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Giri NC, Sun H, Chen H, Costa M, Maroney MJ. X-ray absorption spectroscopy structural investigation of early intermediates in the mechanism of DNA repair by human ABH2. Biochemistry 2011; 50:5067-76. [PMID: 21510633 PMCID: PMC3124014 DOI: 10.1021/bi101668x] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Human ABH2 repairs DNA lesions by using an Fe(II)- and αKG-dependent oxidative demethylation mechanism. The structure of the active site features the facial triad of protein ligands consisting of the side chains of two histidine residues and one aspartate residue that is common to many non-heme Fe(II) oxygenases. X-ray absorption spectroscopy (XAS) of metallated (Fe and Ni) samples of ABH2 was used to investigate the mechanism of ABH2 and its inhibition by Ni(II) ions. The data are consistent with a sequential mechanism that features a five-coordinate metal center in the presence and absence of the α-ketoglutarate cofactor. This aspect is not altered in the Ni(II)-substituted enzyme, and both metals are shown to bind the cofactor. When the substrate is bound to the native Fe(II) complex with α-ketoglutarate bound, a five-coordinate Fe(II) center is retained that features an open coordination position for O(2) binding. However, in the case of the Ni(II)-substituted enzyme, the complex that forms in the presence of the cofactor and substrate is six-coordinate and, therefore, features no open coordination site for oxygen activation at the metal.
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Affiliation(s)
- Nitai Charan Giri
- Department of Chemistry, University of Massachusetts, Amherst, Massachusetts 01003, phone number 413-545-4876, fax number 413-545-4490
| | - Hong Sun
- Department of Environmental Medicine, New York University School of Medicine, New York 10016
| | - Haobin Chen
- Department of Environmental Medicine, New York University School of Medicine, New York 10016
| | - Max Costa
- Department of Environmental Medicine, New York University School of Medicine, New York 10016
| | - Michael J. Maroney
- Department of Chemistry, University of Massachusetts, Amherst, Massachusetts 01003, phone number 413-545-4876, fax number 413-545-4490
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52
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Xuereb DJ, Raja R. Design strategies for engineering selectivity in bio-inspired heterogeneous catalysts. Catal Sci Technol 2011. [DOI: 10.1039/c0cy00088d] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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53
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Sundaravel K, Suresh E, Palaniandavar M. Iron(III) complexes of tridentate N3 ligands as models for catechol dioxygenases: Stereoelectronic effects of pyrazole coordination. Inorganica Chim Acta 2010. [DOI: 10.1016/j.ica.2010.04.025] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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54
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Diebold AR, Neidig ML, Moran GR, Straganz GD, Solomon EI. The three-his triad in Dke1: comparisons to the classical facial triad. Biochemistry 2010; 49:6945-52. [PMID: 20695531 DOI: 10.1021/bi100892w] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The oxygen activating mononuclear non-heme ferrous enzymes catalyze a diverse range of chemistry yet typically maintain a common structural motif: two histidines and a carboxylate coordinating the iron center in a facial triad. A new Fe(II) coordinating triad has been observed in two enzymes, diketone-cleaving dioxygenase, Dke1, and cysteine dioxygenase (CDO), and is composed of three histidine residues. The effect of this three-His motif in Dke1 on the geometric and electronic structure of the Fe(II) center is explored via a combination of absorption, CD, MCD, and VTVH MCD spectroscopies and DFT calculations. This geometric and electronic structure of the three-His triad is compared to that of the classical (2-His-1-carboxylate) facial triad in the alpha-ketoglutarate (alphaKG)-dependent dioxygenases clavaminate synthase 2 (CS2) and hydroxyphenylpyruvate dioxygenase (HPPD). Comparison of the ligand fields at the Fe(II) shows little difference between the three-His and 2-His-1-carboxylate facial triad sites. Acetylacetone, the substrate for Dke1, will also bind to HPPD and is identified as a strong donor, similar to alphaKG. The major difference between the three-His and 2-His-1-carboxylate facial triad sites is in MLCT transitions observed for both types of triads and reflects their difference in charge. These studies provide insight into the effects of perturbation of the facial triad ligation of the non-heme ferrous enzymes on their geometric and electronic structure and their possible contributions to reactivity.
