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Dzyhovskyi V, Stokowa-Sołtys K. Divalent metal ion binding to Staphylococcus aureus FeoB transporter regions. J Inorg Biochem 2023; 244:112203. [PMID: 37018851 DOI: 10.1016/j.jinorgbio.2023.112203] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 03/21/2023] [Accepted: 03/27/2023] [Indexed: 03/31/2023]
Abstract
Transition metal ions such as iron, copper, zinc, manganese or, nickel are essential in many biological processes. Bacteria have developed a number of mechanisms for their acquisition and transport, in which numerous of proteins and smaller molecules are involved. One of the representatives of these proteins is FeoB, which belongs to the Feo (ferrous ion transporter) family. Although ferrous iron transport system is widespread among microorganisms, it is still poorly described in Gram-positive pathogens, such as Staphylococcus aureus. In this work, combined potentiometric and spectroscopic studies (UV-Vis, CD and EPR) were carried out to determine Cu(II), Fe(II) and Zn(II) binding modes to FeoB fragments (Ac-IDYHKLMK-NH2, Ac-ETSHDKY-NH2, and Ac-SFLHMVGS-NH2). For the first time iron(II) complexes with peptides were characterized by potentiometry. All studied ligands are able to form a variety of thermodynamically stable complexes with transition metal ions. It was concluded that among the studied systems, the most effective metal ion binding is observed for the Ac-ETSHDKY-NH2 peptide. Moreover, comparing preferences of all ligands towards different metal ions, copper(II) complexes are the most stable ones at physiological pH.
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2
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Mahto JK, Neetu N, Waghmode B, Kuatsjah E, Sharma M, Sircar D, Sharma AK, Tomar S, Eltis LD, Kumar P. Molecular insights into substrate recognition and catalysis by phthalate dioxygenase from Comamonas testosteroni. J Biol Chem 2021; 297:101416. [PMID: 34800435 PMCID: PMC8649396 DOI: 10.1016/j.jbc.2021.101416] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 11/09/2021] [Accepted: 11/10/2021] [Indexed: 11/19/2022] Open
Abstract
Phthalate, a plasticizer, endocrine disruptor, and potential carcinogen, is degraded by a variety of bacteria. This degradation is initiated by phthalate dioxygenase (PDO), a Rieske oxygenase (RO) that catalyzes the dihydroxylation of phthalate to a dihydrodiol. PDO has long served as a model for understanding ROs despite a lack of structural data. Here we purified PDOKF1 from Comamonas testosteroni KF1 and found that it had an apparent kcat/Km for phthalate of 0.58 ± 0.09 μM-1s-1, over 25-fold greater than for terephthalate. The crystal structure of the enzyme at 2.1 Å resolution revealed that it is a hexamer comprising two stacked α3 trimers, a configuration not previously observed in RO crystal structures. We show that within each trimer, the protomers adopt a head-to-tail configuration typical of ROs. The stacking of the trimers is stabilized by two extended helices, which make the catalytic domain of PDOKF1 larger than that of other characterized ROs. Complexes of PDOKF1 with phthalate and terephthalate revealed that Arg207 and Arg244, two residues on one face of the active site, position these substrates for regiospecific hydroxylation. Consistent with their roles as determinants of substrate specificity, substitution of either residue with alanine yielded variants that did not detectably turnover phthalate. Together, these results provide critical insights into a pollutant-degrading enzyme that has served as a paradigm for ROs and facilitate the engineering of this enzyme for bioremediation and biocatalytic applications.
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Affiliation(s)
- Jai Krishna Mahto
- Department of Biosciences and Bioengineering, IIT Roorkee, Roorkee, India
| | - Neetu Neetu
- Department of Biosciences and Bioengineering, IIT Roorkee, Roorkee, India
| | | | - Eugene Kuatsjah
- Department of Microbiology & Immunology, Life Sciences Institute, The University of British Columbia, Vancouver, Canada
| | - Monica Sharma
- Department of Biosciences and Bioengineering, IIT Roorkee, Roorkee, India
| | - Debabrata Sircar
- Department of Biosciences and Bioengineering, IIT Roorkee, Roorkee, India
| | | | - Shailly Tomar
- Department of Biosciences and Bioengineering, IIT Roorkee, Roorkee, India
| | - Lindsay D Eltis
- Department of Microbiology & Immunology, Life Sciences Institute, The University of British Columbia, Vancouver, Canada
| | - Pravindra Kumar
- Department of Biosciences and Bioengineering, IIT Roorkee, Roorkee, India.
