151
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Molecular insight into bacterial cleavage of oceanic dimethylsulfoniopropionate into dimethyl sulfide. Proc Natl Acad Sci U S A 2014; 111:1026-31. [PMID: 24395783 DOI: 10.1073/pnas.1312354111] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The microbial cleavage of dimethylsulfoniopropionate (DMSP) generates volatile DMS through the action of DMSP lyases and is important in the global sulfur and carbon cycles. When released into the atmosphere from the oceans, DMS is oxidized, forming cloud condensation nuclei that may influence weather and climate. Six different DMSP lyase genes are found in taxonomically diverse microorganisms, and dddQ is among the most abundant in marine metagenomes. Here, we examine the molecular mechanism of DMSP cleavage by the DMSP lyase, DddQ, from Ruegeria lacuscaerulensis ITI_1157. The structures of DddQ bound to an inhibitory molecule 2-(N-morpholino)ethanesulfonic acid and of DddQ inactivated by a Tyr131Ala mutation and bound to DMSP were solved. DddQ adopts a β-barrel fold structure and contains a Zn(2+) ion and six highly conserved hydrophilic residues (Tyr120, His123, His125, Glu129, Tyr131, and His163) in the active site. Mutational and biochemical analyses indicate that these hydrophilic residues are essential to catalysis. In particular, Tyr131 undergoes a conformational change during catalysis, acting as a base to initiate the β-elimination reaction in DMSP lysis. Moreover, structural analyses and molecular dynamics simulations indicate that two loops over the substrate-binding pocket of DddQ can alternate between "open" and "closed" states, serving as a gate for DMSP entry. We also propose a molecular mechanism for DMS production through DMSP cleavage. Our study provides important insight into the mechanism involved in the conversion of DMSP into DMS, which should lead to a better understanding of this globally important biogeochemical reaction.
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152
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Gajewska MJ, Ching WM, Wen YS, Hung CH. Synthesis, structure, and catecholase activity of bispyrazolylacetate copper(ii) complexes. Dalton Trans 2014; 43:14726-36. [DOI: 10.1039/c4dt01467g] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Heteroleptic copper(ii) complexes containing bis(3,5-di-t-butylpyrazol-1-yl)acetate and nitrogen heterocyclic co-ligands identified the influence of co-ligands on the conformation and catecholase-like catalytic activity.
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Affiliation(s)
| | - Wei-Min Ching
- Institute of Chemistry
- Academia Sinica
- Taipei 105, Taiwan
| | - Yuh-Sheng Wen
- Institute of Chemistry
- Academia Sinica
- Taipei 105, Taiwan
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153
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Abstract
It has recently been demonstrated that the genes controlling the epigenetic programmes that are required for maintaining chromatin structure and cell identity include genes that drive human cancer. This observation has led to an increased awareness of chromatin-associated proteins as potentially interesting drug targets. The successful introduction of DNA methylation and histone deacetylase (HDAC) inhibitors for the treatment of specific subtypes of cancer has paved the way for the use of epigenetic therapy. Here, we highlight key biological findings demonstrating the roles of members of the histone lysine demethylase class of enzymes in the development of cancers, discuss the potential and challenges of therapeutically targeting them, and highlight emerging small-molecule inhibitors of these enzymes.
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154
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4-Hydroxyphenylpyruvate dioxygenase and hydroxymandelate synthase: exemplars of the α-keto acid dependent oxygenases. Arch Biochem Biophys 2013; 544:58-68. [PMID: 24211436 DOI: 10.1016/j.abb.2013.10.022] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2013] [Revised: 10/28/2013] [Accepted: 10/30/2013] [Indexed: 11/23/2022]
Abstract
4-Hydroxyphenylpyruvate dioxygenase (HPPD) and hydroxymandelate synthase (HMS) are outliers within the α-keto acid dependent oxygenase (αKAO) family. HPPD and HMS catalyze the chemistry of the majority of enzymes within the αKAO family but are clearly mechanistically convergent, having a grossly different structural topology. Some of the unique characteristics of HPPD and HMS have elucidated select parts of the catalytic cycle that are obscured in other family members. Moreover, the inhibitory chemistry of HPPD is a phenomenon with ever-expanding relevance across all kingdoms of life. This review is a synopsis of the literature pertaining to HPPD and HMS. It is not intended as an exhaustive compilation of all observations made for these enzymes but rather a condensed narrative that connects those studies that have advanced the understanding of the chemistry of both enzymes.
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155
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Souness RJ, Kleffmann T, Tchesnokov EP, Wilbanks SM, Jameson GB, Jameson GNL. Mechanistic implications of persulfenate and persulfide binding in the active site of cysteine dioxygenase. Biochemistry 2013; 52:7606-17. [PMID: 24084026 DOI: 10.1021/bi400661a] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Describing the organization of substrates and substrate analogues in the active site of cysteine dioxygenase identifies potential intermediates in this critical yet poorly understood reaction, the oxidation of cysteine to cysteine sulfinic acid. The fortuitous formation of persulfides under crystallization conditions has allowed their binding in the active site of cysteine dioxygenase to be studied. The crystal structures of cysteine persulfide and 3-mercaptopropionic acid persulfide bound to iron(II) in the active site show that binding of the persulfide occurs via the distal sulfide and, in the case of the cysteine persulfide, the amine also binds. Persulfide was detected by mass spectrometry in both the crystal and the drop, suggesting its origin is chemical rather than enzymatic. A mechanism involving the formation of the relevant disulfide from sulfide produced by hydrolysis of dithionite is proposed. In comparison, persulfenate {observed bound to cysteine dioxygenase [Simmons, C. R., et al. (2008) Biochemistry 47, 11390]} is shown through mass spectrometry to occur only in the crystal and not in the surrounding drop, suggesting that in the crystalline state the persulfenate does not lie on the reaction pathway. Stabilization of both the persulfenate and the persulfides does, however, suggest the position in which dioxygen binds during catalysis.
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Affiliation(s)
- Richard J Souness
- Department of Chemistry and MacDiarmid Institute for Advanced Materials and Nanotechnology and ‡Department of Biochemistry, University of Otago , P.O. Box 56, Dunedin 9054, New Zealand
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156
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Blaesi EJ, Gardner JD, Fox BG, Brunold TC. Spectroscopic and computational characterization of the NO adduct of substrate-bound Fe(II) cysteine dioxygenase: insights into the mechanism of O2 activation. Biochemistry 2013; 52:6040-51. [PMID: 23906193 DOI: 10.1021/bi400825c] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Cysteine dioxygenase (CDO) is a mononuclear nonheme iron(II)-dependent enzyme critical for maintaining appropriate cysteine (Cys) and taurine levels in eukaryotic systems. Because CDO possesses both an unusual 3-His facial ligation sphere to the iron center and a rare Cys-Tyr cross-link near the active site, the mechanism by which it converts Cys and molecular oxygen to cysteine sulfinic acid is of broad interest. However, as of yet, direct experimental support for any of the proposed mechanisms is still lacking. In this study, we have used NO as a substrate analogue for O2 to prepare a species that mimics the geometric and electronic structures of an early reaction intermediate. The resultant unusual S = (1)/2 {FeNO}(7) species was characterized by magnetic circular dichroism, electron paramagnetic resonance, and electronic absorption spectroscopies as well as computational methods including density functional theory and semiempirical calculations. The NO adducts of Cys- and selenocysteine (Sec)-bound Fe(II)CDO exhibit virtually identical electronic properties; yet, CDO is unable to oxidize Sec. To explore the differences in reactivity between Cys- and Sec-bound CDO, the geometries and energies of viable O2-bound intermediates were evaluated computationally, and it was found that a low-energy quintet-spin intermediate on the Cys reaction pathway adopts a different geometry for the Sec-bound adduct. The absence of a low-energy O2 adduct for Sec-bound CDO is consistent with our experimental data and may explain why Sec is not oxidized by CDO.
