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Gałyńska M, de Moraes MMF, Tecmer P, Boguslawski K. Delving into the catalytic mechanism of molybdenum cofactors: a novel coupled cluster study. Phys Chem Chem Phys 2024. [PMID: 38952220 DOI: 10.1039/d4cp01500b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/03/2024]
Abstract
In this work, we use modern electronic structure methods to model the catalytic mechanism of different variants of the molybdenum cofactor (Moco). We investigate the dependence of various Moco model systems on structural relaxation and the importance of environmental effects for five critical points along the reaction coordinate with the DMSO and NO3- substrates. Furthermore, we scrutinize the performance of various coupled-cluster approaches for modeling the relative energies along the investigated reaction paths, focusing on several pair coupled cluster doubles (pCCD) flavors and conventional coupled cluster approximations. Moreover, we elucidate the Mo-O bond formation using orbital-based quantum information measures, which highlight the flow of σM-O bond formation and σN/S-O bond breaking. Our study shows that pCCD-based models are a viable alternative to conventional methods and offer us unique insights into the bonding situation along a reaction coordinate. Finally, this work highlights the importance of environmental effects or changes in the core and, consequently, in the model itself to elucidate the change in activity of different Moco variants.
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Affiliation(s)
- Marta Gałyńska
- Institute of Physics, Faculty of Physics, Astronomy, and Informatics, Nicolaus Copernicus University in Toruń, Grudziądzka 5, 87-100 Toruń, Poland.
| | - Matheus Morato F de Moraes
- Institute of Physics, Faculty of Physics, Astronomy, and Informatics, Nicolaus Copernicus University in Toruń, Grudziądzka 5, 87-100 Toruń, Poland.
| | - Paweł Tecmer
- Institute of Physics, Faculty of Physics, Astronomy, and Informatics, Nicolaus Copernicus University in Toruń, Grudziądzka 5, 87-100 Toruń, Poland.
| | - Katharina Boguslawski
- Institute of Physics, Faculty of Physics, Astronomy, and Informatics, Nicolaus Copernicus University in Toruń, Grudziądzka 5, 87-100 Toruń, Poland.
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Giri NC, Mintmier B, Radhakrishnan M, Mielke JW, Wilcoxen J, Basu P. The critical role of a conserved lysine residue in periplasmic nitrate reductase catalyzed reactions. J Biol Inorg Chem 2024; 29:395-405. [PMID: 38782786 DOI: 10.1007/s00775-024-02057-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Accepted: 04/10/2024] [Indexed: 05/25/2024]
Abstract
Periplasmic nitrate reductase NapA from Campylobacter jejuni (C. jejuni) contains a molybdenum cofactor (Moco) and a 4Fe-4S cluster and catalyzes the reduction of nitrate to nitrite. The reducing equivalent required for the catalysis is transferred from NapC → NapB → NapA. The electron transfer from NapB to NapA occurs through the 4Fe-4S cluster in NapA. C. jejuni NapA has a conserved lysine (K79) between the Mo-cofactor and the 4Fe-4S cluster. K79 forms H-bonding interactions with the 4Fe-4S cluster and connects the latter with the Moco via an H-bonding network. Thus, it is conceivable that K79 could play an important role in the intramolecular electron transfer and the catalytic activity of NapA. In the present study, we show that the mutation of K79 to Ala leads to an almost complete loss of activity, suggesting its role in catalytic activity. The inhibition of C. jejuni NapA by cyanide, thiocyanate, and azide has also been investigated. The inhibition studies indicate that cyanide inhibits NapA in a non-competitive manner, while thiocyanate and azide inhibit NapA in an uncompetitive manner. Neither inhibition mechanism involves direct binding of the inhibitor to the Mo-center. These results have been discussed in the context of the loss of catalytic activity of NapA K79A variant and a possible anion binding site in NapA has been proposed.
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Affiliation(s)
- Nitai C Giri
- Department of Chemistry and Chemical Biology, Indiana University Indianapolis, Indianapolis, IN, USA
| | - Breeanna Mintmier
- Department of Chemistry and Chemical Biology, Indiana University Indianapolis, Indianapolis, IN, USA
| | - Manohar Radhakrishnan
- Department of Chemistry and Chemical Biology, Indiana University Indianapolis, Indianapolis, IN, USA
| | - Jonathan W Mielke
- Department of Chemistry and Biochemistry, University of Wisconsin-Milwaukee, Milwaukee, WI, USA
| | - Jarett Wilcoxen
- Department of Chemistry and Biochemistry, University of Wisconsin-Milwaukee, Milwaukee, WI, USA.
| | - Partha Basu
- Department of Chemistry and Chemical Biology, Indiana University Indianapolis, Indianapolis, IN, USA.