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Characterization of phthalate reductase from Ralstonia eutropha CH34 and in silico study of phthalate dioxygenase and phthalate reductase interaction. J Mol Graph Model 2019; 90:161-170. [DOI: 10.1016/j.jmgm.2019.05.002] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Revised: 05/03/2019] [Accepted: 05/03/2019] [Indexed: 12/17/2022]
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Rogers MS, Lipscomb JD. Salicylate 5-Hydroxylase: Intermediates in Aromatic Hydroxylation by a Rieske Monooxygenase. Biochemistry 2019; 58:5305-5319. [PMID: 31066545 DOI: 10.1021/acs.biochem.9b00292] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Rieske oxygenases (ROs) catalyze a large range of oxidative chemistry. We have shown that cis-dihydrodiol-forming Rieske dioxygenases first react with their aromatic substrates via an active site nonheme Fe(III)-superoxide; electron transfer from the Rieske cluster then completes the product-forming reaction. Alternatively, two-electron-reduced Fe(III)-peroxo or hydroxo-Fe(V)-oxo activated oxygen intermediates are possible and may be utilized by other ROs to expand the catalytic range. Here, the reaction of a Rieske monooxygenase, salicylate 5-hydroxylase, that does not form a cis-dihydrodiol is examined. Single-turnover kinetic studies show fast binding of salicylate and O2. Transfer of the Rieske electron required to form the gentisate product occurs through bonds over ∼12 Å and must also be very fast. However, the observed rate constant for this reaction is much slower than expected and sensitive to substrate type. This suggests that initial reaction with salicylate occurs using the same Fe(III)-superoxo-level intermediate as Rieske dioxygenases and that this reaction limits the observed rate of electron transfer. A transient intermediate (λmax = 700 nm) with an electron paramagnetic resonance (EPR) at g = 4.3 is observed after the product is formed in the active site. The use of 17O2 (I = 5/2) results in hyperfine broadening of the g = 4.3 signal, showing that gentisate binds to the mononuclear iron via its C5-OH in the intermediate. The chromophore and EPR signal allow study of product release in the catalytic cycle. Comparison of the kinetics of single- and multiple-turnover reactions shows that re-reduction of the metal centers accelerates product release ∼300-fold, providing insight into the regulatory mechanism of ROs.
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Affiliation(s)
- Melanie S Rogers
- Department of Biochemistry, Molecular Biology, and Biophysics and Center for Metals in Biocatalysis , University of Minnesota , Minneapolis , Minnesota 55455 , United States
| | - John D Lipscomb
- Department of Biochemistry, Molecular Biology, and Biophysics and Center for Metals in Biocatalysis , University of Minnesota , Minneapolis , Minnesota 55455 , United States
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Fischer AA, Lindeman SV, Fiedler AT. Spectroscopic and computational studies of reversible O2 binding by a cobalt complex of relevance to cysteine dioxygenase. Dalton Trans 2017; 46:13229-13241. [DOI: 10.1039/c7dt01600j] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Spectroscopic and computational studies of reversible O2 binding by a cobalt active-site mimic shed light on the catalytic mechanism of cysteine dioxygenases.