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Affiliation(s)
- Elizabeth J Blaesi
- Department of Chemistry, University of Wisconsin-Madison , Madison, Wisconsin 53706, United States
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157
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Lin JF, Sheih YL, Chang TC, Chang NY, Chang CW, Shen CP, Lee HJ. The interactions in the carboxyl terminus of human 4-hydroxyphenylpyruvate dioxygenase are critical to mediate the conformation of the final helix and the tail to shield the active site for catalysis. PLoS One 2013; 8:e69733. [PMID: 23950902 PMCID: PMC3739788 DOI: 10.1371/journal.pone.0069733] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2013] [Accepted: 06/12/2013] [Indexed: 11/18/2022] Open
Abstract
4-Hydroxylphenylpyruvate dioxygenase (4-HPPD) is an important enzyme for tyrosine catabolism, which catalyzes the conversion of 4-hydroxylphenylpyruvate (4-HPP) to homogentisate. In the present study, human 4-HPPD was cloned and expressed in E. coli. The kinetic parameters for 4-HPP conversion were: k cat=2.2 ± 0.1 s(-1); and K m=0.08 ± 0.02 mM. Sequence alignments show that human 4-HPPD possesses an extended C-terminus compared to other 4-HPPD enzymes. Successive truncation of the disordered tail which follows the final α-helix resulted in no changes in the K m value for 4-HPP substrate but the k cat values were significantly reduced. The results suggest that this disordered C-terminal tail plays an important role in catalysis. For inspection the effect of terminal truncation on protein structure, mutant models were built. These models suggest that the different conformation of E254, R378 and Q375 in the final helix might be the cause of the activity loss. In the structure E254 interacts with R378, the end residue in the final helix; mutation of either one of these residues causes a ca. 95% reductions in k cat values. Q375 provides bifurcate interactions to fix the tail and the final helix in position. The model of the Q375N mutant shows that a solvent accessible channel opens to the putative substrate binding site, suggesting this is responsible for the complete loss of activity. These results highlight the critical role of Q375 in orientating the tail and ensuring the conformation of the terminal α-helix to maintain the integrity of the active site for catalysis.
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Affiliation(s)
- Jang-Foung Lin
- Department of Biochemistry, National Defense Medical Center, Neihu, Taipei, Taiwan
| | - Yung-Lin Sheih
- Department of Biochemistry, National Defense Medical Center, Neihu, Taipei, Taiwan
| | - Tsu-Chung Chang
- Department of Biochemistry, National Defense Medical Center, Neihu, Taipei, Taiwan
| | - Ni-Yuan Chang
- Department of Biochemistry, National Defense Medical Center, Neihu, Taipei, Taiwan
| | - Chiung-Wen Chang
- Department of Biochemistry, National Defense Medical Center, Neihu, Taipei, Taiwan
| | - Chia-Pei Shen
- Department of Biochemistry, National Defense Medical Center, Neihu, Taipei, Taiwan
| | - Hwei-Jen Lee
- Department of Biochemistry, National Defense Medical Center, Neihu, Taipei, Taiwan
- * E-mail:
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158
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Clifton IJ, Ge W, Adlington RM, Baldwin JE, Rutledge PJ. The crystal structure of an isopenicillin N synthase complex with an ethereal substrate analogue reveals water in the oxygen binding site. FEBS Lett 2013; 587:2705-9. [DOI: 10.1016/j.febslet.2013.07.016] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2013] [Revised: 07/04/2013] [Accepted: 07/04/2013] [Indexed: 10/26/2022]
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159
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Light KM, Hangasky JA, Knapp MJ, Solomon EI. Spectroscopic studies of the mononuclear non-heme Fe(II) enzyme FIH: second-sphere contributions to reactivity. J Am Chem Soc 2013; 135:9665-74. [PMID: 23742069 PMCID: PMC3712650 DOI: 10.1021/ja312571m] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Factor inhibiting hypoxia-inducible factor (FIH) is an α-ketoglutarate (αKG)-dependent enzyme which catalyzes hydroxylation of residue Asn803 in the C-terminal transactivation domain (CAD) of hypoxia-inducible factor 1α (HIF-1α) and plays an important role in cellular oxygen sensing and hypoxic response. Circular dichroism (CD), magnetic circular dichroism (MCD), and variable-temperature, variable-field (VTVH) MCD spectroscopies are used to determine the geometric and electronic structures of FIH in its (Fe(II)), (Fe(II)/αKG), and (Fe(II)/αKG/CAD) forms. (Fe(II))FIH and (Fe(II)/αKG)FIH are found to be six-coordinate (6C), whereas (Fe(II)/αKG/CAD)FIH is found to be a 5C/6C mixture. Thus, FIH follows the general mechanistic strategy of non-heme Fe(II) enzymes. Modeling shows that, when Arg238 of FIH is removed, the facial triad carboxylate binds to Fe(II) in a bidentate mode with concomitant lengthening of the Fe(II)/αKG carbonyl bond, which would inhibit the O2 reaction. Correlations over α-keto acid-dependent enzymes and with the extradiol dioxygenases show that members of these families (where both the electron source and O2 bind to Fe(II)) have a second-sphere residue H-bonding to the terminal oxygen of the carboxylate, which stays monodentate. Alternatively, structures of the pterin-dependent and Rieske dioxygenases, which do not have substrate binding to Fe(II), lack H-bonds to the carboxylate and thus allow its bidentate coordination which would direct O2 reactivity. Finally, vis-UV MCD spectra show an unusually high-energy Fe(II) → αKG π* metal-to-ligand charge transfer transition in (Fe(II)/αKG)FIH which is red-shifted upon CAD binding. This red shift indicates formation of H-bonds to the αKG that lower the energy of its carbonyl LUMO, activating it for nucleophilic attack by the Fe-O2 intermediate formed along the reaction coordinate.
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Affiliation(s)
- Kenneth M. Light
- Department of Chemistry, Stanford University, Stanford, CA 94305
| | - John A. Hangasky
- Department of Chemistry, University of Massachusetts, Amherst, MA 01003
| | - Michael J. Knapp
- Department of Chemistry, University of Massachusetts, Amherst, MA 01003
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160
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Moelands MAH, Nijsse S, Folkertsma E, de Bruin B, Lutz M, Spek AL, Klein Gebbink RJM. Bioinspired Nonheme Iron Complexes Derived from an Extended Series of N,N,O-Ligated BAIP Ligands. Inorg Chem 2013; 52:7394-410. [DOI: 10.1021/ic400096e] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- 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
| | - Sjoerd Nijsse
- Organic Chemistry and Catalysis,
Debye Institute for Nanomaterials Science, Faculty of Science, Utrecht University, Universiteitsweg 99, 3584 CG Utrecht,
The Netherlands
| | - Emma Folkertsma
- Organic Chemistry and Catalysis,
Debye Institute for Nanomaterials Science, Faculty of Science, Utrecht University, Universiteitsweg 99, 3584 CG Utrecht,
The Netherlands
| | - Bas de Bruin
- Van’t
Hoff Institute
for Molecular Sciences (HIMS), University of Amsterdam, P.O. Box 94720, 1090 GE Amsterdam, The Netherlands
| | - Martin Lutz
- Van’t
Hoff Institute
for Molecular Sciences (HIMS), University of Amsterdam, P.O. Box 94720, 1090 GE Amsterdam, The Netherlands
- Bijvoet Center for Biomolecular
Research, Crystal and Structural Chemistry, Faculty of Science, Utrecht University, Padualaan 8, 3584 CH Utrecht, The
Netherlands
| | - Anthony L. Spek
- Van’t
Hoff Institute
for Molecular Sciences (HIMS), University of Amsterdam, P.O. Box 94720, 1090 GE Amsterdam, The Netherlands
- Bijvoet Center for Biomolecular
Research, Crystal and Structural Chemistry, Faculty of Science, Utrecht University, Padualaan 8, 3584 CH Utrecht, The
Netherlands
| | - 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
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161
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Bernasconi L, Baerends EJ. A Frontier Orbital Study with ab Initio Molecular Dynamics of the Effects of Solvation on Chemical Reactivity: Solvent-Induced Orbital Control in FeO-Activated Hydroxylation Reactions. J Am Chem Soc 2013; 135:8857-67. [DOI: 10.1021/ja311144d] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Leonardo Bernasconi
- STFC Rutherford Appleton Laboratory, Harwell Oxford, Didcot, OX11 0QX,
United Kingdom
| | - Evert Jan Baerends
- Theoretical
Chemistry Section, Vrije Universiteit Amsterdam, De Boelelaan 1083, 1081
HV Amsterdam, The Netherlands
- WCU program at Department of Chemistry, Pohang University of Science and Technology, Pohang
790-784, South Korea
- Chemistry
Department, Faculty
of Science, King Abdulaziz University,
Jeddah 21589, Saudi Arabia
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162
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Ponnaluri VKC, Maciejewski JP, Mukherji M. A mechanistic overview of TET-mediated 5-methylcytosine oxidation. Biochem Biophys Res Commun 2013; 436:115-20. [PMID: 23727577 DOI: 10.1016/j.bbrc.2013.05.077] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2013] [Accepted: 05/17/2013] [Indexed: 10/26/2022]
Abstract
Methylation of DNA at the carbon-5 position of cytosine plays crucial roles in the epigenetic transcriptional silencing during metazoan development. Recent identification of Ten-Eleven Translocation (TET)-family demethylases have added a new dimension to dynamic regulation of 5-methylcytosine (5mC), and thus, inheritable and somatic gene silencing. The interest in hematology was particularly stimulated by the recent discovery of TET2 mutations in myeloid malignancies which were proven to be leukemogenic in murine knockout models. The TET-family enzymes are Fe(II), 2-oxoglutarate-dependent oxygenases and catalyze demethylation of 5mC by iterative oxidation reactions. In the last decade results from numerous studies have established a key role for these enzymes in epigenetic transcriptional regulation in eukaryotes primarily by hydroxylation reactions. The TET catalyzed hydroxylation and dehydration reactions in the mammalian system exemplify the diversity of oxidation reactions catalyzed by Fe(II), 2-oxoglutarate-dependent oxygenases, and suggest an existence of other types of oxidation reactions catalyzed by these enzymes in the eukaryotes, which are so far only documented in prokaryotes. Here, we review the TET-mediated 5mC oxidation in light of the putative reaction mechanism of Fe(II), 2-oxoglutarate-dependent oxygenases.
