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Krishnan A, Waheed SO, Varghese A, Cherilakkudy FH, Schofield CJ, Karabencheva-Christova TG. Unusual catalytic strategy by non-heme Fe(ii)/2-oxoglutarate-dependent aspartyl hydroxylase AspH. Chem Sci 2024; 15:3466-3484. [PMID: 38455014 PMCID: PMC10915816 DOI: 10.1039/d3sc05974j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Accepted: 02/02/2024] [Indexed: 03/09/2024] Open
Abstract
Biocatalytic C-H oxidation reactions are of important synthetic utility, provide a sustainable route for selective synthesis of important organic molecules, and are an integral part of fundamental cell processes. The multidomain non-heme Fe(ii)/2-oxoglutarate (2OG) dependent oxygenase AspH catalyzes stereoselective (3R)-hydroxylation of aspartyl- and asparaginyl-residues. Unusually, compared to other 2OG hydroxylases, crystallography has shown that AspH lacks the carboxylate residue of the characteristic two-His-one-Asp/Glu Fe-binding triad. Instead, AspH has a water molecule that coordinates Fe(ii) in the coordination position usually occupied by the Asp/Glu carboxylate. Molecular dynamics (MD) and quantum mechanics/molecular mechanics (QM/MM) studies reveal that the iron coordinating water is stabilized by hydrogen bonding with a second coordination sphere (SCS) carboxylate residue Asp721, an arrangement that helps maintain the six coordinated Fe(ii) distorted octahedral coordination geometry and enable catalysis. AspH catalysis follows a dioxygen activation-hydrogen atom transfer (HAT)-rebound hydroxylation mechanism, unusually exhibiting higher activation energy for rebound hydroxylation than for HAT, indicating that the rebound step may be rate-limiting. The HAT step, along with substrate positioning modulated by the non-covalent interactions with SCS residues (Arg688, Arg686, Lys666, Asp721, and Gln664), are essential in determining stereoselectivity, which likely proceeds with retention of configuration. The tetratricopeptide repeat (TPR) domain of AspH influences substrate binding and manifests dynamic motions during catalysis, an observation of interest with respect to other 2OG oxygenases with TPR domains. The results provide unique insights into how non-heme Fe(ii) oxygenases can effectively catalyze stereoselective hydroxylation using only two enzyme-derived Fe-ligating residues, potentially guiding enzyme engineering for stereoselective biocatalysis, thus advancing the development of non-heme Fe(ii) based biomimetic C-H oxidation catalysts, and supporting the proposal that the 2OG oxygenase superfamily may be larger than once perceived.
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Affiliation(s)
- Anandhu Krishnan
- Department of Chemistry, Michigan Technological University Houghton MI 49931 USA
| | - Sodiq O Waheed
- Department of Chemistry, Michigan Technological University Houghton MI 49931 USA
| | - Ann Varghese
- Department of Chemistry, Michigan Technological University Houghton MI 49931 USA
| | | | - Christopher J Schofield
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford OX1 3TA Oxford UK
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2
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Smithwick ER, Wilson RH, Chatterjee S, Pu Y, Dalluge JJ, Damodaran AR, Bhagi-Damodaran A. Electrostatically regulated active site assembly governs reactivity in non-heme iron halogenases. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.25.542349. [PMID: 37292651 PMCID: PMC10245910 DOI: 10.1101/2023.05.25.542349] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Non-heme iron halogenases (NHFe-Hals) catalyze the direct insertion of a chloride/bromide ion at an unactivated carbon position using a high-valent haloferryl intermediate. Despite more than a decade of structural and mechanistic characterization, how NHFe-Hals preferentially bind specific anions and substrates for C-H functionalization remains unknown. Herein, using lysine halogenating BesD and HalB enzymes as model systems, we demonstrate strong positive cooperativity between anion and substrate binding to the catalytic pocket. Detailed computational investigations indicate that a negatively charged glutamate hydrogen-bonded to iron's equatorial-aqua ligand acts as an electrostatic lock preventing both lysine and anion binding in the absence of the other. Using a combination of UV-Vis spectroscopy, binding affinity studies, stopped-flow kinetics investigations, and biochemical assays, we explore the implication of such active site assembly towards chlorination, bromination, and azidation reactivities. Overall, our work highlights previously unknown features regarding how anion-substrate pair binding govern reactivity of iron halogenases that are crucial for engineering next-generation C-H functionalization biocatalysts.
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Affiliation(s)
- Elizabeth R. Smithwick
- Department of Chemistry, University of Minnesota, Twin Cities, Minneapolis, MN 55455, USA
| | - R. Hunter Wilson
- Department of Chemistry, University of Minnesota, Twin Cities, Minneapolis, MN 55455, USA
| | - Sourav Chatterjee
- Department of Chemistry, University of Minnesota, Twin Cities, Minneapolis, MN 55455, USA
| | - Yu Pu
- Department of Chemistry, University of Minnesota, Twin Cities, Minneapolis, MN 55455, USA
| | - Joseph J. Dalluge
- Department of Chemistry, University of Minnesota, Twin Cities, Minneapolis, MN 55455, USA
| | - Anoop Rama Damodaran
- Department of Chemistry, University of Minnesota, Twin Cities, Minneapolis, MN 55455, USA
| | - Ambika Bhagi-Damodaran
- Department of Chemistry, University of Minnesota, Twin Cities, Minneapolis, MN 55455, USA
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3
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Papadopoulou A, Meyer F, Buller RM. Engineering Fe(II)/α-Ketoglutarate-Dependent Halogenases and Desaturases. Biochemistry 2023; 62:229-240. [PMID: 35446547 DOI: 10.1021/acs.biochem.2c00115] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Fe(II)/α-ketoglutarate-dependent dioxygenases (α-KGDs) are widespread enzymes in aerobic biology and serve a remarkable array of biological functions, including roles in collagen biosynthesis, plant and animal development, transcriptional regulation, nucleic acid modification, and secondary metabolite biosynthesis. This functional diversity is reflected in the enzymes' catalytic flexibility as α-KGDs can catalyze an intriguing set of synthetically valuable reactions, such as hydroxylations, halogenations, and desaturations, capturing the interest of scientists across disciplines. Mechanistically, all α-KGDs are understood to follow a similar activation pathway to generate a substrate radical, yet how individual members of the enzyme family direct this key intermediate toward the different reaction outcomes remains elusive, triggering structural, computational, spectroscopic, kinetic, and enzyme engineering studies. In this Perspective, we will highlight how first enzyme and substrate engineering examples suggest that the chemical reaction pathway within α-KGDs can be intentionally tailored using rational design principles. We will delineate the structural and mechanistic investigations of the reprogrammed enzymes and how they begin to inform about the enzymes' structure-function relationships that determine chemoselectivity. Application of this knowledge in future enzyme and substrate engineering campaigns will lead to the development of powerful C-H activation catalysts for chemical synthesis.