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Affiliation(s)
- Adrienne R Diebold
- Department of Chemistry, Stanford University, Stanford, California 94305, USA
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55
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56
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Cisneros GA. DFT study of a model system for the dealkylation step catalyzed by AlkB. Interdiscip Sci 2010; 2:70-7. [PMID: 20640798 DOI: 10.1007/s12539-010-0092-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2009] [Revised: 11/18/2009] [Accepted: 11/25/2009] [Indexed: 11/25/2022]
Abstract
E. coli AlkB is a DNA repair enzyme that catalyzes the de-methylation of DNA by means of a non-heme iron and alpha-keto glutarate as a co-factor. The proposed reaction mechanism can be separated in four stages. The first stage involves the binding of the co-factor and molecular oxygen to the Fe in the active site. This is followed by the formation of a ferryl intermediate in a high-spin state, along with CO(2) and succinate. Subsequently, the O atom on the Fe center is reoriented. The last stage comprises the oxidative de-methylation of the base to produce the native DNA base and formaldehyde. This stage also includes the rate limiting step in the reaction. Here, the last stage of the proposed reaction mechanism of AlkB has been studied for a model of the active site with DFT methods. Minimum structures have been calculated for all intermediates along the path in triplet and quintet spin states. Our results point to the quintet states as more stable, in agreement with previously reported calculations. Potential energy barriers have been obtained for all the steps along this last stage in the quintet state. In the first step the oxygen bound to the Fe center of the ferryl intermediate abstracts a hydrogen atom from the methyl moiety. This first step corresponds to the rate limiting step in the reaction. The calculated barrier for this step is 26.7 kcal/mol. The subsequent steps are highly exoergic. This energetic picture is in qualitative agreement with previously reported results. The calculated energy difference between the ferryl intermediate and the final product is -75.7 kcal/mol for a model with succinate in the active site and -49.3 kcal/mol for a model where the succinate is replaced by water. Our calculated mechanism is slightly different than the previously reported one. These results suggest the possibility of more than one mechanism. This is currently under investigation by ab initio QM/MM methods.
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Affiliation(s)
- G Andrés Cisneros
- Department of Chemistry, Wayne State University, Detroit, MI 48202, USA.
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57
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Dzierzak J, Bottinelli E, Berlier G, Gianotti E, Stulz E, Kowalczyk RM, Raja R. The role of isolated active centres in high-performance bioinspired selective oxidation catalysts. Chem Commun (Camb) 2010; 46:2805-7. [DOI: 10.1039/b926721b] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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58
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Dungan VJ, Ortin Y, Mueller-Bunz H, Rutledge PJ. Design and synthesis of a tetradentate ‘3-amine-1-carboxylate’ ligand to mimic the metal binding environment at the non-heme iron(ii) oxidase active site. Org Biomol Chem 2010; 8:1666-73. [DOI: 10.1039/b921934j] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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59
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Denisov IG, Mak PJ, Makris TM, Sligar SG, Kincaid JR. Resonance Raman characterization of the peroxo and hydroperoxo intermediates in cytochrome P450. J Phys Chem A 2009; 112:13172-9. [PMID: 18630867 DOI: 10.1021/jp8017875] [Citation(s) in RCA: 78] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Resonance Raman (RR) studies of intermediates generated by cryoreduction of the oxyferrous complex of the D251N mutant of cytochrome P450(cam) (CYP101) are reported. Owing to the fact that proton delivery to the active site is hindered in this mutant, the unprotonated peroxo-ferric intermediate is observed as the primary species after radiolytic reduction of the oxy-complex in frozen solutions at 77 K. In as much as previous EPR and ENDOR studies have shown that annealing of this species to approximately 180 K results in protonation of the distal oxygen atom to form the hydroperoxo intermediate, this system has been exploited to permit direct RR interrogation of the changes in the Fe-O and O-O bonds caused by the reduction and subsequent protonation. Our results show that the nu(O-O) mode decreases from a superoxo-like frequency near approximately 1130 cm(-1) to 792 cm(-1) upon reduction. The latter frequency, as well as its lack of sensitivity to H/D exchange, is consistent with heme-bound peroxide formulation. This species also exhibits a nu(Fe-O) mode, the 553 cm(-1) frequency of which is higher than that observed for the nonreduced oxy P450 precursor (537 cm(-1)), implying a strengthened Fe-O linkage upon reduction. Upon subsequent protonation, the resulting Fe-O-OH fragment exhibits a lowered nu(O-O) mode at 774 cm(-1), whereas the nu(Fe-O) increases to 564 cm(-1). Both modes exhibit a downshift upon H/D exchange, as expected for a hydroperoxo-ferric formulation. These experimental RR data are compared with those previously acquired for the wild-type protein, and the shifts observed upon reduction and subsequent protonation are discussed with reference to theoretical predictions.
