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Gatreddi S, Sui D, Hausinger RP, Hu J. Irreversible inactivation of lactate racemase by sodium borohydride reveals reactivity of the nickel-pincer nucleotide cofactor. ACS Catal 2023; 13:1441-1448. [PMID: 37886035 PMCID: PMC10599654 DOI: 10.1021/acscatal.2c05461] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
The nickel-pincer nucleotide (NPN) cofactor discovered in lactate racemase from Lactiplantibacillus plantarum (LarALp) is essential for the activities of racemases/epimerases in the highly diverse LarA superfamily. Prior mechanistic studies have established a proton-coupled hydride-transfer mechanism for LarALp, but direct evidence showing that hydride attacks the C4 atom in the pyridinium ring of NPN has been lacking. Here, we show that sodium borohydride (NaBH4) irreversibly inactivates LarALp accompanied by a rapid color change of the enzyme. The altered ultraviolet-visible spectra during NaBH4 titration supported hydride transfer to C4 of NPN, and the concomitant Ni loss unraveled by mass spectrometry experiments accounted for the irreversible inactivation. High resolution structures of LarALp revealed a substantially weakened C-Ni bond in the metastable sulfite-NPN adduct where the NPN cofactor is in the reduced state. These findings allowed us to propose a mechanism of LarALp inactivation by NaBH4 that provides key insights into the enzyme-catalyzed reaction and sheds light on the reactivity of small molecule NPN mimetics.
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Affiliation(s)
- Santhosh Gatreddi
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, United States
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI 48824, United States
| | - Dexin Sui
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, United States
| | - Robert P. Hausinger
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, United States
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI 48824, United States
| | - Jian Hu
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, United States
- Department of Chemistry, Michigan State University, East Lansing, MI 48824, United States
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Recent progress on group 10 metal complexes of pincer ligands: From synthesis to activities and catalysis. ADVANCES IN ORGANOMETALLIC CHEMISTRY 2021. [DOI: 10.1016/bs.adomc.2021.04.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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Layek S, Agrahari B, Kumar A, Dege N, Pathak DD. Synthesis and X-ray crystal structures of three new nickel(II) complexes of benzoylhydrazones: Catalytic applications in the synthesis of 2-arylbenzoxazoles. Inorganica Chim Acta 2020. [DOI: 10.1016/j.ica.2019.119222] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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Gafurov ZN, Kagilev AA, Kantyukov AO, Balabaev AA, Sinyashin OG, Yakhvarov DG. Classification and synthesis of nickel pincer complexes. Russ Chem Bull 2018. [DOI: 10.1007/s11172-018-2086-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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5
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Schörgenhumer J, Zimmermann A, Waser M. SNS-Ligands for Ru-Catalyzed Homogeneous Hydrogenation and Dehydrogenation Reactions. Org Process Res Dev 2018. [DOI: 10.1021/acs.oprd.8b00142] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Affiliation(s)
- Johannes Schörgenhumer
- Institute of Organic Chemistry, Johannes Kepler University Linz, Altenbergerstr. 69, 4040 Linz, Austria
| | - Axel Zimmermann
- Patheon Austria, part of Thermo Fisher Scientific, St. Peterstr. 25, 4020 Linz, Austria
| | - Mario Waser
- Institute of Organic Chemistry, Johannes Kepler University Linz, Altenbergerstr. 69, 4040 Linz, Austria
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Abstract
Crown ethers are useful macrocycles that act as size-selective binding sites for alkali metals. These frameworks have been incorporated into a number of macromolecular assemblies that use simple cations as reporters and/or activity triggers. Incorporating crown ethers into secondary coordination sphere ligand frameworks for transition metal chemistry will lead to new potential methods for controlling bond formation steps, and routes that couple traditional ligand frameworks with these moieties are highly desirable. Herein we report the syntheses of a family of tridentate phosphine complexes bearing tethered aza-crown ethers (lariats) designed to modularize the variation of aza-crown size, lariat length, and distal phosphine substituents, followed by the synthesis and solid-state structures of Mo(III) complexes bearing cations in the pendent crown ethers.
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Affiliation(s)
- Levente G Pap
- Department of Chemistry, University of Wyoming, Dept. 3838, 1000 E. University Avenue, Laramie, Wyoming 82071, United States
| | - Navamoney Arulsamy
- Department of Chemistry, University of Wyoming, Dept. 3838, 1000 E. University Avenue, Laramie, Wyoming 82071, United States
| | - Elliott B Hulley
- Department of Chemistry, University of Wyoming, Dept. 3838, 1000 E. University Avenue, Laramie, Wyoming 82071, United States
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7
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Yu MJ, Chen SL. From NAD + to Nickel Pincer Complex: A Significant Cofactor Evolution Presented by Lactate Racemase. Chemistry 2017; 23:7545-7557. [PMID: 28374531 DOI: 10.1002/chem.201700405] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2017] [Indexed: 02/02/2023]
Abstract
Lactate racemase (LarA), a new nickel enzyme discovered recently, catalyzes the racemization between d- and l-lactates with a novel nickel pincer cofactor (Ni-PTTMN) derived from nicotinic acid. In this study, by using DFT and a 200-atom active-site model, LarA is revealed to employ a modified proton-coupled hydride-transfer mechanism in which a hydride is transferred to a cofactor pyridine carbon from the substrate α-carbon along with proton transfer from the substrate hydroxy group to a histidine, and then moved back from the opposite side. Tyr294 and Lys298 provide significant acceleration effects by orientating substrates and stabilizing the negative charge developing at the substrate hydroxy oxygen. The barrier was determined to be 12.0 kcal mol-1 , which reveals enhanced racemase activity relative to the LarA reaction using NAD+ -like cofactors. Compared with NAD+ , Ni-PTTMN has a stronger hydride-addition reactivity in moderate and high environmental polarity and may fit perfectly the moderately polar active site of LarA.
