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Park S, Lee K, Padmanaban S, Lee Y. Small Molecule Activation at the acriPNP Pincer-Supported Nickel Sites. Acc Chem Res 2024. [PMID: 39373712 DOI: 10.1021/acs.accounts.4c00401] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/08/2024]
Abstract
ConspectusNickel pincer systems have recently attracted much attention for applications in various organometallic reactions and catalysis involving small molecule activation. Their exploration is in part motivated by the presence of nickel in natural systems for efficient catalysis. Among such systems, the nickel-containing metalloenzyme carbon monoxide dehydrogenase (CODH) efficiently and reversibly converts CO2 to CO at its active site. The generated CO moves through a channel from the CODH active site and is transported to a dinuclear nickel site of acetyl-coenzyme A synthase (ACS), which catalyzes organometallic C-S and C-C bond forming reactions. An analogous C-S bond activation process is also mediated by the nickel containing enzyme methyl-coenzyme M reductase (MCR). The nickel centers in these systems feature sulfur- and nitrogen-rich environments, and in the particular case of lactate racemase, an organometallic nickel pincer motif revealing a Ni-C bond is observed. These bioinorganic systems inspired the development of several nickel pincer scaffolds not only to mimic enzyme active sites and their reactivity but also to further extend low-valent organonickel chemistry. In this Account, we detail our continuing efforts in the chemistry of nickel complexes supported by acridane-based PNP pincer ligands focusing on our long-standing interest in biomimetic small molecule activation. We have employed a series of diphosphinoamide pincer ligands to prepare various nickel(II/I/0) complexes and to study the conversion of C1 chemicals such as CO and CO2 to value-added products. In the transformation of C1 chemicals, the key C-O bond cleavage and C-E bond (E = C, N, O, or S, etc.) formation steps typically require overcoming high activation barriers. Interestingly, enzymatic systems overcome such difficulties for C1 conversion and operate efficiently under ambient conditions with the use of nickel organometallic chemistry. Furthermore, we have extended our efforts to the conversion of NOx anions to NO via the sequential deoxygenation by nickel mediated carbonylation, which was applied to catalytic C-N coupling to produce industrially important organonitrogen compound oximes as a strategy for NOx conversion and utilization (NCU). Notably, the rigidified acriPNP pincer backbone that enforces a planar geometry at nickel was found to be an important factor for diversifying organometallic transformations including (a) homolysis of various σ-bonds mediated by T-shaped nickel(I) metalloradical species, (b) C-H bond activation mediated by a nickel(0) dinitrogen species, (c) selective CO2 reactivity of nickel(0)-CO species, (d) C-C bond formation at low-valent nickel(I or 0)-CO sites with iodoalkanes, and (e) catalytic deoxygenation of NOx anions and subsequent C-N coupling of a nickel-NO species with alkyl halides for oxime production. Broadly, our results highlight the importance of molecular design and the rich chemistry of organonickel species for diverse small molecule transformations.
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Affiliation(s)
- Sanha Park
- Department of Chemistry, Seoul National University, Seoul 08826, Republic of Korea
| | - Kunwoo Lee
- Department of Chemistry, Seoul National University, Seoul 08826, Republic of Korea
| | - Sudakar Padmanaban
- Department of Chemistry, Seoul National University, Seoul 08826, Republic of Korea
| | - Yunho Lee
- Department of Chemistry, Seoul National University, Seoul 08826, Republic of Korea
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2
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Chatterjee S, Nevarez JL, Rankin JA, Hu J, Hausinger RP. Structure of the LarB-Substrate Complex and Identification of a Reaction Intermediate during Nickel-Pincer Nucleotide Cofactor Biosynthesis. Biochemistry 2023; 62:3096-3104. [PMID: 37831946 PMCID: PMC10842510 DOI: 10.1021/acs.biochem.3c00242] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/15/2023]
Abstract
LarB catalyzes the first step of biosynthesis for the nickel-pincer nucleotide cofactor by converting nicotinic acid adenine dinucleotide (NaAD) to AMP and pyridinium-3,5-biscarboxylic acid mononucleotide (P2CMN). Prior studies had shown that LarB uses CO2 for substrate carboxylation and reported the structure of a Lactiplantibacillus plantarum LarB·NAD+ complex, revealing a covalent linkage between Cys221 and C4 of the pyridine ring. This interaction was proposed to promote C5 carboxylation, with C5-carboxylated-NaAD suggested to activate magnesium-bound water, leading to phosphoanhydride hydrolysis. Here, we extended the analysis of wild-type LarB by using ultraviolet-visible spectroscopy to obtain additional evidence for cysteinyl side chain attachment to the ring of NAD+, thus demonstrating that this linkage is not a crystallization artifact. Using the S127A variant of L. plantarum LarB, a form of the enzyme with a reduced rate of NaAD hydrolysis, we examined its interaction with the authentic substrate. The intermediate arising from C5 carboxylation of NaAD, dinicotinic acid adenine dinucleotide (DaAD), was identified by using mass spectrometry. S127A LarB exhibited spectroscopic evidence of a Cys221-NAD+ adduct, but a covalent enzyme-NaAD linkage was not detectable. We determined the S127A LarB·NaAD structure, providing new insights into the enzyme mechanism, and tentatively identified the position and mode of CO2 binding. The crystal structure revealed the location of the side chain for Glu180, which was previously disordered, but showed that it is not well positioned to abstract the C5 proton in the adduct species to restore aromaticity as Cys221 is expelled. Based on these combined results, we propose a revised catalytic mechanism of LarB..