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Affiliation(s)
- V K Chaithanya Ponnaluri
- Division of Pharmaceutical Sciences, School of Pharmacy, University of Missouri-Kansas City, 64108 MO, United States
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163
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Metal vs. chalcogen competition in the catalytic mechanism of cysteine dioxygenase. J Inorg Biochem 2013; 122:1-7. [DOI: 10.1016/j.jinorgbio.2013.01.008] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2012] [Revised: 12/25/2012] [Accepted: 01/11/2013] [Indexed: 11/18/2022]
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164
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CHE XIN, GAO JUN, DU LIKAI, LIU CHENGBU. THEORETICAL INVESTIGATION OF THE HIGH-SPIN "Fe-PROXIMAL OXYGEN" CATALYTIC MECHANISM OF RAT CYSTEINE DIOXYGENASE. JOURNAL OF THEORETICAL & COMPUTATIONAL CHEMISTRY 2013. [DOI: 10.1142/s0219633613500016] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Cysteine dioxygenase (CDO) catalyzes the oxidation of cysteine to cysteine sulfinate, which has crucial roles in the metabolism and bioconversion. The catalyzed reaction mechanism of CDO is currently disputed. Herein, a high-spin " Fe -proximal oxygen" catalytic mechanism of rat CDO is theoretically investigated with an energy barrier of 15.7 kcal⋅mol-1. In the mechanism, the Fe -proximal oxygen atom firstly attacks the sulfur atom of cysteine by the swing of O (1)– O (2) bond, and this makes the Fe -proximal oxygen atom O (1) accessible to S and Fe -terminal oxygen atom O (2) be closed to Fe . Then the generated seven-membered ring intermediate has smaller tension and could help the reaction take place easily. The reaction ends in the formation of the product cysteine sulfinic acid with the second oxygen atom O (2) transferred to S. This study gives an additional insight of the reaction mechanism of CDO, where the " Fe -proximal oxygen" and " Fe -terminal oxygen" mechanisms are both favorable in the catalytic process.
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Affiliation(s)
- XIN CHE
- Key Lab of Colloid and Interface Chemistry, Ministry of Education, Institute of Theoretical Chemistry, School of Chemistry and Chemical Engineering, Shandong University, Jinan, 250100, P. R. China
| | - JUN GAO
- Key Lab of Colloid and Interface Chemistry, Ministry of Education, Institute of Theoretical Chemistry, School of Chemistry and Chemical Engineering, Shandong University, Jinan, 250100, P. R. China
| | - LIKAI DU
- Key Lab of Colloid and Interface Chemistry, Ministry of Education, Institute of Theoretical Chemistry, School of Chemistry and Chemical Engineering, Shandong University, Jinan, 250100, P. R. China
| | - CHENGBU LIU
- Key Lab of Colloid and Interface Chemistry, Ministry of Education, Institute of Theoretical Chemistry, School of Chemistry and Chemical Engineering, Shandong University, Jinan, 250100, P. R. China
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165
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Hangasky JA, Taabazuing CY, Valliere MA, Knapp MJ. Imposing function down a (cupin)-barrel: secondary structure and metal stereochemistry in the αKG-dependent oxygenases. Metallomics 2013; 5:287-301. [PMID: 23446356 PMCID: PMC4109655 DOI: 10.1039/c3mt20153h] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The Fe(ii)/αketoglutarate (αKG) dependent oxygenases catalyze a diverse range of reactions significant in biological processes such as antibiotic biosynthesis, lipid metabolism, oxygen sensing, and DNA and RNA repair. Although functionally diverse, the eight-stranded β-barrel (cupin) and HX(D/E)XnH facial triad motifs are conserved in this super-family of enzymes. Crystal structure analysis of 25 αKG oxygenases reveals two stereoisomers of the Fe cofactor, Anti and Clock, which differ in the relative position of the exchangeable ligand position and the primary substrate. Herein, we discuss the relationship between the chemical mechanism and the secondary coordination sphere of the αKG oxygenases, within the constraints of the stereochemistry of the Fe cofactor. Sequence analysis of the cupin barrel indicates that a small subset of positions constitute the second coordination sphere, which has significant ramifications for the structure of the ferryl intermediate. The competence of both Anti and Clock stereoisomers of Fe points to a ferryl intermediate that is 5 coordinate. The small number of conserved close contacts within the active sites of αKG oxygenases can be extended to chemically related enzymes, such as the αKG-dependent halogenases SyrB2 and CytC3, and the non-αKG dependent dioxygenases isopenicillin N synthase (IPNS) and cysteine dioxygenase (CDO).
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Affiliation(s)
- John A. Hangasky
- Department of Chemistry, University of Massachusetts, Amherst, MA 01003, USA
| | | | - Meaghan A. Valliere
- Department of Chemistry, University of Massachusetts, Amherst, MA 01003, USA
| | - Michael J. Knapp
- Department of Chemistry, University of Massachusetts, Amherst, MA 01003, USA
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166
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Das O, Chatterjee S, Paine TK. Functional models of α-keto acid dependent nonheme iron oxygenases: synthesis and reactivity of biomimetic iron(II) benzoylformate complexes supported by a 2,9-dimethyl-1,10-phenanthroline ligand. J Biol Inorg Chem 2013; 18:401-10. [PMID: 23417539 DOI: 10.1007/s00775-013-0984-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2012] [Accepted: 01/31/2013] [Indexed: 01/12/2023]
Abstract
Two biomimetic iron(II) benzoylformate complexes, [LFe(II)(BF)(2)] (2) and [LFe(II)(NO(3))(BF)] (3) (L is 2,9-dimethyl-1,10-phenanthroline and BF is monoanionic benzoylformate), have been synthesized from an iron(II)-dichloro complex [LFe(II)Cl(2)] (1). All the iron(II) complexes have been structurally and spectroscopically characterized. The iron(II) center in 2 is coordinated by a bidentate NN ligand (2,9-dimethyl-1,10-phenanthroline) and two monoanionic benzoylformates to form a distorted octahedral coordination geometry. One of the benzoylformates binds to the iron in 2 via both carboxylate oxygens but the other one binds in a chelating bidentate fashion via one carboxylate oxygen and the keto oxygen. On the other hand, the iron(II) center in 3 is ligated by one NN ligand, one bidentate nitrate, and one monoanionic chelating benzoylformate. Both iron(II) benzoylformate complexes exhibit the facial NNO donor environment in their solid-state structures. Complexes 2 and 3 are stable in noncoordinating solvents under an inert atmosphere, but react with dioxygen under ambient conditions to undergo oxidative decarboxylation of benzoylformate to benzoate in high yields. Evidence for the formation of an iron(IV)-oxo intermediate upon oxidative decarboxylation of benzoylformate was obtained by interception and labeling experiments. The iron(II) benzoylformate complexes represent the functional models of α-keto acid dependent oxygenases.
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Affiliation(s)
- Oindrila Das
- Department of Inorganic Chemistry, Indian Association for the Cultivation of Science, 2A & 2B Raja S. C. Mullick Road, Jadavpur, 700032, Kolkata, India
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167
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Daruzzaman A, Clifton IJ, Adlington RM, Baldwin JE, Rutledge PJ. The crystal structure of isopenicillin N synthase with a dipeptide substrate analogue. Arch Biochem Biophys 2013; 530:48-53. [DOI: 10.1016/j.abb.2012.12.012] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2012] [Revised: 12/07/2012] [Accepted: 12/09/2012] [Indexed: 11/29/2022]
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168
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Roberts KM, Pavon JA, Fitzpatrick PF. Kinetic mechanism of phenylalanine hydroxylase: intrinsic binding and rate constants from single-turnover experiments. Biochemistry 2013; 52:1062-73. [PMID: 23327364 DOI: 10.1021/bi301675e] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Phenylalanine hydroxylase (PheH) catalyzes the key step in the catabolism of dietary phenylalanine, its hydroxylation to tyrosine using tetrahydrobiopterin (BH(4)) and O(2). A complete kinetic mechanism for PheH was determined by global analysis of single-turnover data in the reaction of PheHΔ117, a truncated form of the enzyme lacking the N-terminal regulatory domain. Formation of the productive PheHΔ117-BH(4)-phenylalanine complex begins with the rapid binding of BH(4) (K(d) = 65 μM). Subsequent addition of phenylalanine to the binary complex to form the productive ternary complex (K(d) = 130 μM) is approximately 10-fold slower. Both substrates can also bind to the free enzyme to form inhibitory binary complexes. O(2) rapidly binds to the productive ternary complex; this is followed by formation of an unidentified intermediate, which can be detected as a decrease in absorbance at 340 nm, with a rate constant of 140 s(-1). Formation of the 4a-hydroxypterin and Fe(IV)O intermediates is 10-fold slower and is followed by the rapid hydroxylation of the amino acid. Product release is the rate-determining step and largely determines k(cat). Similar reactions using 6-methyltetrahydropterin indicate a preference for the physiological pterin during hydroxylation.