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Affiliation(s)
- Athena Papadopoulou
- Competence Center for Biocatalysis, Zurich University of Applied Sciences, Einsiedlerstrasse 31, 8820 Wädenswil, Switzerland
| | - Fabian Meyer
- Competence Center for Biocatalysis, Zurich University of Applied Sciences, Einsiedlerstrasse 31, 8820 Wädenswil, Switzerland
| | - Rebecca M Buller
- Competence Center for Biocatalysis, Zurich University of Applied Sciences, Einsiedlerstrasse 31, 8820 Wädenswil, Switzerland
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4
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Chan NH, Gomez CA, Vennelakanti V, Du Q, Kulik HJ, Lewis JC. Non-Native Anionic Ligand Binding and Reactivity in Engineered Variants of the Fe(II)- and α-Ketoglutarate-Dependent Oxygenase, SadA. Inorg Chem 2022; 61:14477-14485. [PMID: 36044713 PMCID: PMC9789792 DOI: 10.1021/acs.inorgchem.2c02872] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Mononuclear non-heme Fe(II)- and α-ketoglutarate-dependent oxygenases (FeDOs) catalyze a site-selective C-H hydroxylation. Variants of these enzymes in which a conserved Asp/Glu residue in the Fe(II)-binding facial triad is replaced by Ala/Gly can, in some cases, bind various anionic ligands and catalyze non-native chlorination and bromination reactions. In this study, we explore the binding of different anions to an FeDO facial triad variant, SadX, and the effects of that binding on HO• vs X• rebound. We establish not only that chloride and bromide enable non-native halogenation reactions but also that all anions investigated, including azide, cyanate, formate, and fluoride, significantly accelerate and influence the site selectivity of SadX hydroxylation catalysis. Azide and cyanate also lead to the formation of products resulting from N3•, NCO•, and OCN• rebound. While fluoride rebound is not observed, the rate acceleration provided by this ligand leads us to calculate barriers for HO• and F• rebound from a putative Fe(III)(OH)(F) intermediate. These calculations suggest that the lack of fluorination is due to the relative barriers of the HO• and F• rebound transition states rather than an inaccessible barrier for F• rebound. Together, these results improve our understanding of the FeDO facial triad variant tolerance of different anionic ligands, their ability to promote rebound involving these ligands, and inherent rebound preferences relative to HO• that will aid efforts to develop non-native catalysis using these enzymes.
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Affiliation(s)
- Natalie H. Chan
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, USA
| | - Christian A. Gomez
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, USA
| | - Vyshnavi Vennelakanti
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Qian Du
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, USA
| | - Heather J. Kulik
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Jared C. Lewis
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, USA
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5
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Neugebauer ME, Kissman EN, Marchand JA, Pelton JG, Sambold NA, Millar DC, Chang MCY. Reaction pathway engineering converts a radical hydroxylase into a halogenase. Nat Chem Biol 2021; 18:171-179. [PMID: 34937913 DOI: 10.1038/s41589-021-00944-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Accepted: 10/27/2021] [Indexed: 12/16/2022]
Abstract
FeII/α-ketoglutarate (FeII/αKG)-dependent enzymes offer a promising biocatalytic platform for halogenation chemistry owing to their ability to functionalize unactivated C-H bonds. However, relatively few radical halogenases have been identified to date, limiting their synthetic utility. Here, we report a strategy to expand the palette of enzymatic halogenation by engineering a reaction pathway rather than substrate selectivity. This approach could allow us to tap the broader class of FeII/αKG-dependent hydroxylases as catalysts by their conversion to halogenases. Toward this goal, we discovered active halogenases from a DNA shuffle library generated from a halogenase-hydroxylase pair using a high-throughput in vivo fluorescent screen coupled to an alkyne-producing biosynthetic pathway. Insights from sequencing halogenation-active variants along with the crystal structure of the hydroxylase enabled engineering of a hydroxylase to perform halogenation with comparable activity and higher selectivity than the wild-type halogenase, showcasing the potential of harnessing hydroxylases for biocatalytic halogenation.
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Affiliation(s)
- Monica E Neugebauer
- Department of Chemical & Biomolecular Engineering, University of California, Berkeley, Berkeley, CA, USA
| | - Elijah N Kissman
- Department of Chemistry, University of California, Berkeley, Berkeley, CA, USA
| | - Jorge A Marchand
- Department of Chemical & Biomolecular Engineering, University of California, Berkeley, Berkeley, CA, USA
| | - Jeffrey G Pelton
- QB3 Institute, University of California, Berkeley, Berkeley, CA, USA
| | - Nicholas A Sambold
- Department of Molecular & Cell Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Douglas C Millar
- Department of Chemical & Biomolecular Engineering, University of California, Berkeley, Berkeley, CA, USA
| | - Michelle C Y Chang
- Department of Chemical & Biomolecular Engineering, University of California, Berkeley, Berkeley, CA, USA. .,Department of Chemistry, University of California, Berkeley, Berkeley, CA, USA. .,Department of Molecular & Cell Biology, University of California, Berkeley, Berkeley, CA, USA.
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6
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Greve JM, Pinkham AM, Thompson Z, Cowan JA. Active site characterization and activity of the human aspartyl (asparaginyl) β-hydroxylase. Metallomics 2021; 13:6372921. [PMID: 34543426 DOI: 10.1093/mtomcs/mfab056] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Accepted: 09/06/2021] [Indexed: 01/18/2023]
Abstract
Human aspartyl/asparaginyl beta-hydroxylase (HAAH) is a member of the superfamily of nonheme Fe2+/α-ketoglutarate (αKG) dependent oxygenase enzymes with a noncanonical active site. HAAH hydroxylates epidermal growth factor (EGF) like domains to form the β-hydroxylated product from substrate asparagine or aspartic acid and has been suggested to have a negative impact in a variety of cancers. In addition to iron, HAAH also binds divalent calcium, although the role of the latter is not understood. Herein, the metal binding chemistry and influence on enzyme stability and activity have been evaluated by a combined biochemical and biophysical approach. Metal binding parameters for the HAAH active site were determined by use of isothermal titration calorimetry, demonstrating a high-affinity regulatory binding site for Ca2+ in the catalytic domain in addition to the catalytic Fe2+ cofactor. We have analyzed various active site derivatives, utilizing LC-MS and a new HPLC technique to determine the role of metal binding and the second coordination sphere in enzyme activity, discovering a previously unreported residue as vital for HAAH turnover. This analysis of the in vitro biochemical function of HAAH furthers the understanding of its importance to cellular biochemistry and metabolic pathways.