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Affiliation(s)
- Shramana Chatterjee
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI 48824, United States
| | - Jorge L. Nevarez
- Department of Chemistry, Michigan State University, East Lansing, MI 48824, United States
| | - Joel A. Rankin
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI 48824, United States
- Present address: Department of Biochemistry Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota, 55108, United States
| | - Jian Hu
- Department of Chemistry, Michigan State University, East Lansing, MI 48824, United States
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, United States
| | - Robert P. Hausinger
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI 48824, United States
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, United States
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3
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Bhatti T, Kumar A, Parihar A, Moncy HK, Emge TJ, Waldie KM, Hasanayn F, Goldman AS. Metal-Ligand Proton Tautomerism, Electron Transfer, and C(sp 3)-H Activation by a 4-Pyridinyl-Pincer Iridium Hydride Complex. J Am Chem Soc 2023; 145:18296-18306. [PMID: 37552857 PMCID: PMC10450815 DOI: 10.1021/jacs.3c03376] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Indexed: 08/10/2023]
Abstract
The para-N-pyridyl-based PCP pincer proligand 3,5-bis(di-tert-butylphosphinomethyl)-2,6-dimethylpyridine (pN-tBuPCP-H) was synthesized and metalated to give the iridium complex (pN-tBuPCP)IrHCl (2-H). In marked contrast with its phenyl-based congeners, e.g., (tBuPCP)IrHCl and derivatives, 2-H is highly air-sensitive and reacts with oxidants such as ferrocenium, trityl cation, and benzoquinone. These oxidations ultimately lead to intramolecular activation of a phosphino-t-butyl C(sp3)-H bond and cyclometalation. Considering the greater electronegativity of N than C, 2-H is expected to be less easily oxidized than simple PCP derivatives; cyclic voltammetry and DFT calculations support this expectation. However, 2-H is calculated to undergo metal-ligand-proton tautomerism (MLPT) to give an N-protonated complex that can be described with resonance forms representing a zwitterionic complex (with a negative charge on Ir) and a p-N-pyridylidene (a remote N-heterocyclic carbene) Ir(I) complex. One-electron oxidation of this tautomer is calculated to be dramatically more favorable than direct oxidation of 2-H (ΔΔG° = -31.3 kcal/mol). The resulting Ir(II) oxidation product is easily deprotonated to give metalloradical 2• which is observed by NMR spectroscopy. 2• can be further oxidized to give cationic Ir(III) complex, 2+, which can oxidatively add a phosphino-t-butyl C-H bond and undergo deprotonation to give the observed cyclometalated product. DFT calculations indicate that less sterically hindered analogues of 2+ would preferentially undergo intermolecular addition of C(sp3)-H bonds, for example, of n-alkanes. The resulting iridium alkyl complexes could undergo facile β-H elimination to afford olefin, thereby completing a catalytic cycle for alkane dehydrogenation driven by one-electron oxidation and deprotonation, enabled by MLPT.