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Affiliation(s)
- Ilia G Denisov
- Department of Biochemistry, University of Illinois, Urbana, Illinois 61801, USA
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60
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Mayilmurugan R, Visvaganesan K, Suresh E, Palaniandavar M. Iron(III) Complexes of Tripodal Monophenolate Ligands as Models for Non-Heme Catechol Dioxygenase Enzymes: Correlation of Dioxygenase Activity with Ligand Stereoelectronic Properties. Inorg Chem 2009; 48:8771-83. [DOI: 10.1021/ic900969n] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
| | | | - Eringathodi Suresh
- Analytical Science Discipline, Central Salt and Marine Chemicals Research Institute, Bhavnagar − 364 002, India
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61
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Chow MS, Eser BE, Wilson SA, Hodgson KO, Hedman B, Fitzpatrick PF, Solomon EI. Spectroscopy and kinetics of wild-type and mutant tyrosine hydroxylase: mechanistic insight into O2 activation. J Am Chem Soc 2009; 131:7685-98. [PMID: 19489646 DOI: 10.1021/ja810080c] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Tyrosine hydroxylase (TH) is a pterin-dependent nonheme iron enzyme that catalyzes the hydroxylation of L-tyr to L-DOPA in the rate-limiting step of catecholamine neurotransmitter biosynthesis. We have previously shown that the Fe(II) site in phenylalanine hydroxylase (PAH) converts from six-coordinate (6C) to five-coordinate (5C) only when both substrate + cofactor are bound. However, steady-state kinetics indicate that TH has a different co-substrate binding sequence (pterin + O(2) + L-tyr) than PAH (L-phe + pterin + O(2)). Using X-ray absorption spectroscopy (XAS), and variable-temperature-variable-field magnetic circular dichroism (VTVH MCD) spectroscopy, we have investigated the geometric and electronic structure of the wild-type (WT) TH and two mutants, S395A and E332A, and their interactions with substrates. All three forms of TH undergo 6C --> 5C conversion with tyr + pterin, consistent with the general mechanistic strategy established for O(2)-activating nonheme iron enzymes. We have also applied single-turnover kinetic experiments with spectroscopic data to evaluate the mechanism of the O(2) and pterin reactions in TH. When the Fe(II) site is 6C, the two-electron reduction of O(2) to peroxide by Fe(II) and pterin is favored over individual one-electron reactions, demonstrating that both a 5C Fe(II) and a redox-active pterin are required for coupled O(2) reaction. When the Fe(II) is 5C, the O(2) reaction is accelerated by at least 2 orders of magnitude. Comparison of the kinetics of WT TH, which produces Fe(IV)=O + 4a-OH-pterin, and E332A TH, which does not, shows that the E332 residue plays an important role in directing the protonation of the bridged Fe(II)-OO-pterin intermediate in WT to productively form Fe(IV)=O, which is responsible for hydroxylating L-tyr to L-DOPA.
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Affiliation(s)
- Marina S Chow
- Department of Chemistry, Stanford University, Stanford, California 94305, USA
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62
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Solomon EI, Wong SD, Liu LV, Decker A, Chow MS. Peroxo and oxo intermediates in mononuclear nonheme iron enzymes and related active sites. Curr Opin Chem Biol 2009; 13:99-113. [PMID: 19278895 DOI: 10.1016/j.cbpa.2009.02.011] [Citation(s) in RCA: 97] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2008] [Revised: 01/25/2009] [Accepted: 02/02/2009] [Indexed: 10/21/2022]
Abstract
Fe(III)OOH and Fe(IV)O intermediates have now been documented in a number of nonheme iron active sites. In this Current Opinion we use spectroscopy combined with electronic structure calculations to define the frontier molecular orbitals (FMOs) of these species and their contributions to reactivity. For the low-spin Fe(III)OOH species in activated bleomycin we show that the reactivity of this nonheme iron intermediate is very different from that of the analogous Compound 0 of cytochrome P450. For Fe(IV)O S=1 model species we experimentally define the electronic structure and its contribution to reactivity, and computationally evaluate how this would change for the Fe(IV)O S=2 intermediates found in nonheme iron enzymes.
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Affiliation(s)
- Edward I Solomon
- Department of Chemistry, Stanford University, CA 94305, United States.