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Affiliation(s)
- Ming-Jia Yu
- Key Laboratory of Cluster Science of the Ministry of Education, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, 100081, P.R. China
| | - Shi-Lu Chen
- Key Laboratory of Cluster Science of the Ministry of Education, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, 100081, P.R. China
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Xu T, Wodrich MD, Scopelliti R, Corminboeuf C, Hu X. Nickel pincer model of the active site of lactate racemase involves ligand participation in hydride transfer. Proc Natl Acad Sci U S A 2017; 114:1242-1245. [PMID: 28115700 PMCID: PMC5307482 DOI: 10.1073/pnas.1616038114] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Lactate racemase is the first enzyme known to possess a metal pincer active site. The enzyme interconverts d- and l-lactic acid, which is important for the assembly of cell walls in many microorganisms. Here, we report a synthetic model of the active site of lactate racemase, which features a pyridinium-based SCS pincer ligand framework bound to nickel. The model complex mediates the dehydrogenation of alcohols, a reaction relevant to lactate racemization. Experimental and computational data indicate ligand participation in the dehydrogenation reaction.
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Affiliation(s)
- Tao Xu
- Laboratory of Inorganic Synthesis and Catalysis, Institute of Chemical Sciences and Engineering, Ecole Polytechnique Fédérale de Lausanne, Lausanne CH-1015, Switzerland
| | - Matthew D Wodrich
- Laboratory of Inorganic Synthesis and Catalysis, Institute of Chemical Sciences and Engineering, Ecole Polytechnique Fédérale de Lausanne, Lausanne CH-1015, Switzerland
- Laboratory for Computational Molecular Design, Institute of Chemical Sciences and Engineering, Ecole Polytechnique Fédérale de Lausanne, Lausanne CH-1015, Switzerland
| | - Rosario Scopelliti
- Laboratory of Inorganic Synthesis and Catalysis, Institute of Chemical Sciences and Engineering, Ecole Polytechnique Fédérale de Lausanne, Lausanne CH-1015, Switzerland
| | - Clemence Corminboeuf
- Laboratory for Computational Molecular Design, Institute of Chemical Sciences and Engineering, Ecole Polytechnique Fédérale de Lausanne, Lausanne CH-1015, Switzerland
| | - Xile Hu
- Laboratory of Inorganic Synthesis and Catalysis, Institute of Chemical Sciences and Engineering, Ecole Polytechnique Fédérale de Lausanne, Lausanne CH-1015, Switzerland;
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Shopov DY, Sharninghausen LS, Sinha SB, Borowski JE, Mercado BQ, Brudvig GW, Crabtree RH. Synthesis of pyridine-alkoxide ligands for formation of polynuclear complexes. NEW J CHEM 2017. [DOI: 10.1039/c7nj01845b] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A series of novel polydentate N,O-donor ligands strongly favour formation of polynuclear complexes.
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Desguin B, Zhang T, Soumillion P, Hols P, Hu J, Hausinger RP. METALLOPROTEINS. A tethered niacin-derived pincer complex with a nickel-carbon bond in lactate racemase. Science 2015; 349:66-9. [PMID: 26138974 DOI: 10.1126/science.aab2272] [Citation(s) in RCA: 69] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Lactic acid racemization is involved in lactate metabolism and cell wall assembly of many microorganisms. Lactate racemase (Lar) requires nickel, but the nickel-binding site and the role of three accessory proteins required for its activation remain enigmatic. We combined mass spectrometry and x-ray crystallography to show that Lar from Lactobacillus plantarum possesses an organometallic nickel-containing prosthetic group. A nicotinic acid mononucleotide derivative is tethered to Lys(184) and forms a tridentate pincer complex that coordinates nickel through one metal-carbon and two metal-sulfur bonds, with His(200) as another ligand. Although similar complexes have been previously synthesized, there was no prior evidence for the existence of pincer cofactors in enzymes. The wide distribution of the accessory proteins without Lar suggests that it may play a role in other enzymes.
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Affiliation(s)
- Benoît Desguin
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI 48824, USA
| | - Tuo Zhang
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
| | - Patrice Soumillion
- Institute of Life Sciences, Université Catholique de Louvain, B-1348 Louvain-la-Neuve, Belgium
| | - Pascal Hols
- Institute of Life Sciences, Université Catholique de Louvain, B-1348 Louvain-la-Neuve, Belgium
| | - Jian Hu
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA. 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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Arumugam V, Kaminsky W, Nallasamy D. ONO pincer type Pd(ii) complexes: synthesis, crystal structure and catalytic activity towards C-2 arylation of quinoline scaffolds. RSC Adv 2015. [DOI: 10.1039/c5ra15342e] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Four new palladium(ii) complexes featuring ONO pincer type hydrazone ligands were synthesized and characterized by spectroscopic and single-crystal XRD analysis. Utility of these complexes to catalyze C–C bond formation in quinoline scaffolds were assessed.
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Affiliation(s)
- Vignesh Arumugam
- Inorganic & Nanomaterials Research Laboratory
- Department of Chemistry
- Bharathiar University
- Coimbatore 641 046
- India
| | | | - Dharmaraj Nallasamy
- Inorganic & Nanomaterials Research Laboratory
- Department of Chemistry
- Bharathiar University
- Coimbatore 641 046
- India
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