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Affiliation(s)
- Tariq
M. Bhatti
- Department
of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, New Jersey 08854, United States
| | - Akshai Kumar
- Centre
for Nanotechnology, Indian Institute of
Technology Guwahati, Guwahati 781039, Assam, India
| | - Ashish Parihar
- Department
of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, New Jersey 08854, United States
| | - Hellan K. Moncy
- Department
of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, New Jersey 08854, United States
| | - Thomas J. Emge
- Department
of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, New Jersey 08854, United States
| | - Kate M. Waldie
- Department
of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, New Jersey 08854, United States
| | - Faraj Hasanayn
- Department
of Chemistry, American University of Beirut, Beirut 1107 2020, Lebanon
| | - Alan S. Goldman
- Department
of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, New Jersey 08854, United States
- Centre
for Nanotechnology, Indian Institute of
Technology Guwahati, Guwahati 781039, Assam, India
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4
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Parsons LWT, Berben LA. Metallated dihydropyridinates: prospects in hydride transfer and (electro)catalysis. Chem Sci 2023; 14:8234-8248. [PMID: 37564402 PMCID: PMC10411630 DOI: 10.1039/d3sc02080k] [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: 04/22/2023] [Accepted: 07/14/2023] [Indexed: 08/12/2023] Open
Abstract
Hydride transfer (HT) is a fundamental step in a wide range of reaction pathways, including those mediated by dihydropyridinates (DHP-s). Coordination of ions directly to the pyridine ring or functional groups stemming therefrom, provides a powerful approach for influencing the electronic structure and in turn HT chemistry. Much of the work in this area is inspired by the chemistry of bioinorganic systems including NADH. Coordination of metal ions to pyridines lowers the electron density in the pyridine ring and lowers the reduction potential: lower-energy reactions and enhanced selectivity are two outcomes from these modifications. Herein, we discuss approaches for the preparation of DHP-metal complexes and selected examples of their reactivity. We suggest further areas in which these metallated DHP-s could be developed and applied in synthesis and catalysis.
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Affiliation(s)
- Leo W T Parsons
- Department of Chemistry, University of California Davis CA 95616 USA
| | - Louise A Berben
- Department of Chemistry, University of California Davis CA 95616 USA
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5
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Bearne SL. Design and evaluation of substrate-product analog inhibitors for racemases and epimerases utilizing a 1,1-proton transfer mechanism. Methods Enzymol 2023; 690:397-444. [PMID: 37858537 DOI: 10.1016/bs.mie.2023.06.014] [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] [Indexed: 10/21/2023]
Abstract
Racemases and epimerases catalyze the inversion of stereochemistry at asymmetric carbon atoms to generate stereoisomers that often play important roles in normal and pathological physiology. Consequently, there is interest in developing inhibitors of these enzymes for drug discovery. A strategy for the rational design of substrate-product analog (SPA) inhibitors of racemases and epimerases utilizing a direct 1,1-proton transfer mechanism is elaborated. This strategy assumes that two groups on the asymmetric carbon atom remain fixed at active-site binding determinants, while the hydrogen and third, motile group move during catalysis, with the latter potentially traveling between an R- and S-pocket at the active site. SPAs incorporate structural features of the substrate and product, often with geminal disubstitution on the asymmetric carbon atom to simultaneously present the motile group to both the R- and S-pockets. For racemases operating on substrates bearing three polar groups (glutamate, aspartate, and serine racemases) or with compact, hydrophobic binding pockets (proline racemase), substituent motion is limited and the design strategy furnishes inhibitors with poor or modest binding affinities. The approach is most successful when substrates have a large, motile hydrophobic group that binds at a plastic and/or capacious hydrophobic site. Potent inhibitors were developed for mandelate racemase, isoleucine epimerase, and α-methylacyl-CoA racemase using the SPA inhibitor design strategy, exhibiting binding affinities ranging from substrate-like to exceeding that of the substrate by 100-fold. This rational approach for designing inhibitors of racemases and epimerases having the appropriate active-site architectures is a useful strategy for furnishing compounds for drug development.
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Affiliation(s)
- Stephen L Bearne
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS, Canada; Department of Chemistry, Dalhousie University, Halifax, NS, Canada.