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6
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Rhodococcus rhodochrous DSM 43269 3-ketosteroid 9alpha-hydroxylase, a two-component iron-sulfur-containing monooxygenase with subtle steroid substrate specificity. Appl Environ Microbiol 2009; 75:5300-7. [PMID: 19561185 DOI: 10.1128/aem.00066-09] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
This paper reports the biochemical characterization of a purified and reconstituted two-component 3-ketosteroid 9alpha-hydroxylase (KSH). KSH of Rhodococcus rhodochrous DSM 43269, consisting of a ferredoxin reductase (KshB) and a terminal oxygenase (KshA), was heterologously expressed in Escherichia coli. E. coli cell cultures, expressing both KshA and KshB, converted 4-androstene-3,17-dione (AD) into 9alpha-hydroxy-4-AD (9OHAD) with a >60% molar yield over 48 h of incubation. Coexpression and copurification were critical to successfully obtain pure and active KSH. Biochemical analysis revealed that the flavoprotein KshB is an NADH-dependent reductase using flavin adenine dinucleotide as a cofactor. Reconstitution experiments confirmed that KshA, KshB, and NADH are essential for KSH activity with steroid substrates. KSH hydroxylation activity was inhibited by several divalent metal ions, especially by zinc. The reconstituted KSH displayed subtle steroid substrate specificity; a range of 3-ketosteroids, i.e., 5alpha-Eta, 5beta-Eta, Delta1, and Delta4 steroids, could act as KSH substrates, provided that they had a short side chain. The formation of 9OHAD from AD by KSH was confirmed by liquid chromatography-mass spectrometry analysis and by the specific enzymatic conversion of 9OHAD into 3-hydroxy-9,10-secoandrost-1,3,5(10)-triene-9,17-dione using 3-ketosteroid Delta1-dehydrogenase. Only a single KSH is encoded in the genome of the human pathogen Mycobacterium tuberculosis H37Rv, shown to be important for survival in macrophages. Since no human KSH homolog exists, the M. tuberculosis enzyme may provide a novel target for treatment of tuberculosis. Detailed knowledge about the biochemical properties of KSH thus is highly relevant in the research fields of biotechnology and medicine.
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Guo S, Boyd J, Sammynaiken R, Loewen MC. Identification and characterization of a unique cysteine residue proximal to the catalytic site of Arabidopsis thaliana carotenoid cleavage enzyme 1. Biochem Cell Biol 2008; 86:262-70. [DOI: 10.1139/o08-031] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
AtCCD1 and AtNCED3 are related carotenoid cleavage enzymes from Arabidopsis thaliana that catalyze the oxidative cleavage of, respectively, the 9,10 (9′,10′) double bonds of carotenoid substrates such as β-carotene, and the 11,12 double bond of 9-cis epoxycarotenoids. Although the cellular and cleavage functionalities of these enzymes have been reported, their mechanisms and related structural environments mediating these disparate specificities in homologous enzymes have not been well characterized. By relating the differences observed in UV and visible light absorption and Cu(II) electron paramagnetic signals to variations in sequence alignments and 3-D homology models of the two A. thaliana enzymes, we identified a putatively proximal cysteine residue (Cys352) in AtCCD1 that is not conserved in AtNCED3. Spectral analysis of the Cys to Ala mutant confirmed its uniqueness and proximity to the metal binding site, but precluded any role for the residue in the mediation of the observed metal binding affinity or associated steric constraint differences. Further analysis of kinetic substrate cleavage properties indicated a decrease in Vmax and a subtle increase in Km for the C352A mutant compared with those observed for the wild-type, thus confirming catalytic site proximity and suggesting possible roles for the unique cysteine in the modulation of substrate affinity and (or) the reaction rate of AtCCD1.
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Affiliation(s)
- Shukui Guo
- Plant Biotechnology Institute, National Research Council Canada, 110 Gymnasium Place, Saskatoon, SK S7N 0W9, Canada
- SK Structural Science Centre, University of Saskatchewan, 110 Science Place, Saskatoon, SK S7N 5C9, Canada
- Department of Biochemistry, University of Saskatchewan, 107 Wiggins Road, Saskatoon, SK S7N 5E5, Canada
| | - Jason Boyd
- Plant Biotechnology Institute, National Research Council Canada, 110 Gymnasium Place, Saskatoon, SK S7N 0W9, Canada
- SK Structural Science Centre, University of Saskatchewan, 110 Science Place, Saskatoon, SK S7N 5C9, Canada