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Affiliation(s)
- Jenna M Greve
- Department of Chemistry and Biochemistry, The Ohio State University, 100 West 18th Avenue, Columbus, OH 43210, USA
| | - Andrew M Pinkham
- Department of Chemistry and Biochemistry, The Ohio State University, 100 West 18th Avenue, Columbus, OH 43210, USA
| | - Zechariah Thompson
- Department of Chemistry and Biochemistry, The Ohio State University, 100 West 18th Avenue, Columbus, OH 43210, USA
| | - J A Cowan
- Department of Chemistry and Biochemistry, The Ohio State University, 100 West 18th Avenue, Columbus, OH 43210, USA
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7
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Papadopoulou A, Meierhofer J, Meyer F, Hayashi T, Schneider S, Sager E, Buller R. Re‐Programming and Optimization of a
L
‐Proline
cis
‐4‐Hydroxylase for the
cis
‐3‐Halogenation of its Native Substrate. ChemCatChem 2021. [DOI: 10.1002/cctc.202100591] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Athena Papadopoulou
- Competence Center for Biocatalysis Institute of Chemistry and Biotechnology Zurich University of Applied Sciences 8820 Wädenswil Switzerland
| | - Jasmin Meierhofer
- Competence Center for Biocatalysis Institute of Chemistry and Biotechnology Zurich University of Applied Sciences 8820 Wädenswil Switzerland
| | - Fabian Meyer
- Competence Center for Biocatalysis Institute of Chemistry and Biotechnology Zurich University of Applied Sciences 8820 Wädenswil Switzerland
| | - Takahiro Hayashi
- Competence Center for Biocatalysis Institute of Chemistry and Biotechnology Zurich University of Applied Sciences 8820 Wädenswil Switzerland
- Current address: Science & Innovation Center Mitsubishi Chemical Corporation Yokohama Kanagawa 227-8502 Japan
| | - Samuel Schneider
- Competence Center for Biocatalysis Institute of Chemistry and Biotechnology Zurich University of Applied Sciences 8820 Wädenswil Switzerland
| | - Emine Sager
- Novartis Institutes for BioMedical Research Global Discovery Chemistry 4056 Basel Switzerland
| | - Rebecca Buller
- Competence Center for Biocatalysis Institute of Chemistry and Biotechnology Zurich University of Applied Sciences 8820 Wädenswil Switzerland
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8
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Copeland RA, Davis KM, Shoda TKC, Blaesi EJ, Boal AK, Krebs C, Bollinger JM. An Iron(IV)-Oxo Intermediate Initiating l-Arginine Oxidation but Not Ethylene Production by the 2-Oxoglutarate-Dependent Oxygenase, Ethylene-Forming Enzyme. J Am Chem Soc 2021; 143:2293-2303. [PMID: 33522811 DOI: 10.1021/jacs.0c10923] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Ethylene-forming enzyme (EFE) is an ambifunctional iron(II)- and 2-oxoglutarate-dependent (Fe/2OG) oxygenase. In its major (EF) reaction, it converts carbons 1, 2, and 5 of 2OG to CO2 and carbons 3 and 4 to ethylene, a four-electron oxidation drastically different from the simpler decarboxylation of 2OG to succinate mediated by all other Fe/2OG enzymes. EFE also catalyzes a minor reaction, in which the normal decarboxylation is coupled to oxidation of l-arginine (a required activator for the EF pathway), resulting in its conversion to l-glutamate semialdehyde and guanidine. Here we show that, consistent with precedent, the l-Arg-oxidation (RO) pathway proceeds via an iron(IV)-oxo (ferryl) intermediate. Use of 5,5-[2H2]-l-Arg slows decay of the ferryl complex by >16-fold, implying that RO is initiated by hydrogen-atom transfer (HAT) from C5. That this large substrate deuterium kinetic isotope effect has no impact on the EF:RO partition ratio implies that the same ferryl intermediate cannot be on the EF pathway; the pathways must diverge earlier. Consistent with this conclusion, the variant enzyme bearing the Asp191Glu ligand substitution accumulates ∼4 times as much of the ferryl complex as the wild-type enzyme and exhibits a ∼40-fold diminished EF:RO partition ratio. The selective detriment of this nearly conservative substitution to the EF pathway implies that it has unusually stringent stereoelectronic requirements. An active-site, like-charge guanidinium pair, which involves the l-Arg substrate/activator and is unique to EFE among four crystallographically characterized l-Arg-modifying Fe/2OG oxygenases, may serve to selectively stabilize the transition state leading to the unique EF branch.
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9
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Menon BRK, Richmond D, Menon N. Halogenases for biosynthetic pathway engineering: Toward new routes to naturals and non-naturals. CATALYSIS REVIEWS-SCIENCE AND ENGINEERING 2020. [DOI: 10.1080/01614940.2020.1823788] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Binuraj R. K. Menon
- Warwick Integrative Synthetic Biology Centre, School of Life Sciences, University of Warwick, Coventry, UK
| | - Daniel Richmond
- Warwick Integrative Synthetic Biology Centre, School of Life Sciences, University of Warwick, Coventry, UK
| | - Navya Menon
- Warwick Integrative Synthetic Biology Centre, School of Life Sciences, University of Warwick, Coventry, UK
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10
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Exploring the Biocatalytic Potential of Fe/α‐Ketoglutarate‐Dependent Halogenases. Chemistry 2020; 26:7336-7345. [DOI: 10.1002/chem.201905752] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Indexed: 12/18/2022]
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11
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John CW, Hausinger RP, Proshlyakov DA. Structural Origin of the Large Redox-Linked Reorganization in the 2-Oxoglutarate Dependent Oxygenase, TauD. J Am Chem Soc 2019; 141:15318-15326. [PMID: 31475523 PMCID: PMC7092798 DOI: 10.1021/jacs.9b07493] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
2-Oxoglutarate (2OG)-dependent oxygenases catalyze a wide range of chemical transformations via C-H bond activation. Prior studies raised the question of whether substrate hydroxylation by these enzymes occurs via a hydroxyl rebound or alkoxide mechanism and highlighted the need to understand the thermodynamic properties of transient intermediates. A recent spectroelectrochemical investigation of the 2OG-dependent oxygenase, taurine hydroxylase (TauD), revealed a strong link between the redox potential of the Fe(II)/Fe(III) couple and conformational changes of the enzyme. In this study, we show that the redox potential of wild-type TauD varies by 468 mV between the reduction of 2OG-Fe(III)-TauD (-272 mV) and oxidation of 2OG-Fe(II)-TauD (+196 mV). We use active site variants to investigate the structural origin of the redox-linked reorganization and the contributions of the metal-bound residues to the dynamic tuning of the redox potential of TauD. Time-dependent redox titrations show that reorganization occurs as a multistep process. Transient optical absorption and infrared spectroelectrochemistry show that substitution of any metal ligand alters the kinetics and thermodynamics of the reorganization. The H99A variant shows the largest net redox change relative to the wild-type protein, suggesting that redox-coupled protonation of H99 is required for high redox potentials of the metal. The D101Q and H255Q variants also suppress the conformational change, supporting their involvement in the structural rearrangement. Similar redox-linked conformational changes are observed in another 2OG dependent oxygenase, ethylene-forming enzyme, indicating that dynamic structural flexibility and the associated thermodynamic tuning may be a common phenomenon in this family of enzymes.