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63
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Lee YM, Dhuri S, Sawant S, Cho J, Kubo M, Ogura T, Fukuzumi S, Nam W. Water as an Oxygen Source in the Generation of Mononuclear Nonheme Iron(IV) Oxo Complexes. Angew Chem Int Ed Engl 2009. [DOI: 10.1002/ange.200805670] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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64
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Lee YM, Dhuri S, Sawant S, Cho J, Kubo M, Ogura T, Fukuzumi S, Nam W. Water as an Oxygen Source in the Generation of Mononuclear Nonheme Iron(IV) Oxo Complexes. Angew Chem Int Ed Engl 2009; 48:1803-6. [DOI: 10.1002/anie.200805670] [Citation(s) in RCA: 96] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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65
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Annaraj J, Kim S, Seo MS, Lee YM, Kim Y, Kim SJ, Choi YS, Jang HG, Nam W. An iron(II) complex with a N3S2 thioether ligand in the generation of an iron(IV)-oxo complex and its reactivity in olefin epoxidation. Inorganica Chim Acta 2009. [DOI: 10.1016/j.ica.2008.04.018] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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66
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Schroeder S, Lawrence AD, Biedendieck R, Rose RS, Deery E, Graham RM, McLean KJ, Munro AW, Rigby SEJ, Warren MJ. Demonstration that CobG, the monooxygenase associated with the ring contraction process of the aerobic cobalamin (vitamin B12) biosynthetic pathway, contains an Fe-S center and a mononuclear non-heme iron center. J Biol Chem 2008; 284:4796-805. [PMID: 19068481 DOI: 10.1074/jbc.m807184200] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The ring contraction process that occurs during cobalamin (vitamin B(12)) biosynthesis is mediated via the action of two enzymes, CobG and CobJ. The first of these generates a tertiary alcohol at the C-20 position of precorrin-3A by functioning as a monooxygenase, a reaction that also forms a gamma lactone with the acetic acid side chain on ring A. The product, precorrin-3B, is then acted upon by CobJ, which methylates at the C-17 position and promotes ring contraction of the macrocycle by catalyzing a masked pinacol rearrangement. Here, we report the characterization of CobG enzymes from Pseudomonas denitrificans and Brucella melitensis. We show that both contain a [4Fe-4S] center as well as a mononuclear non-heme iron. Although both enzymes are active in vivo, the P. denitrificans enzyme was found to be inactive in vitro. Further analysis of this enzyme revealed that the mononuclear non-heme iron was not reducible, and it was concluded that it is rapidly inactivated once it is released from the bacterial cell. In contrast, the B. melitensis enzyme was found to be fully active in vitro and the mononuclear non-heme iron was reducible by dithionite. The reduced mononuclear non-heme was able to react with the oxygen analogue NO, but only in the presence of the substrate precorrin-3A. The cysteine residues responsible for binding the Fe-S center were identified by site-directed mutagenesis. A mechanism for CobG is presented.
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Affiliation(s)
- Susanne Schroeder
- Protein Science Group, Department of Biosciences, University of Kent, Canterbury, Kent CT27NJ, United Kingdom
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67
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Hewitson KS, Holmes SL, Ehrismann D, Hardy AP, Chowdhury R, Schofield CJ, McDonough MA. Evidence that two enzyme-derived histidine ligands are sufficient for iron binding and catalysis by factor inhibiting HIF (FIH). J Biol Chem 2008; 283:25971-8. [PMID: 18611856 DOI: 10.1074/jbc.m804999200] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
A 2-His-1-carboxylate triad of iron binding residues is present in many non-heme iron oxygenases including the Fe(II) and 2-oxoglutarate (2OG)-dependent dioxygenases. Three variants (D201A, D201E, and D201G) of the iron binding Asp-201 residue of an asparaginyl hydroxylase, factor inhibiting HIF (FIH), were made and analyzed. FIH-D201A and FIH-D201E did not catalyze asparaginyl hydroxylation, but in the presence of a reducing agent, they displayed enhanced 2OG turnover when compared with wild-type FIH. Turnover of 2OG by FIH-D201A was significantly stimulated by the addition of HIF-1alpha(786-826) peptide. Like FIH-D201A and D201E, the D201G variant enhanced 2OG turnover but rather unexpectedly catalyzed asparaginyl hydroxylation. Crystal structures of the FIH-D201A and D201G variants in complex with Fe(II)/Zn(II), 2OG, and HIF-1alpha(786-826/788-806) implied that only two FIH-based residues (His-199 and His-279) are required for metal binding. The results indicate that variation of 2OG-dependent dioxygenase iron-ligating residues as a means of functional assignment should be treated with caution. The results are of mechanistic interest in the light of recent biochemical and structural analyses of non-heme iron and 2OG-dependent halogenases that are similar to the FIH-D201A/G variants in that they use only two His-residues to ligate iron.