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6
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Hausinger RP, Hu J, Desguin B. The nickel-pincer coenzyme of lactate racemase: A case study of uncovering cofactor structure and biosynthesis. Methods Enzymol 2023; 685:341-371. [PMID: 37245907 PMCID: PMC10626555 DOI: 10.1016/bs.mie.2023.03.006] [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] [Indexed: 05/30/2023]
Abstract
Cofactors are essential components of numerous enzymes, therefore their characterization by structural, biophysical, and biochemical approaches is crucial for understanding the resulting catalytic and regulatory mechanisms. In this chapter, we present a case study of a recently discovered cofactor, the nickel-pincer nucleotide (NPN), by demonstrating how we identified and thoroughly characterized this unprecedented nickel-containing coenzyme that is tethered to lactase racemase from Lactiplantibacillus plantarum. In addition, we describe how the NPN cofactor is biosynthesized by a panel of proteins encoded in the lar operon and describe the properties of these novel enzymes. Comprehensive protocols for conducting functional and mechanistic studies of NPN-containing lactate racemase (LarA) and the carboxylase/hydrolase (LarB), sulfur transferase (LarE), and metal insertase (LarC) used for NPN biosynthesis are provided for potential applications towards characterizing enzymes in the same or homologous families.
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Affiliation(s)
- Robert P Hausinger
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, United States; Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, United States.
| | - Jian Hu
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, United States; Department of Chemistry, Michigan State University, East Lansing, MI, United States
| | - Benoît Desguin
- Louvain Institute of Biomolecular Science and Technology, Université catholique de Louvain, Louvain-La-Neuve, Belgium
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7
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Gatreddi S, Urdiain-Arraiza J, Desguin B, Hausinger RP, Hu J. Structural and mutational characterization of a malate racemase from the LarA superfamily. Biometals 2023; 36:303-313. [PMID: 35182264 PMCID: PMC9388697 DOI: 10.1007/s10534-022-00372-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Accepted: 02/07/2022] [Indexed: 01/13/2023]
Abstract
The LarA superfamily consists of nickel-dependent enzymes catalyzing racemization/epimerization reactions using a variety of α-hydroxy acids. The first-characterized LarA, a lactate racemase from Lactobacillus plantarum, led to the discovery of the nickel-pincer nucleotide (NPN) cofactor that is utilized by family members with alternative substrates, including malate racemase from Thermoanaerobacterium thermosaccharolyticum (Mar2). In this work, a higher resolution crystal structure of Mar2 was obtained with better data quality that revealed new structural and dynamic characteristics of the protein. A model of the Mar2 structure with bound cofactor and substrate was generated to uncover the common and the unique features among two distinct subgroups in the LarA superfamily. In addition, structure-guided mutational studies were used to examine the importance of residues that are modeled to interact with NPN and to explore which residues were critical for conferring specificity for malate. In particular, substitution of two residues involved in substrate binding in Mar2 to match the corresponding residues in LarA led to the acquisition of low levels of lactate racemase activity. Of additional interest, the substrate spectrum was expanded to include tartrate, an analog of malate. These new findings will help to better understand structure-function relationships of many other LarA homologs that are broadly distributed in bacterial and archaeal species.
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Affiliation(s)
- Santhosh Gatreddi
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, 48824, USA
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, 48824, USA
| | - Julian Urdiain-Arraiza
- Institute of Biomolecular Science and Technology, Université Catholique de Louvain, 1348, Louvain-La-Neuve, Belgium
| | - Benoît Desguin
- Institute of Biomolecular Science and Technology, Université Catholique de Louvain, 1348, Louvain-La-Neuve, Belgium
| | - Robert P Hausinger
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, 48824, USA.
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, 48824, USA.
| | - 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.
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8
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Hausinger RP. Five decades of metalloenzymology. Enzymes 2023; 54:71-105. [PMID: 37945178 DOI: 10.1016/bs.enz.2023.03.001] [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] [Indexed: 11/12/2023]
Abstract
Metalloenzymes have been detailed in The Enzymes since its inception over half a century ago. Here, I review selected metal-containing enzyme highlights from early chapters in this series and I describe advances made since those contributions. Three topics are emphasized: nickel-containing enzymes, Fe(II)/2-oxoglutarate-dependent oxygenases, and enzymes containing non-canonical iron-sulfur clusters.
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Affiliation(s)
- Robert P Hausinger
- Departments of Microbiology & Molecular Genetics and Biochemistry & Molecular Biology, Michigan State University, East Lansing, MI, United States.
