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Zan X, Yan Y, Chen G, Sun L, Wang L, Wen Y, Xu Y, Zhang Z, Li X, Yang Y, Sun W, Cui F. Recent Advances of Oxalate Decarboxylase: Biochemical Characteristics, Catalysis Mechanisms, and Gene Expression and Regulation. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:10163-10178. [PMID: 38653191 DOI: 10.1021/acs.jafc.4c00172] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/25/2024]
Abstract
Oxalate decarboxylase (OXDC) is a typical Mn2+/Mn3+ dependent metal enzyme and splits oxalate to formate and CO2 without any organic cofactors. Fungi and bacteria are the main organisms expressing the OXDC gene, but with a significantly different mechanism of gene expression and regulation. Many articles reported its potential applications in the clinical treatment of hyperoxaluria, low-oxalate food processing, degradation of oxalate salt deposits, oxalate acid diagnostics, biocontrol, biodemulsifier, and electrochemical oxidation. However, some questions still remain to be clarified about the role of substrate binding and/or protein environment in modulating the redox properties of enzyme-bound Mn(II)/Mn(III), the nature of dioxygen involved in the catalytic mechanism, and how OXDC acquires Mn(II) /Mn(III). This review mainly summarizes its biochemical and structure characteristics, gene expression and regulation, and catalysis mechanism. We also deep-mined oxalate decarboxylase gene data from National Center for Biotechnology Information to give some insights to explore new OXDC with diverse biochemical properties.
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Affiliation(s)
- Xinyi Zan
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang 212013, P. R. China
| | - Ying Yan
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang 212013, P. R. China
| | - Gege Chen
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang 212013, P. R. China
| | - Lei Sun
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang 212013, P. R. China
| | - Linhan Wang
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang 212013, P. R. China
| | - Yixin Wen
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang 212013, P. R. China
| | - Yuting Xu
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang 212013, P. R. China
| | - Ziying Zhang
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang 212013, P. R. China
| | - Xinlin Li
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang 212013, P. R. China
| | - Yumeng Yang
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang 212013, P. R. China
| | - Wenjing Sun
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang 212013, P. R. China
| | - Fengjie Cui
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang 212013, P. R. China
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Paramagnetic resonance investigation of mono- and di-manganese-containing systems in biochemistry. Methods Enzymol 2022; 666:315-372. [DOI: 10.1016/bs.mie.2022.02.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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Riegert AS, Narindoshvili T, Coricello A, Richards NGJ, Raushel FM. Functional Characterization of Two PLP-Dependent Enzymes Involved in Capsular Polysaccharide Biosynthesis from Campylobacter jejuni. Biochemistry 2021; 60:2836-2843. [PMID: 34505775 DOI: 10.1021/acs.biochem.1c00439] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Campylobacter jejuni is a Gram-negative, pathogenic bacterium that causes campylobacteriosis, a form of gastroenteritis. C. jejuni is the most frequent cause of food-borne illness in the world, surpassing Salmonella and E. coli. Coating the surface of C. jejuni is a layer of sugar molecules known as the capsular polysaccharide that, in C. jejuni NCTC 11168, is composed of a repeating unit of d-glycero-l-gluco-heptose, d-glucuronic acid, d-N-acetyl-galactosamine, and d-ribose. The d-glucuronic acid moiety is further amidated with either serinol or ethanolamine. It is unknown how these modifications are synthesized and attached to the polysaccharide. Here, we report the catalytic activities of two previously uncharacterized, pyridoxal phosphate (PLP)-dependent enzymes, Cj1436 and Cj1437, from C. jejuni NCTC 11168. Using a combination of mass spectrometry and nuclear magnetic resonance, we determined that Cj1436 catalyzes the decarboxylation of l-serine phosphate to ethanolamine phosphate. Cj1437 was shown to catalyze the transamination of dihydroxyacetone phosphate to (S)-serinol phosphate in the presence of l-glutamate. The probable routes to the ultimate formation of the glucuronamide substructures in the capsular polysaccharides of C. jejuni are discussed.
