et des Matériaux d'Orsay
- Université Paris Sud
- Orsay 91405 CEDEX
- France
| | - F. Avenier
- Institut de Chimie Moléculaire et des Matériaux d'Orsay
- Université Paris Sud
- Orsay 91405 CEDEX
- France
| | - R. Guillot
- Institut de Chimie Moléculaire et des Matériaux d'Orsay
- Université Paris Sud
- Orsay 91405 CEDEX
- France
| | - A. J. Simaan
- Aix Marseille Université
- Centrale Marseille
- 13397, Marseille
- France
| | - J.-P. Mahy
- Institut de Chimie Moléculaire et des Matériaux d'Orsay
- Université Paris Sud
- Orsay 91405 CEDEX
- France
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140
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Ronau J, Paul LN, Fuchs JE, Liedl K, Abu-Omar MM, Das C. A conserved acidic residue in phenylalanine hydroxylase contributes to cofactor affinity and catalysis. Biochemistry 2014; 53:6834-48. [PMID: 25295853 PMCID: PMC4222540 DOI: 10.1021/bi500734h] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2014] [Revised: 09/22/2014] [Indexed: 01/19/2023]
Abstract
The catalytic domains of aromatic amino acid hydroxylases (AAAHs) contain a non-heme iron coordinated to a 2-His-1-carboxylate facial triad and two water molecules. Asp139 from Chromobacterium violaceum PAH (cPAH) resides within the second coordination sphere and contributes key hydrogen bonds with three active site waters that mediate its interaction with an oxidized form of the cofactor, 7,8-dihydro-l-biopterin, in crystal structures. To determine the catalytic role of this residue, various point mutants were prepared and characterized. Our isothermal titration calorimetry (ITC) analysis of iron binding implies that polarity at position 139 is not the sole criterion for metal affinity, as binding studies with D139E suggest that the size of the amino acid side chain also appears to be important. High-resolution crystal structures of the mutants reveal that Asp139 may not be essential for holding the bridging water molecules together, because many of these waters are retained even in the Ala mutant. However, interactions via the bridging waters contribute to cofactor binding at the active site, interactions for which charge of the residue is important, as the D139N mutant shows a 5-fold decrease in its affinity for pterin as revealed by ITC (compared to a 16-fold loss of affinity in the case of the Ala mutant). The Asn and Ala mutants show a much more pronounced defect in their kcat values, with nearly 16- and 100-fold changes relative to that of the wild type, respectively, indicating a substantial role of this residue in stabilization of the transition state by aligning the cofactor in a productive orientation, most likely through direct binding with the cofactor, supported by data from molecular dynamics simulations of the complexes. Our results indicate that the intervening water structure between the cofactor and the acidic residue masks direct interaction between the two, possibly to prevent uncoupled hydroxylation of the cofactor before the arrival of phenylalanine. It thus appears that the second-coordination sphere Asp residue in cPAH, and, by extrapolation, the equivalent residue in other AAAHs, plays a role in fine-tuning pterin affinity in the ground state via deformable interactions with bridging waters and assumes a more significant role in the transition state by aligning the cofactor through direct hydrogen bonding.
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Affiliation(s)
- Judith
A. Ronau
- Department
of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, Indiana 47907, United States
- Department
of Molecular Biophysics and Biochemistry, Yale University, 266
Whitney Avenue, New Haven, Connecticut 06520, United States
| | - Lake N. Paul
- Bindley
Biosciences Center, Purdue University, West Lafayette, Indiana 47907, United States
| | - Julian E. Fuchs
- Institute
of General, Inorganic and Theoretical Chemistry and Center for Molecular
Biosciences Innsbruck (CMBI), University
of Innsbruck, Innrain
80/82, 6020 Innsbruck, Austria
- Centre
for Molecular Informatics, Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Klaus
R. Liedl
- Institute
of General, Inorganic and Theoretical Chemistry and Center for Molecular
Biosciences Innsbruck (CMBI), University
of Innsbruck, Innrain
80/82, 6020 Innsbruck, Austria
| | - Mahdi M. Abu-Omar
- Department
of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, Indiana 47907, United States
| | - Chittaranjan Das
- Department
of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, Indiana 47907, United States
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141
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Non-Heme Dioxygenase Catalyzes Atypical Oxidations of 6,7-Bicyclic Systems To Form the 6,6-Quinolone Core of Viridicatin-Type Fungal Alkaloids. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201407920] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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142