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Affiliation(s)
- Kirsty S Hewitson
- Chemistry Research Laboratory, The Department of Chemistry, University of Oxford, Mansfield Road, Oxford OX1 3TA, United Kingdom
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68
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Ohta T, Chakrabarty S, Lipscomb JD, Solomon EI. Near-IR MCD of the nonheme ferrous active site in naphthalene 1,2-dioxygenase: correlation to crystallography and structural insight into the mechanism of Rieske dioxygenases. J Am Chem Soc 2008; 130:1601-10. [PMID: 18189388 DOI: 10.1021/ja074769o] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Near-IR MCD and variable temperature, variable field (VTVH) MCD have been applied to naphthalene 1,2-dioxygenase (NDO) to describe the coordination geometry and electronic structure of the mononuclear nonheme ferrous catalytic site in the resting and substrate-bound forms with the Rieske 2Fe2S cluster oxidized and reduced. The structural results are correlated with the crystallographic studies of NDO and other related Rieske nonheme iron oxygenases to develop molecular level insights into the structure/function correlation for this class of enzymes. The MCD data for resting NDO with the Rieske center oxidized indicate the presence of a six-coordinate high-spin ferrous site with a weak axial ligand which becomes more tightly coordinated when the Rieske center is reduced. Binding of naphthalene to resting NDO (Rieske oxidized and reduced) converts the six-coordinate sites into five-coordinate (5c) sites with elimination of a water ligand. In the Rieske oxidized form the 5c sites are square pyramidal but transform to a 1:2 mixture of trigonal bipyramial/square pyramidal sites when the Rieske center is reduced. Thus the geometric and electronic structure of the catalytic site in the presence of substrate can be significantly affected by the redox state of the Rieske center. The catalytic ferrous site is primed for the O2 reaction when substrate is bound in the active site in the presence of the reduced Rieske site. These structural changes ensure that two electrons and the substrate are present before the binding and activation of O2, which avoids the uncontrolled formation and release of reactive oxygen species.
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Affiliation(s)
- Takehiro Ohta
- Department of Chemistry, Stanford University, Stanford, California 94305, USA
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69
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Das S, Bhattacharyya J, Mukhopadhyay S. Mechanistic studies on oxidation of hydrogen peroxide by an oxo-bridged diiron complex in aqueous acidic media. Dalton Trans 2008:6634-40. [DOI: 10.1039/b810011j] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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70
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Bruijnincx PCA, van Koten G, Klein Gebbink RJM. Mononuclear non-heme iron enzymes with the 2-His-1-carboxylate facial triad: recent developments in enzymology and modeling studies. Chem Soc Rev 2008; 37:2716-44. [DOI: 10.1039/b707179p] [Citation(s) in RCA: 412] [Impact Index Per Article: 25.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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71
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Tanase S, Marques-Gallego P, Browne WR, Hage R, Bouwman E, Feringa BL, Reedijk J. Mechanistic implications of the active species involved in the oxidation of hydrocarbons by iron complexes of pyrazine-2-carboxylic acid. Dalton Trans 2008:2026-33. [DOI: 10.1039/b716942f] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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72
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Neidig ML, Brown CD, Light KM, Fujimori DG, Nolan EM, Price JC, Barr EW, Bollinger JM, Krebs C, Walsh CT, Solomon EI. CD and MCD of CytC3 and taurine dioxygenase: role of the facial triad in alpha-KG-dependent oxygenases. J Am Chem Soc 2007; 129:14224-31. [PMID: 17967013 DOI: 10.1021/ja074557r] [Citation(s) in RCA: 79] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The alpha-ketoglutarate (alpha-KG)-dependent oxygenases are a large and diverse class of mononuclear non-heme iron enzymes that require FeII, alpha-KG, and dioxygen for catalysis with the alpha-KG cosubstrate supplying the additional reducing equivalents for oxygen activation. While these systems exhibit a diverse array of reactivities (i.e., hydroxylation, desaturation, ring closure, etc.), they all share a common structural motif at the FeII active site, termed the 2-His-1-carboxylate facial triad. Recently, a new subclass of alpha-KG-dependent oxygenases has been identified that exhibits novel reactivity, the oxidative halogenation of unactivated carbon centers. These enzymes are also structurally unique in that they do not contain the standard facial triad, as a Cl- ligand is coordinated in place of the carboxylate. An FeII methodology involving CD, MCD, and VTVH MCD spectroscopies was applied to CytC3 to elucidate the active-site structural effects of this perturbation of the coordination sphere. A significant decrease in the affinity of FeII for apo-CytC3 was observed, supporting the necessity of the facial triad for iron coordination to form the resting site. In addition, interesting differences observed in the FeII/alpha-KG complex relative to the cognate complex in other alpha-KG-dependent oxygenases indicate the presence of a distorted 6C site with a weak water ligand. Combined with parallel studies of taurine dioxygenase and past studies of clavaminate synthase, these results define a role of the carboxylate ligand of the facial triad in stabilizing water coordination via a H-bonding interaction between the noncoordinating oxygen of the carboxylate and the coordinated water. These studies provide initial insight into the active-site features that favor chlorination by CytC3 over the hydroxylation reactions occurring in related enzymes.