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9
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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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10
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Aleksanyan DV, Churusova SG, Dubasova EV, Ananyev IV, Artyushin OI, Peregudov AS, Klemenkova ZS, Denisov GL, Kozlov VA. Experimental and computational insights into the direct cyclopalladation of different unsymmetrical, yet closely related pincer ligands with thione sulfur donors. Polyhedron 2023. [DOI: 10.1016/j.poly.2023.116303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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11
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Chatterjee S, Gatreddi S, Gupta S, Nevarez JL, Rankin JA, Turmo A, Hu J, Hausinger RP. Unveiling the mechanisms and biosynthesis of a novel nickel-pincer enzyme. Biochem Soc Trans 2022; 50:1187-1196. [PMID: 35960008 PMCID: PMC9880988 DOI: 10.1042/bst20220490] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 07/28/2022] [Accepted: 07/29/2022] [Indexed: 01/31/2023]
Abstract
The nickel-pincer nucleotide (NPN) coenzyme, a substituted pyridinium mononucleotide that tri-coordinates nickel, was first identified covalently attached to a lysine residue in the LarA protein of lactate racemase. Starting from nicotinic acid adenine dinucleotide, LarB carboxylates C5 of the pyridinium ring and hydrolyzes the phosphoanhydride, LarE converts the C3 and C5 carboxylates to thiocarboxylates, and LarC incorporates nickel to form a C-Ni and two S-Ni bonds, during the biosynthesis of this cofactor. LarB uses a novel carboxylation mechanism involving the transient formation of a cysteinyl-pyridinium adduct. Depending on the source of the enzyme, LarEs either catalyze a sacrificial sulfur transfer from a cysteinyl side chain resulting in the formation of dehydroalanine or they utilize a [4Fe-4S] cluster bound by three cysteine residues to accept and transfer a non-core sulfide atom. LarC is a CTP-dependent enzyme that cytidinylylates its substrate, adds nickel, then hydrolyzes the product to release NPN and CMP. Homologs of the four lar genes are widely distributed in microorganisms, with some species containing multiple copies of larA whereas others lack this gene, consistent with the cofactor serving other functions. Several LarA-like proteins were shown to catalyze racemase or epimerase activities using 2-hydroxyacid substrates other than lactic acid. Thus, lactate racemase is the founding member of a large family of NPN-containing enzymes.
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Affiliation(s)
- Shramana Chatterjee
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI 48824, USA
| | - Santhosh Gatreddi
- 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
| | - Swati Gupta
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI 48824, USA
| | - Jorge L. Nevarez
- Department of Chemistry, Michigan State University, East Lansing, MI 48824, USA
| | - Joel A. Rankin
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI 48824, USA
| | - Aiko Turmo
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
| | - 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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12
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Chatterjee S, Parson KF, Ruotolo BT, McCracken J, Hu J, Hausinger RP. Characterization of a [4Fe-4S]-dependent LarE sulfur insertase that facilitates nickel-pincer nucleotide cofactor biosynthesis in Thermotoga maritima. J Biol Chem 2022; 298:102131. [PMID: 35700827 PMCID: PMC9283937 DOI: 10.1016/j.jbc.2022.102131] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Revised: 06/07/2022] [Accepted: 06/10/2022] [Indexed: 11/10/2022] Open
Abstract
Sulfur-insertion reactions are essential for the biosynthesis of several cellular metabolites, including enzyme cofactors. In Lactobacillus plantarum, a sulfur-containing nickel-pincer nucleotide (NPN) cofactor is used as a coenzyme of lactic acid racemase, LarA. During NPN biosynthesis in L. plantarum, sulfur is transferred to a nicotinic acid-derived substrate by LarE, which sacrifices the sulfur atom of its single cysteinyl side chain, forming a dehydroalanine residue. Most LarE homologs contain three conserved cysteine residues that are predicted to cluster at the active site; however, the function of this cysteine cluster is unclear. In this study, we characterized LarE from Thermotoga maritima (LarETm) and show that it uses these three conserved cysteine residues to bind a [4Fe-4S] cluster that is required for sulfur transfer. Notably, we found LarETm retains all side chain sulfur atoms, in contrast to LarELp. We also demonstrate that when provided with L-cysteine and cysteine desulfurase from Escherichia coli (IscSEc), LarETm functions catalytically with IscSEc transferring sulfane sulfur atoms to LarETm. Native mass spectrometry results are consistent with a model wherein the enzyme coordinates sulfide at the nonligated iron atom of the [4Fe-4S] cluster, forming a [4Fe-5S] species, and transferring the noncore sulfide to the activated substrate. This proposed mechanism is like that of TtuA that catalyzes sulfur transfer during 2-thiouridine synthesis. In conclusion, we found that LarE sulfur insertases associated with NPN biosynthesis function either by sacrificial sulfur transfer from the protein or by transfer of a noncore sulfide bound to a [4Fe-4S] cluster.