- Department of Biochemistry, University of Saskatchewan, 107 Wiggins Road, Saskatoon, SK S7N 5E5, Canada
| | - Ramaswami Sammynaiken
- Plant Biotechnology Institute, National Research Council Canada, 110 Gymnasium Place, Saskatoon, SK S7N 0W9, Canada
- SK Structural Science Centre, University of Saskatchewan, 110 Science Place, Saskatoon, SK S7N 5C9, Canada
- Department of Biochemistry, University of Saskatchewan, 107 Wiggins Road, Saskatoon, SK S7N 5E5, Canada
| | - Michèle C. Loewen
- Plant Biotechnology Institute, National Research Council Canada, 110 Gymnasium Place, Saskatoon, SK S7N 0W9, Canada
- SK Structural Science Centre, University of Saskatchewan, 110 Science Place, Saskatoon, SK S7N 5C9, Canada
- Department of Biochemistry, University of Saskatchewan, 107 Wiggins Road, Saskatoon, SK S7N 5E5, Canada
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Ohta T, Chakrabarty S, Lipscomb JD, Solomon EI. Near-IR MCD of the nonheme ferrous active site in naphthalene 1,2-dioxygenase: correlation to crystallography and structural insight into the mechanism of Rieske dioxygenases. J Am Chem Soc 2008; 130:1601-10. [PMID: 18189388 DOI: 10.1021/ja074769o] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Near-IR MCD and variable temperature, variable field (VTVH) MCD have been applied to naphthalene 1,2-dioxygenase (NDO) to describe the coordination geometry and electronic structure of the mononuclear nonheme ferrous catalytic site in the resting and substrate-bound forms with the Rieske 2Fe2S cluster oxidized and reduced. The structural results are correlated with the crystallographic studies of NDO and other related Rieske nonheme iron oxygenases to develop molecular level insights into the structure/function correlation for this class of enzymes. The MCD data for resting NDO with the Rieske center oxidized indicate the presence of a six-coordinate high-spin ferrous site with a weak axial ligand which becomes more tightly coordinated when the Rieske center is reduced. Binding of naphthalene to resting NDO (Rieske oxidized and reduced) converts the six-coordinate sites into five-coordinate (5c) sites with elimination of a water ligand. In the Rieske oxidized form the 5c sites are square pyramidal but transform to a 1:2 mixture of trigonal bipyramial/square pyramidal sites when the Rieske center is reduced. Thus the geometric and electronic structure of the catalytic site in the presence of substrate can be significantly affected by the redox state of the Rieske center. The catalytic ferrous site is primed for the O2 reaction when substrate is bound in the active site in the presence of the reduced Rieske site. These structural changes ensure that two electrons and the substrate are present before the binding and activation of O2, which avoids the uncontrolled formation and release of reactive oxygen species.
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Affiliation(s)
- Takehiro Ohta
- Department of Chemistry, Stanford University, Stanford, California 94305, USA
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Bleijlevens B, Shivarattan T, Sedgwick B, Rigby SEJ, Matthews SJ. Replacement of non-heme Fe(II) with Cu(II) in the alpha-ketoglutarate dependent DNA repair enzyme AlkB: spectroscopic characterization of the active site. J Inorg Biochem 2007; 101:1043-8. [PMID: 17553567 DOI: 10.1016/j.jinorgbio.2007.03.018] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2006] [Revised: 03/24/2007] [Accepted: 03/28/2007] [Indexed: 10/23/2022]
Abstract
The bacterial DNA repair enzyme AlkB is an alpha-ketoglutarate (alphaKG) dependent non-heme Fe(II) containing dioxygenase. Here we describe, for the first time, the preparation of a Cu(II)-reconstituted form of AlkB in various complexes. Spectroscopic characterization showed correct AlkB folding upon incorporation of Cu(II) in the active site. The Cu site was classified as a type 2 site by EPR spectroscopy. The accessibility of the active site metal was studied using imidazole as a probe. Although addition of imidazole did not change the EPR spectrum of the AlkB-Cu-alphaKG complex, the spectrum of the AlkB-Cu-succinate complex clearly changed, indicating binding of imidazole at the Cu site. Binding of substrate (methylated DNA) to the AlkB-Cu-alphaKG complex did not induce changes in the EPR spectrum, demonstrating that the substrate does not bind in the immediate vicinity of the metal centre. This work provides a basis for advanced EPR approaches aimed at studying the interactions and dynamics of AlkB complexes in solution.