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Affiliation(s)
- Kenneth M Roberts
- Department of Biochemistry, University of Texas Health Science Center, San Antonio, TX 78229, USA
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169
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Buongiorno D, Straganz GD. Structure and function of atypically coordinated enzymatic mononuclear non-heme-Fe(II) centers. Coord Chem Rev 2013; 257:541-563. [PMID: 24850951 PMCID: PMC4019311 DOI: 10.1016/j.ccr.2012.04.028] [Citation(s) in RCA: 82] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2012] [Revised: 04/17/2012] [Accepted: 04/18/2012] [Indexed: 11/17/2022]
Abstract
Mononuclear, non-heme-Fe(II) centers are key structures in O2 metabolism and catalyze an impressive variety of enzymatic reactions. While most are bound via two histidines and a carboxylate, some show a different organization. A short overview of atypically coordinated O2 dependent mononuclear-non-heme-Fe(II) centers is presented here Enzymes with 2-His, 3-His, 3-His-carboxylate and 4-His bound Fe(II) centers are discussed with a focus on their reactivity, metal ion promiscuity and recent progress in the elucidation of their enzymatic mechanisms. Observations concerning these and classically coordinated Fe(II) centers are used to understand the impact of the metal binding motif on catalysis.
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Key Words
- 1,3-bis(2-pyridylimino)isoindoline, ind
- 2OH-1,3-Ph2PD, 2-hydroxy-1,3-diphenylpropanedione
- 6-Ph2TPA, N,N-bis[(6-phenyl-2-pyridyl)methyl]-N-[(2-pyridyl)-methyl]amine
- ADO, cysteamine dioxygenase
- AO, apocarotenoid 15,15′-oxygenase
- ARD, aci-reductone dioxygenase
- BsQDO, quercetin 2,3-dioxygenase from Bacillus subtilis
- CD, circular dichroism
- CDO, cysteine dioxygenase
- CGDO, 5-chloro-gentisate 1,2-dioxygenase
- CS2, clavaminate synthase
- CarOs, carotenoid oxygenases
- DFT, density functional theory
- Dioxygen activation
- Dioxygenase
- Dke1, diketone dioxygenase
- EPR, electron paramagnetic resonance
- EXAFS, extended X-ray absorption fine structure spectroscopy
- Enzyme catalysis
- Facial triad
- GDO, gentisate 1,2-dioxygenase
- HADO, 3-hydroxyanthranilate 3,4-dioxygenase
- HGDO, homogentisate 1,2-dioxygenase
- HNDO, hydroxy-2-naphthoate dioxygenase
- MCD, magnetic circular dichroism
- MNHEs, mononuclear non-heme-Fe(II) dependent enzymes
- Metal binding motif
- NRP, nonribosomal peptide
- OTf-, trifluormethanesulfonate
- PDB, protein data bank
- QDO, quercetin 2,3-dioxygenase
- SDO, salicylate 1,2-dioxygenase
- Structure–function relationships
- TauD, taurine hydroxylase
- XAS, X-ray absorption spectroscopy
- acac, acetylacetone (2,4-pentanedione)
- fla, flavonolate
- α-KG, α-ketoglutarate
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Affiliation(s)
- Daniela Buongiorno
- Institute of Biotechnology and Biochemical Engineering, Graz University of Technology, Petersgasse 12 A-8010 Graz, Austria
| | - Grit D Straganz
- Institute of Biotechnology and Biochemical Engineering, Graz University of Technology, Petersgasse 12 A-8010 Graz, Austria
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170
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Dilley DR, Wang Z, Kadirjan-Kalbach DK, Ververidis F, Beaudry R, Padmanabhan K. 1-Aminocyclopropane-1-carboxylic acid oxidase reaction mechanism and putative post-translational activities of the ACCO protein. AOB PLANTS 2013; 5:plt031. [PMID: 24244837 PMCID: PMC3828642 DOI: 10.1093/aobpla/plt031] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2012] [Accepted: 07/12/2013] [Indexed: 05/22/2023]
Abstract
1-Aminocyclopropane-1-carboxylic acid (ACC) oxidase (ACCO) catalyses the final step in ethylene biosynthesis converting ACC to ethylene, cyanide, CO2, dehydroascorbate and water with inputs of Fe(II), ascorbate, bicarbonate (as activators) and oxygen. Cyanide activates ACCO. A 'nest' comprising several positively charged amino acid residues from the C-terminal α-helix 11 along with Lys158 and Arg299 are proposed as binding sites for ascorbate and bicarbonate to coordinately activate the ACCO reaction. The binding sites for ACC, bicarbonate and ascorbic acid for Malus domestica ACCO1 include Arg175, Arg244, Ser246, Lys158, Lys292, Arg299 and Phe300. Glutamate 297, Phe300 and Glu301 in α-helix 11 are also important for the ACCO reaction. Our proposed reaction pathway incorporates cyanide as an ACCO/Fe(II) ligand after reaction turnover. The cyanide ligand is likely displaced upon binding of ACC and ascorbate to provide a binding site for oxygen. We propose that ACCO may be involved in the ethylene signal transduction pathway not directly linked to the ACCO reaction. ACC oxidase has significant homology with Lycopersicon esculentum cysteine protease LeCp, which functions as a protease and as a regulator of 1-aminocyclopropane-1-carboxylic acid synthase (Acs2) gene expression. ACC oxidase may play a similar role in signal transduction after post-translational processing. ACC oxidase becomes inactivated by fragmentation and apparently has intrinsic protease and transpeptidase activity. ACC oxidase contains several amino acid sequence motifs for putative protein-protein interactions, phosphokinases and cysteine protease. ACC oxidase is subject to autophosphorylaton in vitro and promotes phosphorylation of some apple fruit proteins in a ripening-dependent manner.
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Affiliation(s)
- David R. Dilley
- Department of Horticulture, Michigan State University, East Lansing, MI 48824, USA
- Corresponding author's e-mail address:
| | - Zhenyong Wang
- Ball Horticultural Company, 622 Town Road, West Chicago, IL 60185, USA
| | | | - Fillipos Ververidis
- Department of Plant Sciences, Technological Educational Institute of Crete, Heraklion 71004, Greece
| | - Randolph Beaudry
- Department of Horticulture, Michigan State University, East Lansing, MI 48824, USA
| | - Kallaithe Padmanabhan
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
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171
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McDonald AR, Que L. High-valent nonheme iron-oxo complexes: Synthesis, structure, and spectroscopy. Coord Chem Rev 2013. [DOI: 10.1016/j.ccr.2012.08.002] [Citation(s) in RCA: 397] [Impact Index Per Article: 36.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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172
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Chatterjee S, Sheet D, Paine TK. Catalytic and regiospecific extradiol cleavage of catechol by a biomimetic iron complex. Chem Commun (Camb) 2013; 49:10251-3. [DOI: 10.1039/c3cc44124e] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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173
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McLaughlin MP, Retegan M, Bill E, Payne TM, Shafaat HS, Peña S, Sudhamsu J, Ensign AA, Crane BR, Neese F, Holland PL. Azurin as a protein scaffold for a low-coordinate nonheme iron site with a small-molecule binding pocket. J Am Chem Soc 2012; 134:19746-57. [PMID: 23167247 PMCID: PMC3515693 DOI: 10.1021/ja308346b] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
The apoprotein of Pseudomonas aeruginosa azurin binds iron(II) to give a 1:1 complex, which has been characterized by electronic absorption, Mössbauer, and NMR spectroscopies, as well as X-ray crystallography and quantum-chemical computations. Despite potential competition by water and other coordinating residues, iron(II) binds tightly to the low-coordinate site. The iron(II) complex does not react with chemical redox agents to undergo oxidation or reduction. Spectroscopically calibrated quantum-chemical computations show that the complex has high-spin iron(II) in a pseudotetrahedral coordination environment, which features interactions with side chains of two histidines and a cysteine as well as the C═O of Gly45. In the (5)A(1) ground state, the d(z(2)) orbital is doubly occupied. Mutation of Met121 to Ala leaves the metal site in a similar environment but creates a pocket for reversible binding of small anions to the iron(II) center. Specifically, azide forms a high-spin iron(II) complex and cyanide forms a low-spin iron(II) complex.