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Affiliation(s)
- Alexander S Riegert
- Department of Biochemistry & Biophysics, Texas A&M University, College Station, Texas 77843, United States
| | - Tamari Narindoshvili
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Adriana Coricello
- School of Chemistry, Cardiff University, Cardiff CF10 3AT, United Kingdom
| | - Nigel G J Richards
- School of Chemistry, Cardiff University, Cardiff CF10 3AT, United Kingdom
| | - Frank M Raushel
- Department of Biochemistry & Biophysics, Texas A&M University, College Station, Texas 77843, United States.,Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
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Pastore AJ, Teo RD, Montoya A, Burg MJ, Twahir UT, Bruner SD, Beratan DN, Angerhofer A. Oxalate decarboxylase uses electron hole hopping for catalysis. J Biol Chem 2021; 297:100857. [PMID: 34097877 PMCID: PMC8254039 DOI: 10.1016/j.jbc.2021.100857] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2021] [Revised: 05/28/2021] [Accepted: 06/03/2021] [Indexed: 01/16/2023] Open
Abstract
The hexameric low-pH stress response enzyme oxalate decarboxylase catalyzes the decarboxylation of the oxalate mono-anion in the soil bacterium Bacillus subtilis. A single protein subunit contains two Mn-binding cupin domains, and catalysis depends on Mn(III) at the N-terminal site. The present study suggests a mechanistic function for the C-terminal Mn as an electron hole donor for the N-terminal Mn. The resulting spatial separation of the radical intermediates directs the chemistry toward decarboxylation of the substrate. A π-stacked tryptophan pair (W96/W274) links two neighboring protein subunits together, thus reducing the Mn-to-Mn distance from 25.9 Å (intrasubunit) to 21.5 Å (intersubunit). Here, we used theoretical analysis of electron hole-hopping paths through redox-active sites in the enzyme combined with site-directed mutagenesis and X-ray crystallography to demonstrate that this tryptophan pair supports effective electron hole hopping between the C-terminal Mn of one subunit and the N-terminal Mn of the other subunit through two short hops of ∼8.5 Å. Replacement of W96, W274, or both with phenylalanine led to a large reduction in catalytic efficiency, whereas replacement with tyrosine led to recovery of most of this activity. W96F and W96Y mutants share the wildtype tertiary structure. Two additional hole-hopping networks were identified leading from the Mn ions to the protein surface, potentially protecting the enzyme from high Mn oxidation states during turnover. Our findings strongly suggest that multistep hole-hopping transport between the two Mn ions is required for enzymatic function, adding to the growing examples of proteins that employ aromatic residues as hopping stations.
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Affiliation(s)
- Anthony J Pastore
- Department of Chemistry, University of Florida, Gainesville, Florida, USA
| | - Ruijie D Teo
- Department of Chemistry, Duke University, Durham, North Carolina, USA
| | - Alvaro Montoya
- Department of Chemistry, University of Florida, Gainesville, Florida, USA
| | - Matthew J Burg
- Department of Chemistry, University of Florida, Gainesville, Florida, USA
| | - Umar T Twahir
- Department of Chemistry, University of Florida, Gainesville, Florida, USA
| | - Steven D Bruner
- Department of Chemistry, University of Florida, Gainesville, Florida, USA
| | - David N Beratan
- Department of Chemistry, Duke University, Durham, North Carolina, USA.
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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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Gao S, Radadiya A, Li W, Liu H, Zhu W, de Crécy-Lagard V, Richards NGJ, Naismith JH. Uncovering the chemistry of C-C bond formation in C-nucleoside biosynthesis: crystal structure of a C-glycoside synthase/PRPP complex. Chem Commun (Camb) 2020; 56:7617-7620. [PMID: 32515440 PMCID: PMC8183095 DOI: 10.1039/d0cc02834g] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2020] [Accepted: 05/14/2020] [Indexed: 12/19/2022]
Abstract
The enzyme ForT catalyzes C-C bond formation between 5'-phosphoribosyl-1'-pyrophosphate (PRPP) and 4-amino-1H-pyrazole-3,5-dicarboxylate to make a key intermediate in the biosynthesis of formycin A 5'-phosphate by Streptomyces kaniharaensis. We report the 2.5 Å resolution structure of the ForT/PRPP complex and locate active site residues critical for PRPP recognition and catalysis.