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Affiliation(s)
- Michael L Neidig
- Department of Chemistry, Stanford University, Stanford, California 94305, USA
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73
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74
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Neidig ML, Wecksler AT, Schenk G, Holman TR, Solomon EI. Kinetic and spectroscopic studies of N694C lipoxygenase: a probe of the substrate activation mechanism of a nonheme ferric enzyme. J Am Chem Soc 2007; 129:7531-7. [PMID: 17523638 PMCID: PMC2896304 DOI: 10.1021/ja068503d] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Lipoxygenases (LOs) comprise a class of substrate activating mononuclear nonheme iron enzymes which catalyze the hydroperoxidation of unsaturated fatty acids. A commonly proposed mechanism for LO catalysis involves H-atom abstraction by an FeIII-OH- site, best described as a proton coupled electron transfer (PCET) process, followed by direct reaction of O2 with the resulting substrate radical to yield product. An alternative mechanism that has also been discussed involves the abstraction of a proton from the substrate by the FeIII-OH leading to a sigma-organoiron intermediate, where the subsequent sigma bond insertion of dioxygen into the C-Fe bond completes the reaction. H-atom abstraction is favored by a high E(o) of the FeII/FeIII couple and high pK(a) of water bound to the ferrous state, while an organoiron mechanism would be favored by a low E(o) (to keep the site oxidized) and a high pK(a) of water bound to the ferric state (to deprotonate the substrate). A first coordination sphere mutant of soybean LO (N694C) has been prepared and characterized by near-infrared circular dichroism (CD) and variable-temperature, variable-field (VTVH) magnetic circular dichroism (MCD) spectroscopies (FeII site), as well as UV/vis absorption, UV/vis CD, and electron paramagnetic resonance (EPR) spectroscopies (FeIII site). These studies suggest that N694C has a lowered E degrees of the FeII/FeIII couple and a raised pKa of water bound to the ferric site relative to wild type soybean lipoxygenase-1 (WT sLO-1) which would favor the organoiron mechanism. However, the observation in N694C of a significant deuterium isotope effect, anaerobic reduction of iron by substrate, and a substantial decrease in k(cat) (approximately 3000-fold) support H-atom abstraction as the relevant substrate-activation mechanism in sLO-1.
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Affiliation(s)
- Michael L. Neidig
- Department of Chemistry, Stanford University, Stanford, CA, 94305, USA
| | - Aaron T. Wecksler
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, CA, 95064, USA
| | - Gerhard Schenk
- Department of Chemistry, Stanford University, Stanford, CA, 94305, USA
| | - Theodore R. Holman
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, CA, 95064, USA
| | - Edward I. Solomon
- Department of Chemistry, Stanford University, Stanford, CA, 94305, USA
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75
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Seo M, Kamachi T, Kouno T, Murata K, Park M, Yoshizawa K, Nam W. Experimental and Theoretical Evidence for Nonheme Iron(III) Alkylperoxo Species as Sluggish Oxidants in Oxygenation Reactions. Angew Chem Int Ed Engl 2007. [DOI: 10.1002/ange.200604219] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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76
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Seo MS, Kamachi T, Kouno T, Murata K, Park MJ, Yoshizawa K, Nam W. Experimental and Theoretical Evidence for Nonheme Iron(III) Alkylperoxo Species as Sluggish Oxidants in Oxygenation Reactions. Angew Chem Int Ed Engl 2007; 46:2291-4. [PMID: 17304600 DOI: 10.1002/anie.200604219] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Mi Sook Seo
- Department of Chemistry, Division of Nano Sciences and Center for Biomimetic Systems, Ewha Womans University, Seoul 120-750, Korea.