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Affiliation(s)
- Boris Bleijlevens
- Division of Molecular Biosciences, Faculty of Natural Sciences, Imperial College London, South Kensington Campus, Biochemistry Building, London SW7 2AZ, UK
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Cosper NJ, Eby DM, Kounosu A, Kurosawa N, Neidle EL, Kurtz DM, Iwasaki T, Scott RA. Redox-dependent structural changes in archaeal and bacterial Rieske-type [2Fe-2S] clusters. Protein Sci 2002; 11:2969-73. [PMID: 12441394 PMCID: PMC2373747 DOI: 10.1110/ps.0222402] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Proteins containing Rieske-type [2Fe-2S] clusters play important roles in many biological electron transfer reactions. Typically, [2Fe-2S] clusters are not directly involved in the catalytic transformation of substrate, but rather supply electrons to the active site. We report herein X-ray absorption spectroscopic (XAS) data that directly demonstrate an average increase in the iron-histidine bond length of at least 0.1 A upon reduction of two distantly related Rieske-type clusters in archaeal Rieske ferredoxin from Sulfolobus solfataricus strain P-1 and bacterial anthranilate dioxygenases from Acinetobacter sp. strain ADP1. This localized redox-dependent structural change may fine tune the protein-protein interaction (in the case of ARF) or the interdomain interaction (in AntDO) to facilitate rapid electron transfer between a lower potential Rieske-type cluster and its redox partners, thereby regulating overall oxygenase reactions in the cells.
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Affiliation(s)
- Nathaniel J Cosper
- Center for Metalloenzyme Studies, University of Georgia, Athens 30602, USA.
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12
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Abstract
Our understanding of the biological significance and chemical properties of non-heme iron oxygenases has increased dramatically in recent years. New group members have emerged from genome sequences and biochemical analyses. Spectroscopic and crystallographic studies have provided critical insights into catalysis. Self-hydroxylation reactions, commonplace in these proteins, reveal important features of metallocenter reactivity.
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Affiliation(s)
- Matthew J Ryle
- Department of Microbiology & Molecular Genetics, 160 Giltner Hall, Michigan State University, East Lansing, Michigan 48824, USA
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Van Doorslaer S, Cereghetti GM, Glockshuber R, Schweiger A. Unraveling the Cu2+ Binding Sites in the C-Terminal Domain of the Murine Prion Protein: A Pulse EPR and ENDOR Study. J Phys Chem B 2001. [DOI: 10.1021/jp003115y] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Sabine Van Doorslaer
- Laboratory of Physical Chemistry, ETH Zentrum, CH-8092 Zurich, Switzerland, and Institute of Molecular Biology and Biophysics, ETH Zurich Hönggerberg, CH-8093 Zurich, Switzerland
| | - Grazia M. Cereghetti
- Laboratory of Physical Chemistry, ETH Zentrum, CH-8092 Zurich, Switzerland, and Institute of Molecular Biology and Biophysics, ETH Zurich Hönggerberg, CH-8093 Zurich, Switzerland
| | - Rudi Glockshuber
- Laboratory of Physical Chemistry, ETH Zentrum, CH-8092 Zurich, Switzerland, and Institute of Molecular Biology and Biophysics, ETH Zurich Hönggerberg, CH-8093 Zurich, Switzerland
| | - Arthur Schweiger
- Laboratory of Physical Chemistry, ETH Zentrum, CH-8092 Zurich, Switzerland, and Institute of Molecular Biology and Biophysics, ETH Zurich Hönggerberg, CH-8093 Zurich, Switzerland
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Metzler DE, Metzler CM, Sauke DJ. Electron Transport, Oxidative Phosphorylation, and Hydroxylation. Biochemistry 2001. [DOI: 10.1016/b978-012492543-4/50021-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Sigel H, Kapinos LE. Quantification of isomeric equilibria for metal ion complexes formed in solution by phosphate or phosphonate ligands with a weakly coordinating second site. Coord Chem Rev 2000. [DOI: 10.1016/s0010-8545(00)00307-6] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Solomon EI, Brunold TC, Davis MI, Kemsley JN, Lee SK, Lehnert N, Neese F, Skulan AJ, Yang YS, Zhou J. Geometric and electronic structure/function correlations in non-heme iron enzymes. Chem Rev 2000; 100:235-350. [PMID: 11749238 DOI: 10.1021/cr9900275] [Citation(s) in RCA: 1351] [Impact Index Per Article: 56.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- E I Solomon
- Department of Chemistry, Stanford University, Stanford, California 94305-5080
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