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Affiliation(s)
- Sisi Gao
- Research Complex at Harwell, Didcot, OX11 0FA, UK and BSRC, University of St Andrews, St Andrews, KY16 9ST, UK
| | - Ashish Radadiya
- School of Chemistry, Cardiff University, Cardiff, CF10 3AT, UK
| | - Wenbo Li
- Division of Structural Biology, University of Oxford, Oxford, OX3 7BN, UK.
| | - Huanting Liu
- BSRC, University of St Andrews, St Andrews, KY16 9ST, UK
| | - Wen Zhu
- Department of Chemistry and California Institute for Quantitative Biosciences, University of California, Berkeley, CA 94720, USA
| | | | - Nigel G J Richards
- School of Chemistry, Cardiff University, Cardiff, CF10 3AT, UK and Foundation for Applied Molecular Evolution, Alachua, FL 32615, USA
| | - James H Naismith
- Division of Structural Biology, University of Oxford, Oxford, OX3 7BN, UK. and The Rosalind Franklin Institute, Didcot, OX11 0FA, UK
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Banerjee A, Tolla AS, Stjepanovic S, Sevilla MD, Goodsell JL, Angerhofer A, Brennessel WW, Loloee R, Chavez FA. Structural, Spectroscopic, Electrochemical, and Magnetic Properties for Manganese(II) Triazamacrocyclic Complexes. Inorganica Chim Acta 2019; 486:546-555. [PMID: 33981118 PMCID: PMC8112617 DOI: 10.1016/j.ica.2018.11.013] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
We report the synthesis of [Mn(tacud)2](OTf)2 (1) (tacud = 1,4,8-triazacycloundecane), [Mn(tacd)2](OTf)2 (2) (tacd = 1,4,7-triazacyclodecane), and [Mn(tacn)2](OTf)2 (3) (tacn = 1,4,7-triazacyclononane). Electrochemical measurements on the MnIII/II redox couple show that complex 1 has the largest anodic potential of the set (E 1/2 = 1.16 V vs NHE, ΔE p = 106 mV) compared to 2 (E 1/2 = 0.95 V, ΔE p = 108 mV) and 3 (E 1/2 = 0.93 V, ΔE p = 96 mV). This is due to the fact that 1 has the fewest 5-membered chelate rings and thus is least stabilized. Magnetic studies of 1-3 revealed that all complexes remain high spin throughout the temperature range investigated (2 - 300 K). X-band EPR investigations in methanol glass indicated that the manganese(II) centers for 2 and 3 resided in a more distorted octahedral geometric configuration compared to 1. To ease spectral interpretation and extract ZFS parameters, we performed high-frequency high-field EPR (HFEPR) at frequencies above 200 GHz and a field of 7.5 T. Simulation of the spectral data yielded g = 2.0013 and D = -0.031 cm-1 for 1, g = 2.0008, D = -0.0824 cm-1, |E/D| = 0.12 for 2, and g = 2.00028, D = -0.0884 cm-1 for 3. These results are consistent with 3 possessing the most distorted geometry. Calculations (PBE0/6-31G(d)) were performed on 1-3. Results show that 1 has the largest HOMO-LUMO gap energy (6.37 eV) compared to 2 (6.12 eV) and 3 (6.26 eV). Complex 1 also has the lowest HOMO energies indicating higher stability.