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77
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Pau MYM, Davis MI, Orville AM, Lipscomb JD, Solomon EI. Spectroscopic and electronic structure study of the enzyme-substrate complex of intradiol dioxygenases: substrate activation by a high-spin ferric non-heme iron site. J Am Chem Soc 2007; 129:1944-58. [PMID: 17256852 PMCID: PMC2536531 DOI: 10.1021/ja065671x] [Citation(s) in RCA: 75] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Various mechanisms have been proposed for the initial O(2) attack in intradiol dioxygenases based on different electronic descriptions of the enzyme-substrate (ES) complex. We have examined the geometric and electronic structure of the high-spin ferric ES complex of protocatechuate 3,4-dioxygenase (3,4-PCD) with UV/visible absorption, circular dichroism (CD), magnetic CD (MCD), and variable-temperature variable-field (VTVH) MCD spectroscopies. The experimental data were coupled with DFT and INDO/S-CI calculations, and an experimentally calibrated bonding description was obtained. The broad absorption spectrum for the ES complex in the 6000-31000 cm(-1) region was resolved into at least five individual transitions, assigned as ligand-to-metal charge transfer (LMCT) from the protocatechuate (PCA) substrate and Tyr408. From our DFT calculations, all five LMCT transitions originate from the PCA and Tyr piop orbitals to the ferric dpi orbitals. The strong pi covalent donor interactions dominate the bonding in the ES complex. Using hypothetical Ga(3+)-catecholate/semiquinone complexes as references, 3,4-PCD-PCA was found to be best described as a highly covalent Fe(3+)-catecholate complex. The covalency is distributed unevenly among the four PCA valence orbitals, with the strongest interaction between the piop-sym and Fe dxz orbitals. This strong pi interaction, as reflected in the lowest energy PCA-to-Fe(3+) LMCT transition, is responsible for substrate activation for the O(2) reaction of intradiol dioxygenases. This involves a multi-electron-transfer (one beta and two alpha) mechanism, with Fe3+ acting as a buffer for the spin-forbidden two-electron redox process between PCA and O(2) in the formation of the peroxy-bridged ESO2 intermediate. The Fe ligand field overcomes the spin-forbidden nature of the triplet O(2) reaction, which potentially results in an intermediate spin state (S = 3/2) on the Fe(3+) center which is stabilized by a change in coordination along the reaction coordinate.
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Affiliation(s)
- Monita Y M Pau
- Department of Chemistry, Stanford University, Stanford, California 94305-5080, USA
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78
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Hocking RK, Wasinger EC, Yan YL, Degroot FMF, Walker FA, Hodgson KO, Hedman B, Solomon EI. Fe L-edge X-ray absorption spectroscopy of low-spin heme relative to non-heme Fe complexes: delocalization of Fe d-electrons into the porphyrin ligand. J Am Chem Soc 2007; 129:113-25. [PMID: 17199290 PMCID: PMC2890250 DOI: 10.1021/ja065627h] [Citation(s) in RCA: 93] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Hemes (iron porphyrins) are involved in a range of functions in biology, including electron transfer, small-molecule binding and transport, and O2 activation. The delocalization of the Fe d-electrons into the porphyrin ring and its effect on the redox chemistry and reactivity of these systems has been difficult to study by optical spectroscopies due to the dominant porphyrin pi-->pi(*) transitions, which obscure the metal center. Recently, we have developed a methodology that allows for the interpretation of the multiplet structure of Fe L-edges in terms of differential orbital covalency (i.e., differences in mixing of the d-orbitals with ligand orbitals) using a valence bond configuration interaction (VBCI) model. Applied to low-spin heme systems, this methodology allows experimental determination of the delocalization of the Fe d-electrons into the porphyrin (P) ring in terms of both P-->Fe sigma and pi-donation and Fe-->P pi back-bonding. We find that pi-donation to Fe(III) is much larger than pi back-bonding from Fe(II), indicating that a hole superexchange pathway dominates electron transfer. The implications of the results are also discussed in terms of the differences between heme and non-heme oxygen activation chemistry.