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Affiliation(s)
| | - Marius Retegan
- Max Planck Institute for Chemical Energy Conversion, Mülheim an der Ruhr, Germany
| | - Eckhard Bill
- Max Planck Institute for Chemical Energy Conversion, Mülheim an der Ruhr, Germany
| | - Thomas M. Payne
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853
| | - Hannah S. Shafaat
- Max Planck Institute for Chemical Energy Conversion, Mülheim an der Ruhr, Germany
| | - Salvador Peña
- Department of Chemistry, University of Rochester, Rochester, New York 14618
| | - Jawahar Sudhamsu
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853
| | - Amy A. Ensign
- Department of Chemistry, University of Rochester, Rochester, New York 14618
| | - Brian R. Crane
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853
| | - Frank Neese
- Max Planck Institute for Chemical Energy Conversion, Mülheim an der Ruhr, Germany
| | - Patrick L. Holland
- Department of Chemistry, University of Rochester, Rochester, New York 14618
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174
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Miłaczewska A, Broclawik E, Borowski T. On the Catalytic Mechanism of (S)-2-Hydroxypropylphosphonic Acid Epoxidase (HppE): A Hybrid DFT Study. Chemistry 2012; 19:771-81. [DOI: 10.1002/chem.201202825] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2012] [Indexed: 11/10/2022]
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175
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Kabil O, Banerjee R. Characterization of patient mutations in human persulfide dioxygenase (ETHE1) involved in H2S catabolism. J Biol Chem 2012; 287:44561-7. [PMID: 23144459 DOI: 10.1074/jbc.m112.407411] [Citation(s) in RCA: 100] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Hydrogen sulfide (H(2)S) is a recently described endogenously produced gaseous signaling molecule that influences various cellular processes in the central nervous system, cardiovascular system, and gastrointestinal tract. The biogenesis of H(2)S involves the cytoplasmic transsulfuration enzymes, cystathionine β-synthase and γ-cystathionase, whereas its catabolism occurs in the mitochondrion and couples to the energy-yielding electron transfer chain. Low steady-state levels of H(2)S appear to be controlled primarily by efficient oxygen-dependent catabolism via sulfide quinone oxidoreductase, persulfide dioxygenase (ETHE1), rhodanese, and sulfite oxidase. Mutations in the persulfide dioxgenase, i.e. ETHE1, result in ethylmalonic encephalopathy, an inborn error of metabolism. In this study, we report the biochemical characterization and kinetic properties of human persulfide dioxygenase and describe the biochemical penalties associated with two patient mutations, T152I and D196N. Steady-state kinetic analysis reveals that the T152I mutation results in a 3-fold lower activity, which is correlated with a 3-fold lower iron content compared with the wild-type enzyme. The D196N mutation results in a 2-fold higher K(m) for the substrate, glutathione persulfide.
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Affiliation(s)
- Omer Kabil
- Department of Biological Chemistry, University of Michigan Medical Center, Ann Arbor, Michigan 48109-0600, USA
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176
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Mbughuni MM, Meier KK, Münck E, Lipscomb JD. Substrate-mediated oxygen activation by homoprotocatechuate 2,3-dioxygenase: intermediates formed by a tyrosine 257 variant. Biochemistry 2012; 51:8743-54. [PMID: 23066705 DOI: 10.1021/bi301114x] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Homoprotocatechuate (HPCA; 3,4-dihydroxyphenylacetate or 4-carboxymethyl catechol) and O(2) bind in adjacent ligand sites of the active site Fe(II) of homoprotocatechuate 2,3-dioxygenase (FeHPCD). We have proposed that electron transfer from the chelated aromatic substrate through the Fe(II) to O(2) gives both substrates radical character. This would promote reaction between the substrates to form an alkylperoxo intermediate as the first step in aromatic ring cleavage. Several active site amino acids are thought to promote these reactions through acid/base chemistry, hydrogen bonding, and electrostatic interactions. Here the role of Tyr257 is explored by using the Tyr257Phe (Y257F) variant, which decreases k(cat) by about 75%. The crystal structure of the FeHPCD-HPCA complex has shown that Tyr257 hydrogen bonds to the deprotonated C2-hydroxyl of HPCA. Stopped-flow studies show that at least two reaction intermediates, termed Y257F(Int1)(HPCA) and Y257F(Int2)(HPCA), accumulate during the Y257F-HPCA + O(2) reaction prior to formation of the ring-cleaved product. Y257F(Int1)(HPCA) is colorless and is formed as O(2) binds reversibly to the HPCA−enzyme complex. Y257F(Int2)(HPCA) forms spontaneously from Y257F(Int1)(HPCA) and displays a chromophore at 425 nm (ε(425) = 10 500 M(−1) cm(−1)). Mössbauer spectra of the intermediates trapped by rapid freeze quench show that both intermediates contain Fe(II). The lack of a chromophore characteristic of a quinone or semiquinone form of HPCA, the presence of Fe(II), and the low O(2) affinity suggest that Y257F(Int1)(HPCA) is an HPCA-Fe(II)-O(2) complex with little electron delocalization onto the O(2). In contrast, the intense spectrum of Y257F(Int2)(HPCA) suggests the intermediate is most likely an HPCA quinone-Fe(II)-(hydro)peroxo species. Steady-state and transient kinetic analyses show that steps of the catalytic cycle are slowed by as much as 100-fold by the mutation. These effects can be rationalized by a failure of Y257F to facilitate the observed distortion of the bound HPCA that is proposed to promote transfer of one electron to O(2).
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Affiliation(s)
- Michael M Mbughuni
- Department of Biochemistry, Molecular Biology and Biophysics and Center for Metals in Biocatalysis, University of Minnesota, Minneapolis, Minnesota 55455, United States
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177
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Chakraborty B, Halder P, Banerjee PR, Paine TK. Oxidative C–C Bond Cleavage of α‐Keto Acids by Cobalt(II) Complexes of Nitrogen Donor Ligands. Eur J Inorg Chem 2012. [DOI: 10.1002/ejic.201200663] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Biswarup Chakraborty
- Department of Inorganic Chemistry, Indian Association for the Cultivation of Science, 2A & 2B Raja S. C. Mullick Road, Jadavpur, Kolkata 700032, India, Fax: +91‐33‐2473‐2805
| | - Partha Halder
- Department of Inorganic Chemistry, Indian Association for the Cultivation of Science, 2A & 2B Raja S. C. Mullick Road, Jadavpur, Kolkata 700032, India, Fax: +91‐33‐2473‐2805
| | - Priya Ranjan Banerjee
- Department of Inorganic Chemistry, Indian Association for the Cultivation of Science, 2A & 2B Raja S. C. Mullick Road, Jadavpur, Kolkata 700032, India, Fax: +91‐33‐2473‐2805
| | - Tapan Kanti Paine
- Department of Inorganic Chemistry, Indian Association for the Cultivation of Science, 2A & 2B Raja S. C. Mullick Road, Jadavpur, Kolkata 700032, India, Fax: +91‐33‐2473‐2805
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178
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Huang H, Chang WC, Pai PJ, Romo A, Mansoorabadi SO, Russell DH, Liu HW. Evidence for radical-mediated catalysis by HppE: a study using cyclopropyl and methylenecyclopropyl substrate analogues. J Am Chem Soc 2012; 134:16171-4. [PMID: 23006053 PMCID: PMC3463719 DOI: 10.1021/ja3078126] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
(S)-2-Hydroxypropylphosphonic acid epoxidase (HppE) is an unusual mononuclear iron enzyme that catalyzes the oxidative epoxidation of (S)-2-hydroxypropylphosphonic acid ((S)-HPP) in the biosynthesis of the antibiotic fosfomycin. HppE also recognizes (R)-2-hydroxypropylphosphonic acid ((R)-HPP) as a substrate and converts it to 2-oxo-propylphosphonic acid. To probe the mechanisms of these HppE-catalyzed oxidations, cyclopropyl- and methylenecyclopropyl-containing compounds were synthesized and studied as radical clock substrate analogues. Enzymatic assays indicated that the (S)- and (R)-isomers of the cyclopropyl-containing analogues were efficiently converted to epoxide and ketone products by HppE, respectively. In contrast, the ultrafast methylenecyclopropyl-containing probe inactivated HppE, consistent with a rapid radical-triggered ring-opening process that leads to enzyme inactivation. Taken together, these findings provide, for the first time, experimental evidence for the involvement of a C2-centered radical intermediate with a lifetime on the order of nanoseconds in the HppE-catalyzed oxidation of (R)-HPP.