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Affiliation(s)
- Atanu Banerjee
- Department of Chemistry, Oakland University, Rochester, MI 48309-4477, USA
| | - Azam S Tolla
- Department of Chemistry, Oakland University, Rochester, MI 48309-4477, USA
| | | | - Michael D Sevilla
- Department of Chemistry, Oakland University, Rochester, MI 48309-4477, USA
| | - Justin L Goodsell
- Department of Chemistry, University of Florida, Gainesville, FL 32611-7200, USA
| | | | | | - Reza Loloee
- Department of Physics and Astronomy, Michigan State University, East Lansing, MI 48824-1322, USA
| | - Ferman A Chavez
- Department of Chemistry, Oakland University, Rochester, MI 48309-4477, USA
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8
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Zhu W, Reinhardt LA, Richards NGJ. Second-Shell Hydrogen Bond Impacts Transition-State Structure in Bacillus subtilis Oxalate Decarboxylase. Biochemistry 2018; 57:3425-3432. [DOI: 10.1021/acs.biochem.8b00214] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Wen Zhu
- School of Chemistry, Cardiff University, Park Place, Cardiff CF10 3AT, United Kingdom
| | - Laurie A. Reinhardt
- Institute for Enzyme Research and Department of Biochemistry, University of Wisconsin, Madison, Wisconsin 53726, United States
| | - Nigel G. J. Richards
- School of Chemistry, Cardiff University, Park Place, Cardiff CF10 3AT, United Kingdom
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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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Deshpande AR, Pochapsky TC, Ringe D. The Metal Drives the Chemistry: Dual Functions of Acireductone Dioxygenase. Chem Rev 2017; 117:10474-10501. [PMID: 28731690 DOI: 10.1021/acs.chemrev.7b00117] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Acireductone dioxygenase (ARD) from the methionine salvage pathway (MSP) is a unique enzyme that exhibits dual chemistry determined solely by the identity of the divalent transition-metal ion (Fe2+ or Ni2+) in the active site. The Fe2+-containing isozyme catalyzes the on-pathway reaction using substrates 1,2-dihydroxy-3-keto-5-methylthiopent-1-ene (acireductone) and dioxygen to generate formate and the ketoacid precursor of methionine, 2-keto-4-methylthiobutyrate, whereas the Ni2+-containing isozyme catalyzes an off-pathway shunt with the same substrates, generating methylthiopropionate, carbon monoxide, and formate. The dual chemistry of ARD was originally discovered in the bacterium Klebsiella oxytoca, but it has recently been shown that mammalian ARD enzymes (mouse and human) are also capable of catalyzing metal-dependent dual chemistry in vitro. This is particularly interesting, since carbon monoxide, one of the products of off-pathway reaction, has been identified as an antiapoptotic molecule in mammals. In addition, several biochemical and genetic studies have indicated an inhibitory role of human ARD in cancer. This comprehensive review describes the biochemical and structural characterization of the ARD family, the proposed experimental and theoretical approaches to establishing mechanisms for the dual chemistry, insights into the mechanism based on comparison with structurally and functionally similar enzymes, and the applications of this research to the field of artificial metalloenzymes and synthetic biology.
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Affiliation(s)
- Aditi R Deshpande
- Departments of Biochemistry and ‡Chemistry and §the Rosenstiel Institute for Basic Biomedical Research, Brandeis University , Waltham, Massachusetts 02454, United States
| | - Thomas C Pochapsky
- Departments of Biochemistry and ‡Chemistry and §the Rosenstiel Institute for Basic Biomedical Research, Brandeis University , Waltham, Massachusetts 02454, United States
| | - Dagmar Ringe
- Departments of Biochemistry and ‡Chemistry and §the Rosenstiel Institute for Basic Biomedical Research, Brandeis University , Waltham, Massachusetts 02454, United States
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11
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Sheng X, Zhu W, Huddleston J, Xiang DF, Raushel FM, Richards NGJ, Himo F. A Combined Experimental-Theoretical Study of the LigW-Catalyzed Decarboxylation of 5-Carboxyvanillate in the Metabolic Pathway for Lignin Degradation. ACS Catal 2017. [DOI: 10.1021/acscatal.7b01166] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Xiang Sheng