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Affiliation(s)
- Christopher W. John
- Department of Chemistry, Michigan State University, East Lansing, Michigan 48824, United States
| | - Robert P. Hausinger
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan 48824, United States
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824, United States
| | - Denis A. Proshlyakov
- Department of Chemistry, Michigan State University, East Lansing, Michigan 48824, United States
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12
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Chaplin VD, Hangasky JA, Huang HT, Duan R, Maroney MJ, Knapp MJ. Chloride Supports O 2 Activation in the D201G Facial Triad Variant of Factor-Inhibiting Hypoxia Inducible Factor, an α-Ketoglutarate Dependent Oxygenase. Inorg Chem 2018; 57:12588-12595. [PMID: 30252455 DOI: 10.1021/acs.inorgchem.8b01736] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
α-Ketoglutarate (αKG) dependent oxygenases comprise a large superfamily of enzymes that activate O2 for varied reactions. While most of these enzymes contain a nonheme Fe bound by a His2(Asp/Glu) facial triad, a small number of αKG-dependent halogenases require only the two His ligands to bind Fe and activate O2. The enzyme "factor inhibiting HIF" (FIH) contains a His2Asp facial triad and selectively hydroxylates polypeptides; however, removal of the Asp ligand in the Asp201→Gly variant leads to a highly active enzyme, seemingly without a complete facial triad. Herein, we report on the formation of an Fe-Cl cofactor structure for the Asp201→Gly FIH variant using X-ray absorption spectroscopy (XAS), which provides insight into the structure of the His2Cl facial triad found in halogenases. The Asp201→Gly variant supports anion dependent peptide hydroxylation, demonstrating the requirement for a complete His2X facial triad to support O2 reactivity. Our results indicated that exogenous ligand binding to form a complete His2X facial triad was essential for O2 activation and provides a structural model for the His2Cl-bound nonheme Fe found in halogenases.
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Affiliation(s)
- Vanessa D Chaplin
- Department of Chemistry , University of Massachusetts at Amherst , Amherst , Massachusetts 01003 , United States
| | - John A Hangasky
- Department of Chemistry , University of Massachusetts at Amherst , Amherst , Massachusetts 01003 , United States
| | - Hsin-Ting Huang
- Department of Chemistry , University of Massachusetts at Amherst , Amherst , Massachusetts 01003 , United States
| | - Ran Duan
- Department of Chemistry , University of Massachusetts at Amherst , Amherst , Massachusetts 01003 , United States
| | - Michael J Maroney
- Department of Chemistry , University of Massachusetts at Amherst , Amherst , Massachusetts 01003 , United States
| | - Michael J Knapp
- Department of Chemistry , University of Massachusetts at Amherst , Amherst , Massachusetts 01003 , United States
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13
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Liu X. In Vitro Analysis of Cyanobacterial Nonheme Iron-Dependent Aliphatic Halogenases WelO5 and AmbO5. Methods Enzymol 2018; 604:389-404. [PMID: 29779660 DOI: 10.1016/bs.mie.2018.02.015] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Aliphatic carbon-halogen (C-X) bonds are prevalent in modern pharmaceuticals and bioactive natural products. Three distinct chemical strategies are known in Nature to generate these structural motifs. The first is via the nucleophilic substitution at a prefunctionalized electrophilic carbon center with a halide anion (X-), known for the S-adenosyl-l-methionine-dependent halogenases. The second is via the electrophilic activation of an alkene or its equivalent by a halenium ion (X+) donor, known for the haloperoxidases and flavin-dependent halogenases. The third is via the direct functionalization of an unactivated aliphatic C-H bond with a halogen radical (X) equivalent, known for the 2-oxo-glutarate and nonheme iron-dependent halogenases. Due to the ubiquitous nature of aliphatic C-H groups in organic molecules, transformations that permit chemo-, regio-, and stereo-selective modification(s) at an unactivated sp3-carbon center have been a long sought-after goal in chemical science. Two nonheme iron-dependent halogenases, WelO5 and AmbO5 involved in the biogenesis of cyanobacterial hapalindole-type alkaloids, have been recently shown able to perform this type of challenging transformation. In this chapter, experimental details for the in vitro reconstitution of WelO5 and AmbO5 enzymatic activities are presented.
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Affiliation(s)
- Xinyu Liu
- University of Pittsburgh, Pittsburgh, PA, United States.
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14
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Martinez S, Fellner M, Herr CQ, Ritchie A, Hu J, Hausinger RP. Structures and Mechanisms of the Non-Heme Fe(II)- and 2-Oxoglutarate-Dependent Ethylene-Forming Enzyme: Substrate Binding Creates a Twist. J Am Chem Soc 2017; 139:11980-11988. [PMID: 28780854 PMCID: PMC5599930 DOI: 10.1021/jacs.7b06186] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The ethylene-forming enzyme (EFE) from Pseudomonas syringae pv. phaseolicola PK2 is a member of the mononuclear nonheme Fe(II)- and 2-oxoglutarate (2OG)-dependent oxygenase superfamily. EFE converts 2OG into ethylene plus three CO2 molecules while also catalyzing the C5 hydroxylation of l-arginine (l-Arg) driven by the oxidative decarboxylation of 2OG to form succinate and CO2. Here we report 11 X-ray crystal structures of EFE that provide insight into the mechanisms of these two reactions. Binding of 2OG in the absence of l-Arg resulted in predominantly monodentate metal coordination, distinct from the typical bidentate metal-binding species observed in other family members. Subsequent addition of l-Arg resulted in compression of the active site, a conformational change of the carboxylate side chain metal ligand to allow for hydrogen bonding with the substrate, and creation of a twisted peptide bond involving this carboxylate and the following tyrosine residue. A reconfiguration of 2OG achieves bidentate metal coordination. The dioxygen binding site is located on the metal face opposite to that facing l-Arg, thus requiring reorientation of the generated ferryl species to catalyze l-Arg hydroxylation. Notably, a phenylalanyl side chain pointing toward the metal may hinder such a ferryl flip and promote ethylene formation. Extensive site-directed mutagenesis studies supported the importance of this phenylalanine and confirmed the essential residues used for substrate binding and catalysis. The structural and functional characterization described here suggests that conversion of 2OG to ethylene, atypical among Fe(II)/2OG oxygenases, is facilitated by the binding of l-Arg which leads to an altered positioning of the carboxylate metal ligand, a resulting twisted peptide bond, and the off-line geometry for dioxygen coordination.
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Affiliation(s)
- Salette Martinez
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan 48824
| | - Matthias Fellner
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824
| | - Caitlyn Q Herr
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824
| | - Anastasia Ritchie
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan 48824
| | - Jian Hu
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824
- Department of Chemistry, Michigan State University, East Lansing, Michigan 48824
| | - Robert P. Hausinger
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan 48824
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824
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15
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Mitchell AJ, Dunham NP, Bergman JA, Wang B, Zhu Q, Chang WC, Liu X, Boal AK. Structure-Guided Reprogramming of a Hydroxylase To Halogenate Its Small Molecule Substrate. Biochemistry 2017; 56:441-444. [PMID: 28029241 DOI: 10.1021/acs.biochem.6b01173] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Enzymatic installation of chlorine/bromine into unactivated carbon centers provides a versatile, selective, and environmentally friendly alternative to chemical halogenation. Iron(II) and 2-(oxo)-glutarate (FeII/2OG)-dependent halogenases are powerful biocatalysts that are capable of cleaving aliphatic C-H bonds to introduce useful functional groups, including halogens. Using the structure of the Fe/2OG halogenase, WelO5, in complex with its small molecule substrate, we identified a similar N-acyl amino acid hydroxylase, SadA, and reprogrammed it to halogenate its substrate, thereby generating a new chiral haloalkyl center. The work highlights the potential of FeII/2OG enzymes as platforms for development of novel stereospecific catalysts for late-stage C-H functionalization.