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Ishikawa N, Tanaka H, Koyama F, Noguchi H, Wang CCC, Hotta K, Watanabe K. Non-Heme Dioxygenase Catalyzes Atypical Oxidations of 6,7-Bicyclic Systems To Form the 6,6-Quinolone Core of Viridicatin-Type Fungal Alkaloids. Angew Chem Int Ed Engl 2014; 53:12880-4. [DOI: 10.1002/anie.201407920] [Citation(s) in RCA: 89] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2014] [Indexed: 01/11/2023]
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143
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Bryliakov KP, Talsi EP. Active sites and mechanisms of bioinspired oxidation with H2O2, catalyzed by non-heme Fe and related Mn complexes. Coord Chem Rev 2014. [DOI: 10.1016/j.ccr.2014.06.009] [Citation(s) in RCA: 189] [Impact Index Per Article: 18.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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144
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Blaesi EJ, Fox BG, Brunold TC. Spectroscopic and computational investigation of iron(III) cysteine dioxygenase: implications for the nature of the putative superoxo-Fe(III) intermediate. Biochemistry 2014; 53:5759-70. [PMID: 25093959 PMCID: PMC4165443 DOI: 10.1021/bi500767x] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
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Cysteine dioxygenase (CDO) is a mononuclear,
non-heme iron-dependent
enzyme that converts exogenous cysteine (Cys) to cysteine sulfinic
acid using molecular oxygen. Although the complete catalytic mechanism
is not yet known, several recent reports presented evidence for an
Fe(III)-superoxo reaction intermediate. In this work, we have utilized
spectroscopic and computational methods to investigate the as-isolated
forms of CDO, as well as Cys-bound Fe(III)CDO, both in the absence
and presence of azide (a mimic of superoxide). An analysis of our
electronic absorption, magnetic circular dichroism, and electron paramagnetic
resonance data of the azide-treated as-isolated forms of CDO within
the framework of density functional theory (DFT) computations reveals
that azide coordinates directly to the Fe(III), but not the Fe(II)
center. An analogous analysis carried out for Cys-Fe(III)CDO provides
compelling evidence that at physiological pH, the iron center is six
coordinate, with hydroxide occupying the sixth coordination site.
Upon incubation of this species with azide, the majority of the active
sites retain hydroxide at the iron center. Nonetheless, a modest perturbation
of the electronic structure of the Fe(III) center is observed, indicating
that azide ions bind near the active site. Additionally, for a small
fraction of active sites, azide displaces hydroxide and coordinates
directly to the Cys-bound Fe(III) center to generate a low-spin (S = 1/2) Fe(III) complex. In the DFT-optimized
structure of this complex, the central nitrogen atom of the azide
moiety lies within 3.12 Å of the cysteine sulfur. A similar orientation
of the superoxide ligand in the putative Fe(III)-superoxo reaction
intermediate would promote the attack of the distal oxygen atom on
the sulfur of substrate Cys.
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Affiliation(s)
- Elizabeth J Blaesi
- Departments of †Chemistry and ‡Biochemistry, University of Wisconsin-Madison , Madison, Wisconsin 53706, United States
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145
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Balamurugan M, Vadivelu P, Palaniandavar M. Iron(iii) complexes of tripodal tetradentate 4N ligands as functional models for catechol dioxygenases: the electronic vs. steric effect on extradiol cleavage. Dalton Trans 2014; 43:14653-68. [DOI: 10.1039/c3dt52145a] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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146
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Pabis A, Geronimo I, York DM, Paneth P. Molecular Dynamics Simulation of Nitrobenzene Dioxygenase Using AMBER Force Field. J Chem Theory Comput 2014; 10:2246-2254. [PMID: 24955078 PMCID: PMC4059247 DOI: 10.1021/ct500205z] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2014] [Indexed: 12/03/2022]
Abstract
Molecular dynamics simulation of the oxygenase component of nitrobenzene dioxygenase (NBDO) system, a member of the naphthalene family of Rieske nonheme iron dioxygenases, has been carried out using the AMBER force field combined with a new set of parameters for the description of the mononuclear nonheme iron center and iron-sulfur Rieske cluster. Simulation results provide information on the structure and dynamics of nitrobenzene dioxygenase in an aqueous environment and shed light on specific interactions that occur in its catalytic center. The results suggest that the architecture of the active site is stabilized by key hydrogen bonds, and Asn258 positions the substrate for oxidation. Analysis of protein-water interactions reveal the presence of a network of solvent molecules at the entrance to the active site, which could be of potential catalytic importance.