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Affiliation(s)
- Shramana Chatterjee
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan, USA
| | - Kristine F Parson
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan, USA
| | - Brandon T Ruotolo
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan, USA
| | - John McCracken
- Department of Chemistry, Michigan State University, East Lansing, Michigan, USA
| | - Jian Hu
- Department of Chemistry, Michigan State University, East Lansing, Michigan, USA; Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan, USA
| | - Robert P Hausinger
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan, USA; Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan, USA.
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13
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Turmo A, Hu J, Hausinger RP. Characterization of the nickel-inserting cyclometallase LarC from Moorella thermoacetica and identification of a cytidinylylated reaction intermediate. Metallomics 2022; 14:6539348. [PMID: 35225337 PMCID: PMC8962377 DOI: 10.1093/mtomcs/mfac014] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Accepted: 02/19/2022] [Indexed: 11/13/2022]
Abstract
LarC catalyzes the CTP-dependent insertion of nickel ion into pyridinium-3,5-bisthiocarboxylic acid mononucleotide (P2TMN), the final biosynthetic step for generating the nickel-pincer nucleotide (NPN) enzyme cofactor. In this study, we characterized a LarC homolog from Moorella thermoacetica (LarCMt) and characterized selected properties of the protein. We ruled out the hypothesis that enzyme inhibition by its product pyrophosphate accounts for its apparent single-turnover activity. Most notably, we identified a cytidinylylated-substrate intermediate that is formed during the reaction of LarCMt. Selected LarCMt variants with substitutions at the predicted CTP-binding site retained substantial amounts of activity, but exhibited greatly reduced levels of the CMP-P2TMN intermediate. In contrast, enhanced amounts of the CMP-P2TMN intermediate were generated when using LarCMt from cells grown on medium without supplemental nickel. On the basis of these results, we propose a functional role for CTP in the unprecedented nickel-insertase reaction during NPN biosynthesis.
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Affiliation(s)
- Aiko Turmo
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
| | - 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
- Correspondence: 567 Wilson Rd, Room 2215, Biomedical Physical Sciences, East Lansing, MI 48824, USA. E-mail:
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14
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Ahmed KM, Amani K. Synthesis, characterization, and reactivity of a novel magnetically recyclable triazine‐based Cu‐
NNN
‐pincer complex. Appl Organomet Chem 2022. [DOI: 10.1002/aoc.6630] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Karzan Mahmood Ahmed
- Department of Chemistry, Faculty of Sciences University of Kurdistan Sanandaj Iran
- Department of Chemistry College of Education, University of Garmian Kalar Kurdistan Region Iraq
| | - Kamal Amani
- Department of Chemistry, Faculty of Sciences University of Kurdistan Sanandaj Iran
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15
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Biosynthesis and Degradation of Sulfur Modifications in tRNAs. Int J Mol Sci 2021; 22:ijms222111937. [PMID: 34769366 PMCID: PMC8584467 DOI: 10.3390/ijms222111937] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 10/30/2021] [Accepted: 11/01/2021] [Indexed: 12/23/2022] Open
Abstract
Various sulfur-containing biomolecules include iron–sulfur clusters that act as cofactors for enzymes, sulfur-containing vitamins such as thiamin, and sulfur-modified nucleosides in RNA, in addition to methionine and cysteine in proteins. Sulfur-containing nucleosides are post-transcriptionally introduced into tRNA molecules, where they ensure precise codon recognition or stabilization of tRNA structure, thereby maintaining cellular proteome integrity. Modulating sulfur modification controls the translation efficiency of specific groups of genes, allowing organisms to adapt to specific environments. The biosynthesis of tRNA sulfur nucleosides involves elaborate ‘sulfur trafficking systems’ within cellular sulfur metabolism and ‘modification enzymes’ that incorporate sulfur atoms into tRNA. This review provides an up-to-date overview of advances in our knowledge of the mechanisms involved. It covers the functions, biosynthesis, and biodegradation of sulfur-containing nucleosides as well as the reaction mechanisms of biosynthetic enzymes catalyzed by the iron–sulfur clusters, and identification of enzymes involved in the de-modification of sulfur atoms of RNA. The mechanistic similarity of these opposite reactions is discussed. Mutations in genes related to these pathways can cause human diseases (e.g., cancer, diabetes, and mitochondrial diseases), emphasizing the importance of these pathways.