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Affiliation(s)
| | | | | | | | - Qin Zhu
- Department of Chemistry, University of Pittsburgh , Pittsburgh, Pennsylvania 15260, United States
| | | | - Xinyu Liu
- Department of Chemistry, University of Pittsburgh , Pittsburgh, Pennsylvania 15260, United States
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16
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Jakubczyk D, Caputi L, Stevenson CEM, Lawson DM, O'Connor SE. Structural characterization of EasH (Aspergillus japonicus) - an oxidase involved in cycloclavine biosynthesis. Chem Commun (Camb) 2016; 52:14306-14309. [PMID: 27885368 PMCID: PMC5317212 DOI: 10.1039/c6cc08438a] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2016] [Accepted: 11/22/2016] [Indexed: 01/08/2023]
Abstract
Aj_EasH is a non-heme iron- and α-keto-glutarate-dependent oxidase that is responsible for an unusual cyclopropyl ring formation in the biosynthesis of the fungal ergot alkaloid cycloclavine. The three dimensional structure of Aj_EasH (2.2 Å resolution) reported here provides insight into the mechanism of this unusual and complex reaction.
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Affiliation(s)
- Dorota Jakubczyk
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK.
| | - Lorenzo Caputi
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK.
| | - Clare E M Stevenson
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK.
| | - David M Lawson
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK.
| | - Sarah E O'Connor
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK.
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17
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Proshlyakov DA, McCracken J, Hausinger RP. Spectroscopic analyses of 2-oxoglutarate-dependent oxygenases: TauD as a case study. J Biol Inorg Chem 2016; 22:367-379. [PMID: 27812832 DOI: 10.1007/s00775-016-1406-3] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2016] [Accepted: 10/25/2016] [Indexed: 11/28/2022]
Abstract
A wide range of spectroscopic approaches have been used to interrogate the mononuclear iron metallocenter in 2-oxoglutarate (2OG)-dependent oxygenases. The results from these spectroscopic studies have provided valuable insights into the structural changes at the active site during substrate binding and catalysis, thus providing critical information that complements investigations of these enzymes by X-ray crystallography, biochemical, and computational approaches. This mini-review highlights taurine hydroxylase (taurine:2OG dioxygenase, TauD) as a case study to illustrate the wealth of knowledge that can be generated by applying a diverse array of spectroscopic investigations to a single enzyme. In particular, electronic absorption, circular dichroism, magnetic circular dichroism, conventional and pulse electron paramagnetic, Mössbauer, X-ray absorption, and resonance Raman methods have been exploited to uncover the properties of the metal site in TauD.
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Affiliation(s)
- Denis A Proshlyakov
- Department of Chemistry, Michigan State University, East Lansing, MI, 48824, USA
| | - John McCracken
- Department of Chemistry, Michigan State University, East Lansing, MI, 48824, USA
| | - Robert P Hausinger
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, 48824, USA. .,Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, 48824, USA.
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18
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The different catalytic roles of the metal-binding ligands in human 4-hydroxyphenylpyruvate dioxygenase. Biochem J 2016; 473:1179-89. [PMID: 26936969 DOI: 10.1042/bcj20160146] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Accepted: 03/02/2016] [Indexed: 11/17/2022]
Abstract
4-Hydroxyphenylpyruvate dioxygenase (HPPD) is a non-haem iron(II)-dependent oxygenase that catalyses the conversion of 4-hydroxyphenylpyruvate (HPP) to homogentisate (HG). In the active site, a strictly conserved 2-His-1-Glu facial triad co-ordinates the iron ready for catalysis. Substitution of these residues resulted in about a 10-fold decrease in the metal binding affinity, as measured by isothermal titration calorimetry, and a large reduction in enzyme catalytic efficiencies. The present study revealed the vital role of the ligand Glu(349) in enzyme function. Replacing this residue with alanine resulted in loss of activity. The E349G variant retained 5% activity for the coupled reaction, suggesting that co-ordinating water may be able to support activation of the trans-bound dioxygen upon substrate binding. The reaction catalysed by the H183A variant was fully uncoupled. H183A variant catalytic activity resulted in protein cleavage between Ile(267) and Ala(268) and the production of an N-terminal fragment. The H266A variant was able to produce 4-hydroxyphenylacetate (HPA), demonstrating that decarboxylation had occurred but that there was no subsequent product formation. Structural modelling of the variant enzyme with bound dioxygen revealed the rearrangement of the co-ordination environment and the dynamic behaviour of bound dioxygen in the H266A and H183A variants respectively. These models suggest that the residues regulate the geometry of the reactive oxygen intermediate during the oxidation reaction. The mutagenesis and structural simulation studies demonstrate the critical and unique role of each ligand in the function of HPPD, and which correlates with their respective co-ordination position.
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19
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Kim YJ, Wu W, Chun SE, Whitacre JF, Bettinger CJ. Catechol-mediated reversible binding of multivalent cations in eumelanin half-cells. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2014; 26:6572-6579. [PMID: 25155817 DOI: 10.1002/adma.201402295] [Citation(s) in RCA: 64] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2014] [Revised: 07/19/2014] [Indexed: 06/03/2023]
Abstract
Electrochemical storage systems that utilize divalent cations such as Mg2+ can improve the volumetric charge storage capacities compared to those that use monovalent ions. Here, a cathode based on naturally derived melanin pigments is used in secondary Mg2+ batteries. Redox active catechol groups in melanins permit efficient and reversible exchange of divalent Mg2+ cations to preserve charge storage capacity in biopolymer cathodes for more than 500 cycles.
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Affiliation(s)
- Young Jo Kim
- Department of Materials Science and Engineering, Carnegie Mellon University, Pittsburgh, PA, 15213, USA
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20
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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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21
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Kulik HJ, Drennan CL. Substrate placement influences reactivity in non-heme Fe(II) halogenases and hydroxylases. J Biol Chem 2013; 288:11233-41. [PMID: 23449977 DOI: 10.1074/jbc.m112.415570] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
We employ error-corrected density functional theory methods to map out the dependence of reactivity on substrate position for SyrB2, a member of a family of non-heme iron halogenases and hydroxylases that are only reactive toward amino acid substrates delivered via prosthetic phosphopantetheine arms. For the initial hydrogen abstraction step, the inherent flexibility of the phosphopantetheine molecule weakens the position dependence for both the native substrate (threonine for SyrB2) and alternative substrates. Over a 5 Å window of substrate positions, the tethered hydrogen abstraction step proceeds with nearly identical activation energies and donor-acceptor distances in the transition state. The propensity of a particular substrate toward halogenation or hydroxylation is found to depend strongly on the substrate placement following hydrogen abstraction, with deeper substrate delivery into the active (for native substrates) site favoring halogenation and shallower substrate delivery favoring hydroxylation.