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Affiliation(s)
- Hui Huang
- Division of Medicinal Chemistry, College of Pharmacy, and Department of Chemistry and Biochemistry, University of Texas at Austin, Austin, Texas 78712, United States
| | - Wei-chen Chang
- Division of Medicinal Chemistry, College of Pharmacy, and Department of Chemistry and Biochemistry, University of Texas at Austin, Austin, Texas 78712, United States
| | - Pei-Jing Pai
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Anthony Romo
- Division of Medicinal Chemistry, College of Pharmacy, and Department of Chemistry and Biochemistry, University of Texas at Austin, Austin, Texas 78712, United States
| | - Steven O. Mansoorabadi
- Division of Medicinal Chemistry, College of Pharmacy, and Department of Chemistry and Biochemistry, University of Texas at Austin, Austin, Texas 78712, United States
| | - David H. Russell
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Hung-wen Liu
- Division of Medicinal Chemistry, College of Pharmacy, and Department of Chemistry and Biochemistry, University of Texas at Austin, Austin, Texas 78712, United States
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179
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Du L, Gao J, Liu Y, Liu C. Water-Dependent Reaction Pathways: An Essential Factor for the Catalysis in HEPD Enzyme. J Phys Chem B 2012; 116:11837-44. [DOI: 10.1021/jp305454m] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Likai Du
- Key Laboratory of Colloid and Interface Chemistry, Ministry of Education, Institute of Theoretical Chemistry, School of Chemistry & Chemical Engineering, Shandong University, Jinan, 250100, P. R. China
| | - Jun Gao
- Key Laboratory of Colloid and Interface Chemistry, Ministry of Education, Institute of Theoretical Chemistry, School of Chemistry & Chemical Engineering, Shandong University, Jinan, 250100, P. R. China
- Key Laboratory of Theoretical and Computational Chemistry in Universities of Shandong (Shandong University), Jinan, 250100, P. R. China
| | - Yongjun Liu
- Key Laboratory of Colloid and Interface Chemistry, Ministry of Education, Institute of Theoretical Chemistry, School of Chemistry & Chemical Engineering, Shandong University, Jinan, 250100, P. R. China
- Key Laboratory of Theoretical and Computational Chemistry in Universities of Shandong (Shandong University), Jinan, 250100, P. R. China
| | - Chengbu Liu
- Key Laboratory of Colloid and Interface Chemistry, Ministry of Education, Institute of Theoretical Chemistry, School of Chemistry & Chemical Engineering, Shandong University, Jinan, 250100, P. R. China
- Key Laboratory of Theoretical and Computational Chemistry in Universities of Shandong (Shandong University), Jinan, 250100, P. R. China
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180
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Structural Insight into the Prolyl Hydroxylase PHD2: A Molecular Dynamics and DFT Study. Eur J Inorg Chem 2012. [DOI: 10.1002/ejic.201200391] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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181
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Abstract
The S-oxygenation of cysteine with dioxygen to give cysteine sulfinic acid occurs at the non-heme iron active site of cysteine dioxygenase. Similar S-oxygenation events occur in other non-heme iron enzymes, including nitrile hydratase and isopenicillin N synthase, and these enzymes have inspired the development of a class of [N(x)S(y)]-Fe model complexes. Certain members of this class have provided some intriguing examples of S-oxygenation, and this article summarizes these results, focusing on the non-heme iron(II/III)-thiolate model complexes that are known to react with O(2) or other O-atom transfer oxidants to yield sulfur oxygenates. Key aspects of the synthesis, structure, and reactivity of these systems are presented, along with any mechanistic information available on the oxygenation reactions. A number of iron(III)-thiolate complexes react with O(2) to give S-oxygenates, and the degree to which the thiolate sulfur donors are oxidized varies among the different complexes, depending upon the nature of the ligand, metal geometry, and spin state. The first examples of iron(II)-thiolate complexes that react with O(2) to give selective S-oxygenation are just emerging. Mechanistic information on these transformations is limited, with isotope labeling studies providing much of the current mechanistic data. The many questions that remain unanswered for both models and enzymes provide strong motivation for future work in this area.
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Affiliation(s)
- Alison C. McQuilken
- Department of Chemistry, The Johns Hopkins University, Baltimore, Maryland 21218, USA
| | - David P. Goldberg
- Department of Chemistry, The Johns Hopkins University, Baltimore, Maryland 21218, USA
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182
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Yoshioka Y, Kosaka N, Ochiya T, Kato T. Micromanaging Iron Homeostasis: hypoxia-inducible micro-RNA-210 suppresses iron homeostasis-related proteins. J Biol Chem 2012; 287:34110-9. [PMID: 22896707 DOI: 10.1074/jbc.m112.356717] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Iron is fundamental for sustaining life for living organisms, and the iron metabolism is finely regulated at different levels. In cancer cells, deregulation of the iron metabolism induces oxidative stress and drives tumor progression and metastasis; however, the molecular mechanisms of iron homeostasis are not fully understood. Here we found that iron deficiency as well as hypoxia promoted microRNA-210 (miR-210) expression. A central mediator of miR-210 transcriptional activation is the hypoxia-inducible factor (HIF)-1α, and the hypoxia-response element in the miR-210 promoter is confirmed experimentally. This is in agreement with the data from in vivo studies that have demonstrated the presence of miR-210-expressing cells at the chronic hypoxic regions of xenografted tumors. Furthermore we found two essential molecules for iron homeostasis, iron-sulfur cluster scaffold protein (ISCU) and transferrin receptor 1 (TfR), are a direct target of miR-210. Transfection of miR-210 decreases the uptake of transferrin by inhibiting the expression of TfR. In addition, inhibition of miR-210 by anti-miR-210 up-regulates ISCU expression. These findings suggest that miR-210 works as an iron sensor and is involved in the maintenance of iron homeostasis by sustaining the TfR expression level to stimulate cell proliferation and promote cell survival in the hypoxic region within tumors.
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Affiliation(s)
- Yusuke Yoshioka
- Integrative Bioscience and Biomedical Engineering, Graduate School of Science and Engineering, Waseda University, 2-2 Wakamatsu, Shinjuku, Tokyo 162-8480, Japan
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184
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Che X, Gao J, Zhang D, Liu C. How Do the Thiolate Ligand and Its Relative Position Control the Oxygen Activation in the Cysteine Dioxygenase Model? J Phys Chem A 2012; 116:5510-7. [DOI: 10.1021/jp3001515] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Xin Che
- Key Laboratory of Colloid and Interface Chemistry, Ministry of Education, Institute of Theoretical Chemistry, School of Chemistry & Chemical Engineering, Shandong University, Jinan 250100, P. R. China
| | - Jun Gao
- Key Laboratory of Colloid and Interface Chemistry, Ministry of Education, Institute of Theoretical Chemistry, School of Chemistry & Chemical Engineering, Shandong University, Jinan 250100, P. R. China
| | - Dongju Zhang
- Key Laboratory of Colloid and Interface Chemistry, Ministry of Education, Institute of Theoretical Chemistry, School of Chemistry & Chemical Engineering, Shandong University, Jinan 250100, P. R. China
| | - Chengbu Liu
- Key Laboratory of Colloid and Interface Chemistry, Ministry of Education, Institute of Theoretical Chemistry, School of Chemistry & Chemical Engineering, Shandong University, Jinan 250100, P. R. China
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185
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Borowski T, Wójcik A, Miłaczewska A, Georgiev V, Blomberg MRA, Siegbahn PEM. The alkenyl migration mechanism catalyzed by extradiol dioxygenases: a hybrid DFT study. J Biol Inorg Chem 2012; 17:881-90. [DOI: 10.1007/s00775-012-0904-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2011] [Accepted: 05/09/2012] [Indexed: 10/28/2022]
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186
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Dke1--structure, dynamics, and function: a theoretical and experimental study elucidating the role of the binding site shape and the hydrogen-bonding network in catalysis. J Biol Inorg Chem 2012; 17:801-15. [PMID: 22526564 DOI: 10.1007/s00775-012-0898-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2011] [Accepted: 03/29/2012] [Indexed: 10/28/2022]
Abstract
This study elucidates the role of the protein structure in the catalysis of β-diketone cleavage at the three-histidine metal center of diketone cleaving enzyme (Dke1) by computational methods in correlation with kinetic and mutational analyses. Molecular dynamics simulations, using quantum mechanically deduced parameters for the nonheme Fe(II) cofactor, were performed and showed a distinct organization of the hydrophilic triad in the free and substrate-ligated wild-type enzyme. It is shown that in the free species, the Fe(II) center is coordinated to three histidines and one glutamate, whereas the substrate-ligated, catalytically competent enzyme-substrate complex has an Fe(II) center with three-histidine coordination, with a small fraction of three-histidine, one-glutamate coordination. The substrate binding modes and channels for the traffic of water and ligands (2,4-pentandionyl anion, methylglyoxal, and acetate) were identified. To characterize the impact of the hydrophobic protein environment around the metal center on catalysis, a set of hydrophobic residues close to the active site were targeted. The variations resulted in an up to tenfold decrease of the O(2) reduction rates for the mutants. Molecular dynamics studies revealed an impact of the hydrophobic residues on the substrate stabilization in the active site as well as on the orientations of Glu98 and Arg80, which have previously been shown to be crucial for catalysis. Consequently, the Glu98-His104 interaction in the variants is weaker than in the wild-type complex. The role of protein structure in stabilizing the primary O(2) reduction step in Dke1 is discussed on the basis of our results.