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16
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The LarB carboxylase/hydrolase forms a transient cysteinyl-pyridine intermediate during nickel-pincer nucleotide cofactor biosynthesis. Proc Natl Acad Sci U S A 2021; 118:2106202118. [PMID: 34548397 DOI: 10.1073/pnas.2106202118] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/23/2021] [Indexed: 11/18/2022] Open
Abstract
Enzymes possessing the nickel-pincer nucleotide (NPN) cofactor catalyze C2 racemization or epimerization reactions of α-hydroxyacid substrates. LarB initiates synthesis of the NPN cofactor from nicotinic acid adenine dinucleotide (NaAD) by performing dual reactions: pyridinium ring C5 carboxylation and phosphoanhydride hydrolysis. Here, we show that LarB uses carbon dioxide, not bicarbonate, as the substrate for carboxylation and activates water for hydrolytic attack on the AMP-associated phosphate of C5-carboxylated-NaAD. Structural investigations show that LarB has an N-terminal domain of unique fold and a C-terminal domain homologous to aminoimidazole ribonucleotide carboxylase/mutase (PurE). Like PurE, LarB is octameric with four active sites located at subunit interfaces. The complex of LarB with NAD+, an analog of NaAD, reveals the formation of a covalent adduct between the active site Cys221 and C4 of NAD+, resulting in a boat-shaped dearomatized pyridine ring. The formation of such an intermediate with NaAD would enhance the reactivity of C5 to facilitate carboxylation. Glu180 is well positioned to abstract the C5 proton, restoring aromaticity as Cys221 is expelled. The structure of as-isolated LarB and its complexes with NAD+ and the product AMP identify additional residues potentially important for substrate binding and catalysis. In combination with these findings, the results from structure-guided mutagenesis studies lead us to propose enzymatic mechanisms for both the carboxylation and hydrolysis reactions of LarB that are distinct from that of PurE.
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17
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Edmonds KA, Jordan MR, Giedroc DP. COG0523 proteins: a functionally diverse family of transition metal-regulated G3E P-loop GTP hydrolases from bacteria to man. Metallomics 2021; 13:6327566. [PMID: 34302342 PMCID: PMC8360895 DOI: 10.1093/mtomcs/mfab046] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Accepted: 07/15/2021] [Indexed: 01/13/2023]
Abstract
Transition metal homeostasis ensures that cells and organisms obtain sufficient metal to meet cellular demand while dispensing with any excess so as to avoid toxicity. In bacteria, zinc restriction induces the expression of one or more Zur (zinc-uptake repressor)-regulated Cluster of Orthologous Groups (COG) COG0523 proteins. COG0523 proteins encompass a poorly understood sub-family of G3E P-loop small GTPases, others of which are known to function as metallochaperones in the maturation of cobalamin (CoII) and NiII cofactor-containing metalloenzymes. Here, we use genomic enzymology tools to functionally analyse over 80 000 sequences that are evolutionarily related to Acinetobacter baumannii ZigA (Zur-inducible GTPase), a COG0523 protein and candidate zinc metallochaperone. These sequences segregate into distinct sequence similarity network (SSN) clusters, exemplified by the ZnII-Zur-regulated and FeIII-nitrile hydratase activator CxCC (C, Cys; X, any amino acid)-containing COG0523 proteins (SSN cluster 1), NiII-UreG (clusters 2, 8), CoII-CobW (cluster 4), and NiII-HypB (cluster 5). A total of five large clusters that comprise ≈ 25% of all sequences, including cluster 3 which harbors the only structurally characterized COG0523 protein, Escherichia coli YjiA, and many uncharacterized eukaryotic COG0523 proteins. We also establish that mycobacterial-specific protein Y (Mpy) recruitment factor (Mrf), which promotes ribosome hibernation in actinomycetes under conditions of ZnII starvation, segregates into a fifth SSN cluster (cluster 17). Mrf is a COG0523 paralog that lacks all GTP-binding determinants as well as the ZnII-coordinating Cys found in CxCC-containing COG0523 proteins. On the basis of this analysis, we discuss new perspectives on the COG0523 proteins as cellular reporters of widespread nutrient stress induced by ZnII limitation.