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Affiliation(s)
- Heather J Kulik
- Department of Chemistry, Stanford University, Stanford, California 94305, USA
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22
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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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23
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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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24
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Crawford JA, Li W, Pierce BS. Single turnover of substrate-bound ferric cysteine dioxygenase with superoxide anion: enzymatic reactivation, product formation, and a transient intermediate. Biochemistry 2011; 50:10241-53. [PMID: 21992268 DOI: 10.1021/bi2011724] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Cysteine dioxygenase (CDO) is a non-heme mononuclear iron enzyme that catalyzes the O(2)-dependent oxidation of L-cysteine (Cys) to produce cysteine sulfinic acid (CSA). In this study we demonstrate that the catalytic cycle of CDO can be "primed" by one electron through chemical oxidation to produce CDO with ferric iron in the active site (Fe(III)-CDO, termed 2). While catalytically inactive, the substrate-bound form of Fe(III)-CDO (2a) is more amenable to interrogation by UV-vis and EPR spectroscopy than the 'as-isolated' Fe(II)-CDO enzyme (1). Chemical-rescue experiments were performed in which superoxide (O(2)(•-)) anions were introduced to 2a to explore the possibility that a Fe(III)-superoxide species represents the first intermediate within the catalytic pathway of CDO. In principle, O(2)(•-) can serve as a suitable acceptor for the remaining 3-electrons necessary for CSA formation and regeneration of the active Fe(II)-CDO enzyme (1). Indeed, addition of O(2)(•-) to 2a resulted in the rapid formation of a transient species (termed 3a) observable at 565 nm by UV-vis spectroscopy. The subsequent decay of 3a is kinetically matched to CSA formation. Moreover, a signal attributed to 3a was also identified using parallel mode X-band EPR spectroscopy (g ~ 11). Spectroscopic simulations, observed temperature dependence, and the microwave power saturation behavior of 3a are consistent with a ground state S = 3 from a ferromagnetically coupled (J ~ -8 cm(-1)) high-spin ferric iron (S(A) = 5/2) with a bound radical (S(B) = 1/2), presumably O(2)(•-). Following treatment with O(2)(•-), the specific activity of recovered CDO increased to ~60% relative to untreated enzyme.
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Affiliation(s)
- Joshua A Crawford
- Department of Chemistry and Biochemistry, College of Sciences, The University of Texas at Arlington, Arlington, Texas 76019, United States
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25
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Di Giuro CML, Buongiorno D, Leitner E, Straganz GD. Exploring the catalytic potential of the 3-His mononuclear nonheme Fe(II) center: discovery and characterization of an unprecedented maltol cleavage activity. J Inorg Biochem 2011; 105:1204-11. [PMID: 21718656 DOI: 10.1016/j.jinorgbio.2011.05.018] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2011] [Revised: 05/24/2011] [Accepted: 05/26/2011] [Indexed: 11/16/2022]
Abstract
Mononuclear nonheme iron enzymes (MNHEs) catalyze a range of very diverse reactions in O(2) metabolism, but they share a common principle active-site organization. To investigate a putative catalytic promiscuity of these enzymatic metal centers, we studied the reactivity of the 3-His ligated metal center of diketone cleaving enzyme (Dke1) toward non-native substrates, with a focus on alternative O(2) dependent reactions. From a screening approach, which aims at eliminating steric factors by including minimal substrate-substructures, three alternative, 'non-β-dicarbonyl-cleavage' reactions are identified, among them an unprecedented oxygenation of maltol. Maltol cleavage is characterized by steady state and fast kinetic measurements and shows an O(2) concentration dependent rate determining step k(cat)/K(M)(O(2)) of 0.3mM(-1)s(-1) and a strict coupling of O(2) reduction and substrate oxidation. Furthermore, the catalytic potential of the 3-His metal center for O(2) dependent catechol ring-cleavage and phenylpyruvate oxidation (PP) is demonstrated.
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Affiliation(s)
- Cristiana M L Di Giuro
- Institute for Biotechnology and Biochemical Engineering, Graz University of Technology, Petersgasse 12, A-8010 Graz, Austria
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26
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Gattis SG, Hernick M, Fierke CA. Active site metal ion in UDP-3-O-((R)-3-hydroxymyristoyl)-N-acetylglucosamine deacetylase (LpxC) switches between Fe(II) and Zn(II) depending on cellular conditions. J Biol Chem 2010; 285:33788-96. [PMID: 20709752 DOI: 10.1074/jbc.m110.147173] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
UDP-3-O-((R)-3-hydroxymyristoyl)-N-acetylglucosamine deacetylase (LpxC) catalyzes the deacetylation of UDP-3-O-((R)-3-hydroxymyristoyl)-N-acetylglucosamine to form UDP-3-O-myristoylglucosamine and acetate in Gram-negative bacteria. This second, and committed, step in lipid A biosynthesis is a target for antibiotic development. LpxC was previously identified as a mononuclear Zn(II) metalloenzyme; however, LpxC is 6-8-fold more active with the oxygen-sensitive Fe(II) cofactor (Hernick, M., Gattis, S. G., Penner-Hahn, J. E., and Fierke, C. A. (2010) Biochemistry 49, 2246-2255). To analyze the native metal cofactor bound to LpxC, we developed a pulldown method to rapidly purify tagged LpxC under anaerobic conditions. The metal bound to LpxC purified from Escherichia coli grown in minimal medium is mainly Fe(II). However, the ratio of iron/zinc bound to LpxC varies with the metal content of the medium. Furthermore, the iron/zinc ratio bound to native LpxC, determined by activity assays, has a similar dependence on the growth conditions. LpxC has significantly higher affinity for Zn(II) compared with Fe(II) with K(D) values of 60 ± 20 pM and 110 ± 40 nM, respectively. However, in vivo concentrations of readily exchangeable iron are significantly higher than zinc, suggesting that Fe(II) is the thermodynamically favored metal cofactor for LpxC under cellular conditions. These data indicate that LpxC expressed in E. coli grown in standard medium predominantly exists as the Fe(II)-enzyme. However, the metal cofactor in LpxC can switch between iron and zinc in response to perturbations in available metal ions. This alteration may be important for regulating the LpxC activity upon changes in environmental conditions and may be a general mechanism of regulating the activity of metalloenzymes.
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Affiliation(s)
- Samuel G Gattis
- Departments of Biological Chemistry, University of Michigan, Ann Arbor, Michigan 48109, USA
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27
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Grzyska PK, Hausinger RP, Proshlyakov DA. Metal and substrate binding to an Fe(II) dioxygenase resolved by UV spectroscopy with global regression analysis. Anal Biochem 2009; 399:64-71. [PMID: 19932076 DOI: 10.1016/j.ab.2009.11.022] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2009] [Revised: 11/09/2009] [Accepted: 11/14/2009] [Indexed: 11/15/2022]
Abstract
The addition of divalent metal ions or substrate taurine to TauD, an alpha-ketoglutarate-dependent dioxygenase, alters its UV absorption, as clearly observed by monitoring the protein's difference spectra. Binding of metal ions leads to a decrease in absorption at approximately 297 nm and modulation of other features. A separate signature with enhanced absorption at approximately 295 nm is identified for binding of taurine. These narrow ( approximately 700 cm(-1)) and intense ( approximately 0.5mM(-1) cm(-1)) spectral changes are attributed to ligand-induced protein conformational changes affecting the environment of aromatic residues. The changes in the UV difference spectra were exploited to assess directly the thermodynamics and kinetics of ligand interactions in wild-type TauD and selected variants. This approach holds promise as a new tool to probe ligand-induced conformational changes in a wide range of other proteins. Experimental and quantification approaches for a reliable analysis of protein absorption below 320 nm are presented.