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Affiliation(s)
- Rosalie K Hocking
- Department of Chemistry, Stanford University, Stanford, California 94305, USA
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79
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80
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Nehru K, Seo MS, Kim J, Nam W. Oxidative N-Dealkylation Reactions by Oxoiron(IV) Complexes of Nonheme and Heme Ligands. Inorg Chem 2006; 46:293-8. [PMID: 17198439 DOI: 10.1021/ic0614014] [Citation(s) in RCA: 91] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Nonheme and heme iron monooxygenases participate in oxidative N-dealkylation reactions in nature, and high-valent oxoiron(IV) species have been invoked as active oxidants that effect the oxygenation of organic substrates. The present study describes the first example of the oxidative N-dealkylation of N,N-dialkylamines by synthetic nonheme oxoiron(IV) complexes and the reactivity comparisons of nonheme and heme oxoiron(IV) complexes. Detailed mechanistic studies were performed with various N,N-dialkylaniline substrates such as para-substituted N,N-dimethylanilines, para-chloro-N-ethyl-N-methylaniline, para-chloro-N-cyclopropyl-N-isopropylaniline, and deuteriated N,N-dimethylanilines. The results of a linear free-energy correlation, inter- and intramolecular kinetic isotope effects, and product analysis studied with the mechanistic probes demonstrate that the oxidative N-dealkylation reactions by nonheme and heme oxoiron(IV) complexes occur via an electron transfer-proton transfer (ET-PT) mechanism.
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Affiliation(s)
- Kasi Nehru
- Department of Chemistry, Division of Nano Sciences, and Center for Biomimetic Systems, Ewha Womans University, Seoul 120-750, Korea
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81
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Neidig ML, Decker A, Choroba OW, Huang F, Kavana M, Moran GR, Spencer JB, Solomon EI. Spectroscopic and electronic structure studies of aromatic electrophilic attack and hydrogen-atom abstraction by non-heme iron enzymes. Proc Natl Acad Sci U S A 2006; 103:12966-73. [PMID: 16920789 PMCID: PMC1559736 DOI: 10.1073/pnas.0605067103] [Citation(s) in RCA: 126] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
(4-Hydroxy)mandelate synthase (HmaS) and (4-hydroxyphenyl)pyruvate dioxygenase (HPPD) are two alpha-keto acid dependent mononuclear non-heme iron enzymes that use the same substrate, (4-hydroxyphenyl)pyruvate, but exhibit two different general reactivities. HmaS performs hydrogen-atom abstraction to yield benzylic hydroxylated product (S)-(4-hydroxy)mandelate, whereas HPPD utilizes an electrophilic attack mechanism that results in aromatic hydroxylated product homogentisate. These enzymes provide a unique opportunity to directly evaluate the similarities and differences in the reaction pathways used for these two reactivities. An Fe(II) methodology using CD, magnetic CD, and variable-temperature, variable-field magnetic CD spectroscopies was applied to HmaS and compared with that for HPPD to evaluate the factors that affect substrate interactions at the active site and to correlate these to the different reactivities exhibited by HmaS and HPPD to the same substrate. Combined with density functional theory calculations, we found that HmaS and HPPD have similar substrate-bound complexes and that the role of the protein pocket in determining the different reactivities exhibited by these enzymes (hydrogen-atom abstraction vs. aromatic electrophilic attack) is to properly orient the substrate, allowing for ligand field geometric changes along the reaction coordinate. Elongation of the Fe(IV) O bond in the transition state leads to dominant Fe(III) O(*-) character, which significantly contributes to the reactivity with either the aromatic pi-system or the C H sigma-bond.
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Affiliation(s)
| | - Andrea Decker
- Department of Chemistry, Stanford University, Stanford, CA 94306
| | - Oliver W. Choroba
- Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom; and
| | - Fanglu Huang
- Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom; and
| | - Michael Kavana
- Department of Chemistry and Biochemistry, University of Wisconsin, Milwaukee, WI 53211
| | - Graham R. Moran
- Department of Chemistry and Biochemistry, University of Wisconsin, Milwaukee, WI 53211
| | - Jonathan B. Spencer
- Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom; and
| | - Edward I. Solomon
- Department of Chemistry, Stanford University, Stanford, CA 94306
- To whom correspondence should be addressed: E-mail:
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82
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de Visser SP. Differences in and Comparison of the Catalytic Properties of Heme and Non-Heme Enzymes with a Central Oxo–Iron Group. Angew Chem Int Ed Engl 2006. [DOI: 10.1002/ange.200503841] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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83
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de Visser SP. Differences in and Comparison of the Catalytic Properties of Heme and Non-Heme Enzymes with a Central Oxo–Iron Group. Angew Chem Int Ed Engl 2006; 45:1790-3. [PMID: 16470900 DOI: 10.1002/anie.200503841] [Citation(s) in RCA: 88] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Sam P de Visser
- Manchester Interdisciplinary Biocentre and the School of Chemical Engineering and Analytical Science, University of Manchester, UK.
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