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187
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Nepravishta R, Polizio F, Paci M, Melino S. A metal-binding site in the RTN1-C protein: new perspectives on the physiological role of a neuronal protein. Metallomics 2012; 4:480-7. [PMID: 22522967 DOI: 10.1039/c2mt20035j] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Reticulon 1-C (RTN1-C) is an ER-associated neuronal protein characterized by horse-shoe-like topology with two transmembrane helices and the N- and C-terminal regions which are supposed in the cytosolic side of ER. The physiological role of this protein is not completely clarified, but several studies have suggested its involvement in the neuronal differentiation, membrane vesicle trafficking and induction of apoptosis. The C-terminal region of RTN1-C is characterized by the presence of a H4 histone consensus sequence that makes it able to interact with nucleic acids and HDAC enzymes both in vitro and in vivo. In the present study a potential metal ion binding motif (HxE/D) at the C-terminal of the RTN1-C has been identified and its capability to bind metals investigated by UV-vis, CD, multidimensional NMR spectroscopy and biological assays. The results suggest a possible implication of the metal ions in the mechanisms of formation of the recently observed RTNs multiprotein complexes contributing to understand the structure and function of this neuronal membrane protein, suggesting a possible effect of the metal binding property on its biological function.
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Affiliation(s)
- Ridvan Nepravishta
- Department of Sciences and Chemical Technologies, University of Rome Tor Vergata, via della Ricerca Scientifica, 00133 Rome, Italy
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188
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Li T, Huo L, Pulley C, Liu A. Decarboxylation mechanisms in biological system. Bioorg Chem 2012; 43:2-14. [PMID: 22534166 DOI: 10.1016/j.bioorg.2012.03.001] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2011] [Revised: 03/04/2012] [Accepted: 03/19/2012] [Indexed: 11/30/2022]
Abstract
This review examines the mechanisms propelling cofactor-independent, organic cofactor-dependent and metal-dependent decarboxylase chemistry. Decarboxylation, the removal of carbon dioxide from organic acids, is a fundamentally important reaction in biology. Numerous decarboxylase enzymes serve as key components of aerobic and anaerobic carbohydrate metabolism and amino acid conversion. In the past decade, our knowledge of the mechanisms enabling these crucial decarboxylase reactions has continued to expand and inspire. This review focuses on the organic cofactors biotin, flavin, NAD, pyridoxal 5'-phosphate, pyruvoyl, and thiamin pyrophosphate as catalytic centers. Significant attention is also placed on the metal-dependent decarboxylase mechanisms.
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Affiliation(s)
- Tingfeng Li
- Department of Biochemistry, University of Mississippi Medical Center, 2500 North State Street, Jackson, MS 39216, USA
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189
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Dungan VJ, Wong SM, Barry SM, Rutledge PJ. l-Proline-derived ligands to mimic the ‘2-His-1-carboxylate’ triad of the non-haem iron oxidase active site. Tetrahedron 2012. [DOI: 10.1016/j.tet.2012.02.031] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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190
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Mantri M, Zhang Z, McDonough MA, Schofield CJ. Autocatalysed oxidative modifications to 2-oxoglutarate dependent oxygenases. FEBS J 2012; 279:1563-75. [DOI: 10.1111/j.1742-4658.2012.08496.x] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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191
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McDonald AR, Guo Y, Vu VV, Bominaar EL, Münck E, Que L. A Mononuclear Carboxylate-Rich Oxoiron(IV) Complex: a Structural and Functional Mimic of TauD Intermediate 'J'. Chem Sci 2012; 3:1680-1693. [PMID: 23267430 DOI: 10.1039/c2sc01044e] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The pentadentate ligand (n)Bu-P2DA (2(b), (n)Bu-P2DA = N-(1',1'-bis(2-pyridyl)pentyl)iminodiacetate) was designed to bind an iron center in a carboxylate-rich environment similar to that found in the active sites of TauD and other α-ketoglutarate-dependent mononuclear non-heme iron enzymes. The iron(II) complex (n)Bu(4)N[Fe(II)(Cl)((n)Bu-P2DA)] (3(b)-Cl) was synthesized and crystallographically characterized to have a 2-pyridine-2-carboxylate donor set in the plane perpendicular to the Fe-Cl bond. Reaction of 3(b)-Cl with N-heterocyclic amines such as pyridine or imidazole yielded the N-heterocyclic amine adducts [Fe(II)(N)((n)Bu-P2DA)]. These adducts in turn reacted with oxo-transfer reagents at -95 °C to afford a short-lived oxoiron(IV) complex [Fe(IV)(O)((n)Bu-P2DA)] (5(b)) in yields as high as 90% depending on the heterocycle used. Complex 5(b) exhibits near-IR absorption features (λ(max) = 770 nm) and Mossbauer parameters (δ = 0.04 mm/s; ΔE(Q) = 1.13 mm/s; D = 27±2 cm(-1)) characteristic of an S = 1 oxoiron(IV) species. Direct evidence for an Fe=O bond of 1.66 Å was found from EXAFS analysis. DFT calculations on 5(b) in its S =1 spin state afforded a geometry-optimized structure consistent with the EXAFS data. They further demonstrated that the replacement of two pyridine donors in [Fe(IV)(O)(N4Py)](2+) (N4Py = N,N-(bis(2-pyridyl)methyl)N-bis(2-pyridylmethyl)amine) with carboxylate donors in 5(b) decreased the energy gap between the ground S = 1 and the excited S = 2 states, reflecting the weaker equatorial ligand field of 5(b) and accounting for its larger D value. Complex 5(b) reacted readily with dihydrotoluene, methyldiphenylphosphine and ferrocene at -60 °C, and in all cases was approximately a 5-fold more reactive oxidant than [Fe(IV)(O)(N4Py)](2+). The reactivity differences between these two complexes may arise from a combination of electronic and steric factors. Carboxylate-rich 5(b) represents the closest structural mimic reported thus far of the oxoiron(IV) intermediate ('J') found in TauD and provides us with vital insights into the role carboxylate ligands play in modulating the spectroscopic and reactivity properties of the non-heme oxoiron(IV) moiety.
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Affiliation(s)
- Aidan R McDonald
- Department of Chemistry and Center for Metals in Biocatalysis, University of Minnesota, 207 Pleasant Street S.E., Minneapolis, MN 55455
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192
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Daughtry KD, Xiao Y, Stoner-Ma D, Cho E, Orville AM, Liu P, Allen KN. Quaternary ammonium oxidative demethylation: X-ray crystallographic, resonance Raman, and UV-visible spectroscopic analysis of a Rieske-type demethylase. J Am Chem Soc 2012; 134:2823-34. [PMID: 22224443 DOI: 10.1021/ja2111898] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Herein, the structure resulting from in situ turnover in a chemically challenging quaternary ammonium oxidative demethylation reaction was captured via crystallographic analysis and analyzed via single-crystal spectroscopy. Crystal structures were determined for the Rieske-type monooxygenase, stachydrine demethylase, in the unliganded state (at 1.6 Å resolution) and in the product complex (at 2.2 Å resolution). The ligand complex was obtained from enzyme aerobically cocrystallized with the substrate stachydrine (N,N-dimethylproline). The ligand electron density in the complex was interpreted as proline, generated within the active site at 100 K by the absorption of X-ray photon energy and two consecutive demethylation cycles. The oxidation state of the Rieske iron-sulfur cluster was characterized by UV-visible spectroscopy throughout X-ray data collection in conjunction with resonance Raman spectra collected before and after diffraction data. Shifts in the absorption band wavelength and intensity as a function of absorbed X-ray dose demonstrated that the Rieske center was reduced by solvated electrons generated by X-ray photons; the kinetics of the reduction process differed dramatically for the liganded complex compared to unliganded demethylase, which may correspond to the observed turnover in the crystal.