- Department
of Organic Chemistry, Arrhenius Laboratory, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Wen Zhu
- School
of Chemistry, Cardiff University, Park Place, Cardiff CF10 3AT, U.K
| | - Jamison Huddleston
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Dao Fen Xiang
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Frank M. Raushel
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | | | - Fahmi Himo
- Department
of Organic Chemistry, Arrhenius Laboratory, Stockholm University, SE-106 91 Stockholm, Sweden
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12
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Biological functions controlled by manganese redox changes in mononuclear Mn-dependent enzymes. Essays Biochem 2017; 61:259-270. [PMID: 28487402 DOI: 10.1042/ebc20160070] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2016] [Revised: 03/05/2017] [Accepted: 03/17/2017] [Indexed: 02/06/2023]
Abstract
Remarkably few enzymes are known to employ a mononuclear manganese ion that undergoes changes in redox state during catalysis. Many questions remain to be answered about the role of substrate binding and/or protein environment in modulating the redox properties of enzyme-bound Mn(II), the nature of the dioxygen species involved in the catalytic mechanism, and how these enzymes acquire Mn(II) given that many other metal ions in the cell form more stable protein complexes. Here, we summarize current knowledge concerning the structure and mechanism of five mononuclear manganese-dependent enzymes: superoxide dismutase, oxalate oxidase (OxOx), oxalate decarboxylase (OxDC), homoprotocatechuate 3,4-dioxygenase, and lipoxygenase (LOX). Spectroscopic measurements and/or computational studies suggest that Mn(III)/Mn(II) are the catalytically active oxidation states of the metal, and the importance of 'second-shell' hydrogen bonding interactions with metal ligands has been demonstrated for a number of examples. The ability of these enzymes to modulate the redox properties of the Mn(III)/Mn(II) couple, thereby allowing them to generate substrate-based radicals, appears essential for accessing diverse chemistries of fundamental importance to organisms in all branches of life.
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13
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Goodwin JM, Rana H, Ndungu J, Chakrabarti G, Moomaw EW. Hydrogen peroxide inhibition of bicupin oxalate oxidase. PLoS One 2017; 12:e0177164. [PMID: 28486485 PMCID: PMC5423638 DOI: 10.1371/journal.pone.0177164] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2016] [Accepted: 04/24/2017] [Indexed: 01/28/2023] Open
Abstract
Oxalate oxidase is a manganese containing enzyme that catalyzes the oxidation of oxalate to carbon dioxide in a reaction that is coupled with the reduction of oxygen to hydrogen peroxide. Oxalate oxidase from Ceriporiopsis subvermispora (CsOxOx) is the first fungal and bicupin enzyme identified that catalyzes this reaction. Potential applications of oxalate oxidase for use in pancreatic cancer treatment, to prevent scaling in paper pulping, and in biofuel cells have highlighted the need to understand the extent of the hydrogen peroxide inhibition of the CsOxOx catalyzed oxidation of oxalate. We apply a membrane inlet mass spectrometry (MIMS) assay to directly measure initial rates of carbon dioxide formation and oxygen consumption in the presence and absence of hydrogen peroxide. This work demonstrates that hydrogen peroxide is both a reversible noncompetitive inhibitor of the CsOxOx catalyzed oxidation of oxalate and an irreversible inactivator. The build-up of the turnover-generated hydrogen peroxide product leads to the inactivation of the enzyme. The introduction of catalase to reaction mixtures protects the enzyme from inactivation allowing reactions to proceed to completion. Circular dichroism spectra indicate that no changes in global protein structure take place in the presence of hydrogen peroxide. Additionally, we show that the CsOxOx catalyzed reaction with the three carbon substrate mesoxalate consumes oxygen which is in contrast to previous proposals that it catalyzed a non-oxidative decarboxylation with this substrate.