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Affiliation(s)
- Anna Pabis
- Institute
of Applied Radiation Chemistry, Lodz University
of Technology, Zeromskiego
116, 90-924 Lodz, Poland
- Department
of Chemistry and Chemical Biology, Center for Integrative Proteomics
Research and BioMaPS Institute for Quantitative Biology, Rutgers, The State University of New Jersey, 174 Frelinghuysen Road, Piscataway, New Jersey 08854, United States
| | - Inacrist Geronimo
- Institute
of Applied Radiation Chemistry, Lodz University
of Technology, Zeromskiego
116, 90-924 Lodz, Poland
| | - Darrin M. York
- Department
of Chemistry and Chemical Biology, Center for Integrative Proteomics
Research and BioMaPS Institute for Quantitative Biology, Rutgers, The State University of New Jersey, 174 Frelinghuysen Road, Piscataway, New Jersey 08854, United States
| | - Piotr Paneth
- Institute
of Applied Radiation Chemistry, Lodz University
of Technology, Zeromskiego
116, 90-924 Lodz, Poland
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147
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Lu L, Zhu C, Xia B, Yi C. Oxidative Demethylation of DNA and RNA Mediated by Non-Heme Iron-Dependent Dioxygenases. Chem Asian J 2014; 9:2018-29. [DOI: 10.1002/asia.201402148] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2014] [Indexed: 11/10/2022]
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148
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3-Ketosteroid 9α-hydroxylase enzymes: Rieske non-heme monooxygenases essential for bacterial steroid degradation. Antonie van Leeuwenhoek 2014; 106:157-72. [PMID: 24846050 PMCID: PMC4064121 DOI: 10.1007/s10482-014-0188-2] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/30/2014] [Accepted: 04/25/2014] [Indexed: 12/26/2022]
Abstract
Various micro-organisms are able to use sterols/steroids as carbon- and energy sources for growth. 3-Ketosteroid 9α-hydroxylase (KSH), a two component Rieske non-heme monooxygenase comprised of the oxygenase KshA and the reductase KshB, is a key-enzyme in bacterial steroid degradation. It initiates opening of the steroid polycyclic ring structure. The enzyme has industrial relevance in the synthesis of pharmaceutical steroids. Deletion of KSH activity in sterol degrading bacteria results in blockage of steroid ring opening and is used to produce valuable C19-steroids such as 4-androstene-3,17-dione and 1,4-androstadiene-3,17-dione. Interestingly, KSH activity is essential for the pathogenicity of Mycobacterium tuberculosis. Detailed information about KSH thus is of medical relevance, and KSH inhibitory compounds may find application in combatting tuberculosis. In recent years, the 3D structure of the KshA protein of M. tuberculosis H37Rv has been elucidated and various studies report biochemical characteristics and possible physiological roles of KSH. The current knowledge is reviewed here and forms a solid basis for further studies on this highly interesting enzyme. Future work may result in the construction of KSH mutants capable of production of specific bioactive steroids. Furthermore, KSH provides an promising target for drugs against the pathogenic agent M. tuberculosis.
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149
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Hirao H, Thellamurege N, Zhang X. Applications of density functional theory to iron-containing molecules of bioinorganic interest. Front Chem 2014; 2:14. [PMID: 24809043 PMCID: PMC4010748 DOI: 10.3389/fchem.2014.00014] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2013] [Accepted: 03/10/2014] [Indexed: 12/29/2022] Open
Abstract
The past decades have seen an explosive growth in the application of density functional theory (DFT) methods to molecular systems that are of interest in a variety of scientific fields. Owing to its balanced accuracy and efficiency, DFT plays particularly useful roles in the theoretical investigation of large molecules. Even for biological molecules such as proteins, DFT finds application in the form of, e.g., hybrid quantum mechanics and molecular mechanics (QM/MM), in which DFT may be used as a QM method to describe a higher prioritized region in the system, while a MM force field may be used to describe remaining atoms. Iron-containing molecules are particularly important targets of DFT calculations. From the viewpoint of chemistry, this is mainly because iron is abundant on earth, iron plays powerful (and often enigmatic) roles in enzyme catalysis, and iron thus has the great potential for biomimetic catalysis of chemically difficult transformations. In this paper, we present a brief overview of several recent applications of DFT to iron-containing non-heme synthetic complexes, heme-type cytochrome P450 enzymes, and non-heme iron enzymes, all of which are of particular interest in the field of bioinorganic chemistry. Emphasis will be placed on our own work.
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Affiliation(s)
- Hajime Hirao
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological UniversitySingapore, Singapore
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150
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Etzbach L, Plaza A, Garcia R, Baumann S, Müller R. Cystomanamides: structure and biosynthetic pathway of a family of glycosylated lipopeptides from myxobacteria. Org Lett 2014; 16:2414-7. [PMID: 24735013 DOI: 10.1021/ol500779s] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Cystomanamides A-D were isolated as novel natural product scaffolds from Cystobacter fuscus MCy9118, and their structures were established by spectroscopic techniques including 2D NMR, LC-SPE-NMR/-MS, and HR-MS. The cystomanamides contain β-hydroxy amino acids along with 3-amino-9-methyldecanoic acid that is N-glycosylated in cystomanamide C and D. The gene cluster for cystomanamide biosynthesis was identified by gene disruption as PKS/NRPS hybrid incorporating an iso-fatty acid as starter unit and including a reductive amination step at the interface of the PKS and NRPS modules.
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Affiliation(s)
- Lena Etzbach
- Department of Microbial Natural Products, Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI) and Pharmaceutical Biotechnology, Saarland University , Campus C2 3, 66123 Saarbrücken, Germany
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