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Affiliation(s)
- Piotr K Grzyska
- Department of Biochemistry & Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
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28
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Gorres KL, Pua KH, Raines RT. Stringency of the 2-His-1-Asp active-site motif in prolyl 4-hydroxylase. PLoS One 2009; 4:e7635. [PMID: 19890397 PMCID: PMC2767507 DOI: 10.1371/journal.pone.0007635] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2009] [Accepted: 10/06/2009] [Indexed: 11/18/2022] Open
Abstract
The non-heme iron(II) dioxygenase family of enzymes contain a common 2-His-1-carboxylate iron-binding motif. These enzymes catalyze a wide variety of oxidative reactions, such as the hydroxylation of aliphatic C-H bonds. Prolyl 4-hydroxylase (P4H) is an alpha-ketoglutarate-dependent iron(II) dioxygenase that catalyzes the post-translational hydroxylation of proline residues in protocollagen strands, stabilizing the ensuing triple helix. Human P4H residues His412, Asp414, and His483 have been identified as an iron-coordinating 2-His-1-carboxylate motif. Enzymes that catalyze oxidative halogenation do so by a mechanism similar to that of P4H. These halogenases retain the active-site histidine residues, but the carboxylate ligand is replaced with a halide ion. We replaced Asp414 of P4H with alanine (to mimic the active site of a halogenase) and with glycine. These substitutions do not, however, convert P4H into a halogenase. Moreover, the hydroxylase activity of D414A P4H cannot be rescued with small molecules. In addition, rearranging the two His and one Asp residues in the active site eliminates hydroxylase activity. Our results demonstrate a high stringency for the iron-binding residues in the P4H active site. We conclude that P4H, which catalyzes an especially demanding chemical transformation, is recalcitrant to change.
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Affiliation(s)
- Kelly L. Gorres
- Department of Biochemistry, University of Wisconsin–Madison, Madison, Wisconsin, United States of America
| | - Khian Hong Pua
- Department of Biochemistry, University of Wisconsin–Madison, Madison, Wisconsin, United States of America
| | - Ronald T. Raines
- Department of Biochemistry, University of Wisconsin–Madison, Madison, Wisconsin, United States of America
- Department of Chemistry, University of Wisconsin–Madison, Madison, Wisconsin, United States of America
- * E-mail:
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29
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Kulik HJ, Blasiak LC, Marzari N, Drennan CL. First-principles study of non-heme Fe(II) halogenase SyrB2 reactivity. J Am Chem Soc 2009; 131:14426-33. [PMID: 19807187 PMCID: PMC2760000 DOI: 10.1021/ja905206k] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We present here a computational study of reactions at a model complex of the SyrB2 enzyme active site. SyrB2, which chlorinates L-threonine in the syringomycin biosynthetic pathway, belongs to a recently discovered class of alpha-ketoglutarate (alphaKG), non-heme Fe(II)-dependent halogenases that share many structural and chemical similarities with hydroxylases. Namely, halogenases and hydroxylases alike decarboxylate the alphaKG co-substrate, facilitating formation of a high-energy ferryl-oxo intermediate that abstracts a hydrogen from the reactant complex. The reaction mechanisms differ at this point, and mutation of active site residues (Asp for the hydroxylase to Ala or Ala to Asp/Glu for halogenase) fails to reproduce hydroxylating activity in SyrB2 or halogenating activity in similar hydroxylases. Using a density functional theory approach with a recently implemented Hubbard U correction for accurate treatment of transition-metal chemistry, we explore probable reaction pathways and mechanisms via a model complex consisting of only the iron center and its direct ligands. We show that the first step, alphaKG decarboxylation, is barrierless and exothermic, but the subsequent hydrogen abstraction step has an energetic barrier consistent with that accessible under biological conditions. In the model complex we use, radical chlorination is barrierless and exothermic, whereas the analogous hydroxylation is found to have a small energetic barrier. The hydrogen abstraction and radical chlorination steps are strongly coupled: the barrier for the hydrogen abstraction step is reduced when carried out concomitantly with the exothermic chlorination step. Our work suggests that the lack of chlorination in mutant hydroxylases is most likely due to poor binding of chlorine in the active site, whereas mutant halogenases do not hydroxylate for energetic reasons. Although secondary shell residues undoubtedly modulate the overall reactivity and binding of relevant substrates, we show that a small model compound consisting exclusively of the direct ligands to the metal can help explain reactivity heretofore not yet understood in the halogenase SyrB2.
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Affiliation(s)
- Heather J Kulik
- Department of Materials Science & Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, USA.
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30
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Wong C, Fujimori DG, Walsh CT, Drennan CL. Structural analysis of an open active site conformation of nonheme iron halogenase CytC3. J Am Chem Soc 2009; 131:4872-9. [PMID: 19281171 PMCID: PMC2663892 DOI: 10.1021/ja8097355] [Citation(s) in RCA: 65] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
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CytC3, a member of the recently discovered class of nonheme Fe(II) and α-ketoglutarate (αKG)-dependent halogenases, catalyzes the double chlorination of l-2-aminobutyric acid (Aba) to produce a known Streptomyces antibiotic, γ,γ-dichloroaminobutyrate. Unlike the majority of the Fe(II)-αKG-dependent enzymes that catalyze hydroxylation reactions, halogenases catalyze a transfer of halides. To examine the important enzymatic features that discriminate between chlorination and hydroxylation, the crystal structures of CytC3 both with and without αKG/Fe(II) have been solved to 2.2 Å resolution. These structures capture CytC3 in an open active site conformation, in which no chloride is bound to iron. Comparison of the open conformation of CytC3 with the closed conformation of another nonheme iron halogenase, SyrB2, suggests two important criteria for creating an enzyme-bound Fe—Cl catalyst: (1) the presence of a hydrogen-bonding network between the chloride and surrounding residues, and (2) the presence of a hydrophobic pocket in which the chloride resides.