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Maia LB. Bringing Nitric Oxide to the Molybdenum World-A Personal Perspective. Molecules 2023; 28:5819. [PMID: 37570788 PMCID: PMC10420851 DOI: 10.3390/molecules28155819] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Revised: 07/29/2023] [Accepted: 07/30/2023] [Indexed: 08/13/2023] Open
Abstract
Molybdenum-containing enzymes of the xanthine oxidase (XO) family are well known to catalyse oxygen atom transfer reactions, with the great majority of the characterised enzymes catalysing the insertion of an oxygen atom into the substrate. Although some family members are known to catalyse the "reverse" reaction, the capability to abstract an oxygen atom from the substrate molecule is not generally recognised for these enzymes. Hence, it was with surprise and scepticism that the "molybdenum community" noticed the reports on the mammalian XO capability to catalyse the oxygen atom abstraction of nitrite to form nitric oxide (NO). The lack of precedent for a molybdenum- (or tungsten) containing nitrite reductase on the nitrogen biogeochemical cycle contributed also to the scepticism. It took several kinetic, spectroscopic and mechanistic studies on enzymes of the XO family and also of sulfite oxidase and DMSO reductase families to finally have wide recognition of the molybdoenzymes' ability to form NO from nitrite. Herein, integrated in a collection of "personal views" edited by Professor Ralf Mendel, is an overview of my personal journey on the XO and aldehyde oxidase-catalysed nitrite reduction to NO. The main research findings and the path followed to establish XO and AO as competent nitrite reductases are reviewed. The evidence suggesting that these enzymes are probable players of the mammalian NO metabolism is also discussed.
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Affiliation(s)
- Luisa B Maia
- LAQV, REQUIMTE, Department of Chemistry, NOVA School of Science and Technology (FCT NOVA), 2829-516 Caparica, Portugal
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Nemykin VN, Sabin JR, Kail BW, Upadhyay A, Hendrich MP, Basu P. Influence of the ligand-field on EPR parameters of cis- and trans-isomers in Mo V systems relevant to molybdenum enzymes: Experimental and density functional theory study. J Inorg Biochem 2023; 245:112228. [PMID: 37149488 PMCID: PMC10330323 DOI: 10.1016/j.jinorgbio.2023.112228] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 04/12/2023] [Accepted: 04/12/2023] [Indexed: 05/08/2023]
Abstract
The electron paramagnetic resonance (EPR) investigation of mononuclear cis- and trans-(L1O)MoOCl2 complexes [L1OH = bis(3,5-dimethylpyrazolyl)-3-tert-butyl-2-hydroxy-5-methylphenyl)methane] reveals a significant difference in their spin Hamiltonian parameters which reflect different equatorial and axial ligand fields created by the heteroscorpionate donor atoms. Density functional theory (DFT) was used to calculate the values of principal components and relative orientations of the g and A tensors, and the molecular framework in four pairs of isomeric mononuclear oxo‑molybdenum(V) complexes (cis- and trans-(L1O)MoOCl2, cis,cis- and cis,trans-(L-N2S2)MoOCl [L-N2S2H2 = N,N'-dimethyl-N,N'-bis(mercaptophenyl)ethylenediamine], cis,cis- and cis,trans-(L-N2S2)MoO(SCN), and cis- and trans-[(dt)2MoO(OMe)]2- [dtH2 = 2,3-dimercapto-2-butene]). Scalar relativistic DFT calculations were conducted using three different exchange-correlation functionals. It was found that the use of hybrid exchange-correlation functional with 25% of the Hartree-Fock exchange leads to the best quantitative agreement between theory and experiment. A simplified ligand-field approach was used to analyze the influence of the ligand fields in all cis- and trans-isomers on energies and contributions of molybdenum d-orbital manifold to g and A tensors and relative orientations. Specifically, contributions that originated from the spin-orbit coupling of the dxz, dyz, and dx2-y2 orbitals into the ground state have been discussed. The new findings are discussed in the context of the experimental data of mononuclear molybdoenzyme, DMSO reductase.
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Affiliation(s)
- Victor N Nemykin
- Department of Chemistry, University of Tennessee - Knoxville, Knoxville, TN 37996, USA; Department of Chemistry and Biochemistry, University of Minnesota Duluth, Duluth, MN 55812, USA.
| | - Jared R Sabin
- Department of Chemistry and Biochemistry, University of Minnesota Duluth, Duluth, MN 55812, USA
| | - Brian W Kail
- Department of Chemistry and Biochemistry, Duquesne University, Pittsburgh, PA 15216, USA
| | - Anup Upadhyay
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, PA 15213, USA
| | - Michael P Hendrich
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, PA 15213, USA.
| | - Partha Basu
- Department of Chemistry and Biochemistry, Duquesne University, Pittsburgh, PA 15216, USA; Department of Chemistry and Chemical Biology, Indiana University Purdue University Indianapolis, Indianapolis, IN 46202, USA.