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Affiliation(s)
- Kelly D Daughtry
- Department of Physiology and Biophysics, Boston University School of Medicine, Boston, Massachusetts 02218, USA
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193
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Structural and molecular genetic analyses of the bacterial carbazole degradation system. Biosci Biotechnol Biochem 2012; 76:1-18. [PMID: 22232235 DOI: 10.1271/bbb.110620] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Carbazole degradation by several bacterial strains, including Pseudomonas resinovorans CA10, has been investigated over the last two decades. As the initial reaction in degradation pathways, carbazole is commonly oxygenated at angular (C9a) and adjacent (C1) carbons as two hydroxyl groups in a cis configuration. This type of dioxygenation is termed "angular dioxygenation," and is catalyzed by carbazole 1,9a-dioxygenase (CARDO), consisting of terminal oxygenase, ferredoxin, and ferredoxin reductase components. The crystal structures of all components and the electron transfer complex between terminal oxygenase and ferredoxin indicate substrate recognition mechanisms suitable for angular dioxygenation and specific electron transfer among the three components. In contrast, the carbazole degradative car operon of CA10 is located on IncP-7 conjugative plasmid pCAR1. Together with conventional molecular genetic and biochemical investigations, recent genome sequencing and RNA mapping studies have clarified that transcriptional cross-regulation via nucleoid-associated proteins is established between pCAR1 and the host chromosome.
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194
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Metlitzky M, Puehringer S, J. Fisher S. Crystal structure of PqqB from <i>Pseudomonas putida</i> at 2.2 Å resolution. ACTA ACUST UNITED AC 2012. [DOI: 10.4236/jbpc.2012.32023] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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195
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Barry SM, Mueller-Bunz H, Rutledge PJ. Investigating the oxidation of alkenes by non-heme iron enzyme mimics. Org Biomol Chem 2012; 10:7372-81. [DOI: 10.1039/c2ob25834j] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
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196
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Sydor PK, Challis GL. Oxidative tailoring reactions catalyzed by nonheme iron-dependent enzymes: streptorubin B biosynthesis as an example. Methods Enzymol 2012; 516:195-218. [PMID: 23034230 DOI: 10.1016/b978-0-12-394291-3.00002-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/09/2022]
Abstract
Tailoring enzymes catalyze reactions that modify natural product backbone structures before, during, or after their biosynthesis to create a final product with specific biological activities. Such reactions can be catalyzed by a myriad of different enzyme families and are responsible for a wide variety of transformations including regio- and/or stereospecific acylation, alkylation, glycosylation, halogenation, and oxidation. Within a broad group of oxidative tailoring enzymes, there is a rapidly growing family of nonheme iron- and oxygen-dependent enzymes that catalyze a variety of remarkable hydroxylation, desaturation, halogenation, and oxidative cyclization reaction in the biosynthesis of several important metabolites, including carbapenems, penicillins, cephalosporins, clavams, prodiginines, fosfomycin, syringomycin, and coronatine. In this chapter, we report an expedient method for analyzing tailoring enzymes that catalyze oxidative cyclization reactions in prodiginine biosynthesis via expression of the corresponding genes in a heterologous host, feeding of putative biosynthetic intermediates to the resulting strains, and liquid chromatography-mass spectrometry analyses of the metabolites produced.
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Affiliation(s)
- Paulina K Sydor
- Department of Chemistry, University of Warwick, Coventry, United Kingdom
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197
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Jones MW, Baldwin JE, Cowley AR, Dilworth JR, Karpov A, Smiljanic N, Thompson AL, Adlington RM. Synthesis of new bulky bis(pyrazolyl)methane carboxylate (heteroscorpionate) ligands and their complexes with iron, manganese and nickel. Dalton Trans 2012; 41:14068-86. [DOI: 10.1039/c2dt31859h] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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198
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Clifton IJ, Ge W, Adlington RM, Baldwin JE, Rutledge PJ. The crystal structure of isopenicillin N synthase with δ-(l-α-aminoadipoyl)-l-cysteinyl-d-methionine reveals thioether coordination to iron. Arch Biochem Biophys 2011; 516:103-7. [DOI: 10.1016/j.abb.2011.09.014] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2011] [Revised: 09/28/2011] [Accepted: 09/30/2011] [Indexed: 12/01/2022]
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199
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Diebold AR, Brown-Marshall CD, Neidig ML, Brownlee JM, Moran GR, Solomon EI. Activation of α-keto acid-dependent dioxygenases: application of an {FeNO}7/{FeO2}8 methodology for characterizing the initial steps of O2 activation. J Am Chem Soc 2011; 133:18148-60. [PMID: 21981763 PMCID: PMC3212634 DOI: 10.1021/ja202549q] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The α-keto acid-dependent dioxygenases are a major subgroup within the O(2)-activating mononuclear nonheme iron enzymes. For these enzymes, the resting ferrous, the substrate plus cofactor-bound ferrous, and the Fe(IV)═O states of the reaction have been well studied. The initial O(2)-binding and activation steps are experimentally inaccessible and thus are not well understood. In this study, NO is used as an O(2) analogue to probe the effects of α-keto acid binding in 4-hydroxyphenylpyruvate dioxygenase (HPPD). A combination of EPR, UV-vis absorption, magnetic circular dichroism (MCD), and variable-temperature, variable-field (VTVH) MCD spectroscopies in conjunction with computational models is used to explore the HPPD-NO and HPPD-HPP-NO complexes. New spectroscopic features are present in the α-keto acid bound {FeNO}(7) site that reflect the strong donor interaction of the α-keto acid with the Fe. This promotes the transfer of charge from the Fe to NO. The calculations are extended to the O(2) reaction coordinate where the strong donation associated with the bound α-keto acid promotes formation of a new, S = 1 bridged Fe(IV)-peroxy species. These studies provide insight into the effects of a strong donor ligand on O(2) binding and activation by Fe(II) in the α-keto acid-dependent dioxygenases and are likely relevant to other subgroups of the O(2) activating nonheme ferrous enzymes.
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Affiliation(s)
- Adrienne R. Diebold
- Department of Chemistry, Stanford University, Stanford, California 94305, USA
| | | | - Michael L. Neidig
- Department of Chemistry, Stanford University, Stanford, California 94305, USA
| | - June M. Brownlee
- Department of Chemistry and Biochemistry, University of Wisconsin-Madison, Milwaukee, Wisconsin 53211, USA
| | - Graham R. Moran
- Department of Chemistry and Biochemistry, University of Wisconsin-Madison, Milwaukee, Wisconsin 53211, USA
| | - Edward I. Solomon
- Department of Chemistry, Stanford University, Stanford, California 94305, USA
- Stanford Synchrotron Radiation Lightsource, SLAC, Stanford, CA 94309
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200
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Mbughuni MM, Chakrabarti M, Hayden JA, Meier KK, Dalluge JJ, Hendrich MP, Münck E, Lipscomb JD. Oxy intermediates of homoprotocatechuate 2,3-dioxygenase: facile electron transfer between substrates. Biochemistry 2011; 50:10262-74. [PMID: 22011290 DOI: 10.1021/bi201436n] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Substrates homoprotocatechuate (HPCA) and O(2) bind to the Fe(II) of homoprotocatechuate 2,3-dioxygenase (FeHPCD) in adjacent coordination sites. Transfer of an electron(s) from HPCA to O(2) via the iron is proposed to activate the substrates for reaction with each other to initiate aromatic ring cleavage. Here, rapid-freeze-quench methods are used to trap and spectroscopically characterize intermediates in the reactions of the HPCA complexes of FeHPCD and the variant His200Asn (FeHPCD−HPCA and H200N−HPCA, respectively) with O(2). A blue intermediate forms within 20 ms of mixing of O(2) with H200N−HPCA (H200N(Int1)(HPCA)). Parallel mode electron paramagnetic resonance and Mössbauer spectroscopies show that this intermediate contains high-spin Fe(III) (S = 5/2) antiferromagnetically coupled to a radical (S(R) = 1/2) to yield an S = 2 state. Together, optical and Mössbauer spectra of the intermediate support assignment of the radical as an HPCA semiquinone, implying that oxygen is bound as a (hydro)peroxo ligand. H200N(Int1)(HPCA) decays over the next 2 s, possibly through an Fe(II) intermediate (H200N(Int2)(HPCA)), to yield the product and the resting Fe(II) enzyme. Reaction of FeHPCD−HPCA with O(2) results in rapid formation of a colorless Fe(II) intermediate (FeHPCD(Int1)(HPCA)). This species decays within 1 s to yield the product and the resting enzyme. The absence of a chromophore from a semiquinone or evidence of a spin-coupled species in FeHPCD(Int1)(HPCA) suggests it is an intermediate occurring after O(2) activation and attack. The similar Mössbauer parameters for FeHPCD(Int1)(HPCA) and H200N(Int2)(HPCA) suggest these are similar intermediates. The results show that transfer of an electron from the substrate to the O(2) via the iron does occur, leading to aromatic ring cleavage.
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Affiliation(s)
- Michael M Mbughuni
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota 55455, United States
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