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Affiliation(s)
- Cintyu Wong
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Ave., Cambridge, Massachusetts 02139, USA
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Biochemical characterization and mutational analysis of the mononuclear non-haem Fe2+ site in Dke1, a cupin-type dioxygenase from Acinetobacter johnsonii. Biochem J 2009; 418:403-11. [PMID: 18973472 DOI: 10.1042/bj20081161] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
beta-diketone-cleaving enzyme Dke1 is a homotetrameric Fe2+-dependent dioxygenase from Acinetobacter johnsonii. The Dke1protomer adopts a single-domain beta-barrel fold characteristic of the cupin superfamily of proteins and features a mononuclear non-haem Fe2+ centre where a triad of histidine residues, His-62, His-64 and His-104, co-ordinate the catalytic metal. To provide structure-function relationships for the peculiar metal site of Dke1 in relation to the more widespread 2-His-1-Glu/Asp binding site for non-haem Fe2+,we replaced each histidine residue individually with glutamate and asparagine and compared binding of Fe2+ and four non-native catalytically inactive metals with purified apo-forms of wild-type and mutant enzymes. Results from anaerobic equilibrium microdialysis (Fe2+) and fluorescence titration (Fe2+, Cu2+, Ni2+, Mn2+ and Zn2+) experiments revealed the presence of two broadly specific metal-binding sites in native Dke1 that bind Fe2+ with a dissociation constant (Kd) of 5 microM (site I) and approximately 0.3 mM (site II). Each mutation, except for the substitution of asparagine for His-104, disrupted binding of Fe2+, but not that of the other bivalent metal ions, at site I,while leaving metal binding at site II largely unaffected. Dke1 mutants harbouring glutamate substitutions were completely inactive and not functionally complemented by external Fe2+.The Fe2+ catalytic centre activity (kcat) of mutants with asparagine substitution of His-62 and His-104 was decreased 140- and 220-fold respectively, compared with the kcat value of 8.5 s(-1) for the wild-type enzyme in the reaction with pentane-2,4-dione.The H64N mutant was not catalytically competent, except in the presence of external Fe2+ (1 mM) which elicited about 1/1000 of wild-type activity. Therefore co-ordination of Fe2+ by Dke1 requires an uncharged metallocentre, and three histidine ligands are needed for the assembly of a fully functional catalytic site. Oxidative inactivation of Dke1 was shown to involve conversion of enzyme-bound Fe2+ into Fe3+, which is then released from the metal centre.
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de Visser SP, Straganz GD. Why Do Cysteine Dioxygenase Enzymes Contain a 3-His Ligand Motif Rather than a 2His/1Asp Motif Like Most Nonheme Dioxygenases? J Phys Chem A 2009; 113:1835-46. [DOI: 10.1021/jp809700f] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Sam P. de Visser
- The Manchester Interdisciplinary Biocenter and the School of Chemical Engineering and Analytical Science, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, United Kingdom, and Graz University of Technology, Institute of Biotechnology and Biochemical Engineering, Petersgasse 12, A-8010 Graz, Austria
| | - Grit D. Straganz
- The Manchester Interdisciplinary Biocenter and the School of Chemical Engineering and Analytical Science, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, United Kingdom, and Graz University of Technology, Institute of Biotechnology and Biochemical Engineering, Petersgasse 12, A-8010 Graz, Austria
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Structural and functional comparison of 2-His-1-carboxylate and 3-His metallocentres in non-haem iron(II)-dependent enzymes. Biochem Soc Trans 2009; 36:1180-6. [PMID: 19021520 DOI: 10.1042/bst0361180] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The canonical structural motif for co-ordination of non-haem ferrous iron in metal-dependent oxygenases is a facial triad of two histidine residues and one aspartate or glutamate residue. This so-called 2-His-1-carboxylate metallocentre is often accommodated in a double-stranded beta-helix fold with the iron-co-ordinating residues located in the rigid core structure of the protein. At the sequence level, the metal ligands are arranged in a HXD/E...H motif (where the distance between the conserved histidine residues is variable). Interestingly, cysteine dioxygenase, among a growing number of other iron(II) oxygenases, has the carboxylate residue replaced by another histidine. In the present review, we compare the properties of 3-His and 2-His-1-carboxylate sites based on current evidence from high-resolution crystal structures, spectroscopic characterization of the metal centres and results from mutagenesis studies. Although the overall conformation of the two metal sites is quite similar, the carboxylate residue seems to accommodate a slightly closer co-ordination distance than the counterpart histidine. The ability of the 2-His-1-carboxylate site to fit a site-directed substitution by an alternatively co-ordinating or non-co-ordinating residue with retention of metal-binding capacity and catalytic function varies among different enzymes. However, replacement by histidine disrupted the activity in the three iron(II) oxygenases examined so far.
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Li J, Fitzpatrick PF. Characterization of metal ligand mutants of phenylalanine hydroxylase: Insights into the plasticity of a 2-histidine-1-carboxylate triad. Arch Biochem Biophys 2008; 475:164-8. [PMID: 18477464 PMCID: PMC2518327 DOI: 10.1016/j.abb.2008.04.029] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2008] [Revised: 04/23/2008] [Accepted: 04/24/2008] [Indexed: 11/30/2022]
Abstract
The iron atom in the nonheme iron monooxygenase phenylalanine hydroxylase is bound on one face by His285, His290, and Glu330. This arrangement of metal ligands is conserved in the other aromatic amino acid hydroxylases, tyrosine hydroxylase and tryptophan hydroxylase. A similar 2-His-1-carboxylate facial triad of two histidines and an acidic residue are the ligands to the iron in other nonheme iron enzymes, including the alpha-ketoglutarate-dependent hydroxylases and the extradiol dioxygenases. Previous studies of the effects of conservative mutations of the iron ligands in tyrosine hydroxylase established that there is some plasticity in the nature of the ligands and that the three ligands differ in their sensitivity to mutagenesis. To determine the generality of this finding for enzymes containing a 2-His-1-carboxylate facial triad, the His285, His290, and Glu330 in rat phenylalanine hydroxylase were mutated to glutamine, glutamate, and histidine. All of the mutant proteins had low but measurable activities for tyrosine formation. In general, mutation of Glu330 had the greatest effect on activity and mutation of His290 the least. All of the mutations resulted in an excess of tetrahydropterin oxidized relative to tyrosine formation, with mutation of His285 having the greatest effect on the coupling of the two partial reactions. The H285Q enzyme had the highest activity as tetrahydropterin oxidase at 20% the wild-type value. All of the mutations greatly decreased the affinity for iron, with mutation of Glu330 the most deleterious. The results complement previous results with tyrosine hydroxylase in establishing the plasticity of the individual iron ligands in this enzyme family.
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Affiliation(s)
- Jun Li
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843-2128
| | - Paul F. Fitzpatrick
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843-2128
- Department of Chemistry, Texas A&M University, College Station, TX 77843-2128
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Grzyska PK, Hausinger RP. Cr(II) reactivity of taurine/alpha-ketoglutarate dioxygenase. Inorg Chem 2007; 46:10087-92. [PMID: 17973473 DOI: 10.1021/ic700383q] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The interaction of CrII with taurine/alpha-ketoglutarate (alphaKG) dioxygenase (TauD) was examined. CrII replaces FeII and binds stoichiometrically with alphaKG to the FeII/alphaKG binding site of the protein, with additional CrII used to generate a chromophore attributed to a CrIII-semiquinone in a small percentage of the sample. Formation of the latter oxygen-sensitive species requires the dihydroxyphenylalanine (DOPA) quinone form of Tyr-73. This preformed side chain is generated by intracellular self-hydroxylation of Tyr-73 to form DOPA, which is subsequently oxidized to the quinone. No chromophore is generated when using NaBH4-treated sample, protein isolated from anaerobically grown cells, inactive TauD variants that are incapable of self-hydroxylation, or the Y73F active mutant of TauD. A CrIII-DOPA semiquinone also was observed in the herbicide hydroxylase SdpA.
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Affiliation(s)
- Piotr K Grzyska
- Department of Microbiology & Molecular Genetics, Michigan State University, East Lansing, Michigan 48824-4320, USA
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