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Beliaeva M, Seebeck FP. Discovery and Characterization of the Metallopterin-Dependent Ergothioneine Synthase from Caldithrix abyssi. JACS AU 2022; 2:2098-2107. [PMID: 36186560 PMCID: PMC9516567 DOI: 10.1021/jacsau.2c00365] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 08/04/2022] [Accepted: 08/05/2022] [Indexed: 05/29/2023]
Abstract
Ergothioneine is a histidine derivative with a 2-mercaptoimidazole side chain and a trimethylated α-amino group. Although the physiological function of this natural product is not yet understood, the facts that many bacteria, some archaea, and most fungi produce ergothioneine and that plants and animals have specific mechanisms to absorb and distribute ergothioneine in specific tissues suggest a fundamental role in cellular life. The observation that ergothioneine biosynthesis has emerged multiple times in molecular evolution points to the same conclusion. Aerobic bacteria and fungi attach sulfur to the imidazole ring of trimethylhistidine via an O2-dependent reaction that is catalyzed by a mononuclear non-heme iron enzyme. Green sulfur bacteria and archaea use a rhodanese-like sulfur transferase to attach sulfur via oxidative polar substitution. In this report, we describe a third unrelated class of enzymes that catalyze sulfur transfer in ergothioneine production. The metallopterin-dependent ergothioneine synthase from Caldithrix abyssi contains an N-terminal module that is related to the tungsten-dependent acetylene hydratase and a C-terminal domain that is a functional cysteine desulfurase. The two modules cooperate to transfer sulfur from cysteine onto trimethylhistidine. Inactivation of the C-terminal desulfurase blocks ergothioneine production but maintains the ability of the metallopterin to exchange sulfur between ergothioneine and trimethylhistidine. Homologous bifunctional enzymes are encoded exclusively in anaerobic bacterial and archaeal species.
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Affiliation(s)
- Mariia
A. Beliaeva
- Department
of Chemistry, University of Basel, Mattenstrasse 24a, 4002 Basel, Switzerland
- Molecular
Systems Engineering, National Competence
Center in Research (NCCR), 4058 Basel, Switzerland
| | - Florian P. Seebeck
- Department
of Chemistry, University of Basel, Mattenstrasse 24a, 4002 Basel, Switzerland
- Molecular
Systems Engineering, National Competence
Center in Research (NCCR), 4058 Basel, Switzerland
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Maiti BK, Maia LB, Moura JJG. Sulfide and transition metals - A partnership for life. J Inorg Biochem 2021; 227:111687. [PMID: 34953313 DOI: 10.1016/j.jinorgbio.2021.111687] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Revised: 11/24/2021] [Accepted: 11/28/2021] [Indexed: 12/13/2022]
Abstract
Sulfide and transition metals often came together in Biology. The variety of possible structural combinations enabled living organisms to evolve an array of highly versatile metal-sulfide centers to fulfill different physiological roles. The ubiquitous iron‑sulfur centers, with their structural, redox, and functional diversity, are certainly the best-known partners, but other metal-sulfide centers, involving copper, nickel, molybdenum or tungsten, are equally crucial for Life. This review provides a concise overview of the exclusive sulfide properties as a metal ligand, with emphasis on the structural aspects and biosynthesis. Sulfide as catalyst and as a substrate is discussed. Different enzymes are considered, including xanthine oxidase, formate dehydrogenases, nitrogenases and carbon monoxide dehydrogenases. The sulfide effect on the activity and function of iron‑sulfur, heme and zinc proteins is also addressed.
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Affiliation(s)
- Biplab K Maiti
- National Institute of Technology Sikkim, Department of Chemistry, Ravangla Campus, Barfung Block, Ravangla Sub Division, South Sikkim 737139, India.
| | - Luisa B Maia
- LAQV, REQUIMTE, Department of Chemistry, NOVA School of Science and Technology (FCT NOVA), Universidade NOVA de Lisboa, Campus de Caparica, Portugal.
| | - José J G Moura
- LAQV, REQUIMTE, Department of Chemistry, NOVA School of Science and Technology (FCT NOVA), Universidade NOVA de Lisboa, Campus de Caparica, Portugal.
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