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Affiliation(s)
- John M. Goodwin
- Department of Chemistry and Biochemistry, Kennesaw State University, Kennesaw, GA, United States of America
| | - Hassan Rana
- Department of Chemistry and Biochemistry, Kennesaw State University, Kennesaw, GA, United States of America
| | - Joan Ndungu
- Department of Chemistry and Biochemistry, Kennesaw State University, Kennesaw, GA, United States of America
| | - Gaurab Chakrabarti
- Department of Pharmacology, Oncology and Radiation Oncology, University of Texas Southwestern Medical Center, Dallas, TX, United States of America
- Laboratory of Molecular Stress Responses, University of Texas Southwestern Medical Center, Dallas, TX, United States of America
- Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX, United States of America
| | - Ellen W. Moomaw
- Department of Chemistry and Biochemistry, Kennesaw State University, Kennesaw, GA, United States of America
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14
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Li A, Ziehr JL, Johnson KA. A new general method for simultaneous fitting of temperature and concentration dependence of reaction rates yields kinetic and thermodynamic parameters for HIV reverse transcriptase specificity. J Biol Chem 2017; 292:6695-6702. [PMID: 28255091 DOI: 10.1074/jbc.m116.760827] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2016] [Revised: 02/21/2017] [Indexed: 11/06/2022] Open
Abstract
Recent studies have demonstrated the dominant role of induced fit in enzyme specificity of HIV reverse transcriptase and many other enzymes. However, relevant thermodynamic parameters are lacking, and equilibrium thermodynamic methods are of no avail because the key parameters can only be determined by kinetic measurement. By modifying KinTek Explorer software, we present a new general method for globally fitting data collected over a range of substrate concentrations and temperatures and apply it to HIV reverse transcriptase. Fluorescence stopped-flow methods were used to record the kinetics of enzyme conformational changes that monitor nucleotide binding and incorporation. The nucleotide concentration dependence was measured at temperatures ranging from 5 to 37 °C, and the raw data were fit globally to derive a single set of rate constants at 37 °C and a set of activation enthalpy terms to account for the kinetics at all other temperatures. This comprehensive analysis afforded thermodynamic parameters for nucleotide binding (Kd , ΔG, ΔH, and ΔS at 37 °C) and kinetic parameters for enzyme conformational changes and chemistry (rate constants and activation enthalpy). Comparisons between wild-type enzyme and a mutant resistant to nucleoside analogs used to treat HIV infections reveal that the ground state binding is weaker and the activation enthalpy for the conformational change step is significantly larger for the mutant. Further studies to explore the structural underpinnings of the observed thermodynamics and kinetics of the conformational change step may help to design better analogs to treat HIV infections and other diseases. Our new method is generally applicable to enzyme and chemical kinetics.
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Affiliation(s)
- An Li
- From the Institute for Cell and Molecular Biology, Molecular Biosciences Department, University of Texas at Austin, Austin, Texas 78712
| | - Jessica L Ziehr
- From the Institute for Cell and Molecular Biology, Molecular Biosciences Department, University of Texas at Austin, Austin, Texas 78712
| | - Kenneth A Johnson
- From the Institute for Cell and Molecular Biology, Molecular Biosciences Department, University of Texas at Austin, Austin, Texas 78712
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15
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Oxygen activation by mononuclear Mn, Co, and Ni centers in biology and synthetic complexes. J Biol Inorg Chem 2016; 22:407-424. [PMID: 27853875 DOI: 10.1007/s00775-016-1402-7] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2016] [Accepted: 10/21/2016] [Indexed: 10/20/2022]
Abstract
The active sites of metalloenzymes that catalyze O2-dependent reactions generally contain iron or copper ions. However, several enzymes are capable of activating O2 at manganese or nickel centers instead, and a handful of dioxygenases exhibit activity when substituted with cobalt. This minireview summarizes the catalytic properties of oxygenases and oxidases with mononuclear Mn, Co, or Ni active sites, including oxalate-degrading oxidases, catechol dioxygenases, and quercetin dioxygenase. In addition, recent developments in the O2 reactivity of synthetic Mn, Co, or Ni complexes are described, with an emphasis on the nature of reactive intermediates featuring superoxo-, peroxo-, or oxo-ligands. Collectively, the biochemical and synthetic studies discussed herein reveal the possibilities and limitations of O2 activation at these three "overlooked" metals.
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16
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Twahir UT, Ozarowski A, Angerhofer A. Redox Cycling, pH Dependence, and Ligand Effects of Mn(III) in Oxalate Decarboxylase from Bacillus subtilis. Biochemistry 2016; 55:6505-6516. [DOI: 10.1021/acs.biochem.6b00891] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Umar T. Twahir
- Department
of Chemistry, University of Florida, Gainesville, Florida 32611-7200, United States
| | - Andrew Ozarowski
- National High Magnetic Field Laboratory, 1800 East Paul Dirac Drive, Tallahassee, Florida 32310, United States
| | - Alexander Angerhofer
- Department
of Chemistry, University of Florida, Gainesville, Florida 32611-7200, United States
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