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Affiliation(s)
- Katherine A Edmonds
- Department of Chemistry, Indiana University, Bloomington, IN 47405-7102, USA
| | - Matthew R Jordan
- Department of Chemistry, Indiana University, Bloomington, IN 47405-7102, USA.,Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, IN 47405, USA
| | - David P Giedroc
- Department of Chemistry, Indiana University, Bloomington, IN 47405-7102, USA.,Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, IN 47405, USA
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18
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Efficient long-range conduction in cable bacteria through nickel protein wires. Nat Commun 2021; 12:3996. [PMID: 34183682 PMCID: PMC8238962 DOI: 10.1038/s41467-021-24312-4] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Accepted: 06/09/2021] [Indexed: 02/06/2023] Open
Abstract
Filamentous cable bacteria display long-range electron transport, generating electrical currents over centimeter distances through a highly ordered network of fibers embedded in their cell envelope. The conductivity of these periplasmic wires is exceptionally high for a biological material, but their chemical structure and underlying electron transport mechanism remain unresolved. Here, we combine high-resolution microscopy, spectroscopy, and chemical imaging on individual cable bacterium filaments to demonstrate that the periplasmic wires consist of a conductive protein core surrounded by an insulating protein shell layer. The core proteins contain a sulfur-ligated nickel cofactor, and conductivity decreases when nickel is oxidized or selectively removed. The involvement of nickel as the active metal in biological conduction is remarkable, and suggests a hitherto unknown form of electron transport that enables efficient conduction in centimeter-long protein structures.
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19
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Lau S, Gasperini D, Webster RL. Amine-Boranes as Transfer Hydrogenation and Hydrogenation Reagents: A Mechanistic Perspective. Angew Chem Int Ed Engl 2021; 60:14272-14294. [PMID: 32935898 PMCID: PMC8248159 DOI: 10.1002/anie.202010835] [Citation(s) in RCA: 57] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Indexed: 11/10/2022]
Abstract
Transfer hydrogenation (TH) has historically been dominated by Meerwein-Ponndorf-Verley (MPV) reactions. However, with growing interest in amine-boranes, not least ammonia-borane (H3 N⋅BH3 ), as potential hydrogen storage materials, these compounds have also started to emerge as an alternative reagent in TH reactions. In this Review we discuss TH chemistry using H3 N⋅BH3 and their analogues (amine-boranes and metal amidoboranes) as sacrificial hydrogen donors. Three distinct pathways were considered: 1) classical TH, 2) nonclassical TH, and 3) hydrogenation. Simple experimental mechanistic probes can be employed to distinguish which pathway is operating and computational analysis can corroborate or discount mechanisms. We find that the pathway in operation can be perturbed by changing the temperature, solvent, amine-borane, or even the substrate used in the system, and subsequently assignment of the mechanism can become nontrivial.
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Affiliation(s)
- Samantha Lau
- Department of ChemistryUniversity of BathClaverton DownBathUK
| | | | - Ruth L. Webster
- Department of ChemistryUniversity of BathClaverton DownBathUK
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20
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Yang J, Ma Z. Research progress on the effects of nickel on hormone secretion in the endocrine axis and on target organs. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2021; 213:112034. [PMID: 33581486 DOI: 10.1016/j.ecoenv.2021.112034] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Revised: 01/27/2021] [Accepted: 02/02/2021] [Indexed: 05/29/2023]
Abstract
BACKGROUND Nickel, as one of the most abundant elements in the earth's crust, plays many roles in human reproduction and life. It is an essential trace element for the human body, but can be harmful in excess amounts. Nickel has a significant impact on endocrine hormones in humans and animals, potentially causing abnormal secretions and changing the structure and function of endocrine organs. This article systematically reviews the effects of nickel on hormone secretion and target organs in the endocrine system and identifies areas of insufficient research. METHODS All data in this article were extracted from peer-reviewed articles. The PubMed, SciFinder, Google Scholar, Web of Science, and China National Knowledge Infrastructure databases were searched for relevant articles. Data on nickel's effect on endocrine system hormones and target organs were retrieved, and manually sorted prior to inclusion in this review. RESULTS Nickel acts on the endocrine system and affects the release and regulation of endocrine hormones. Disorders of endocrine hormones may lead to retardation of human growth and mental development, disturbance of water and salt regulation, and even a decline in reproductive ability. Nickel affects the hypothalamus and pituitary gland by regulating organs upstream of the endocrine axis; it can cause abnormal secretion of pituitary hormones, which affects target organs of the endocrine axis, resulting in dysfunction therein and abnormal secretion of related hormones. Nickel also damages target organs, mainly by inducing apoptosis, which triggers oxidative stress, cell autophagy, free radical release, and DNA damage. However, there are few studies on the endocrine axis, and some of the data are contradictory. Nevertheless, it is clear that nickel affects the endocrine system. CONCLUSIONS Nickel can damage organs in the endocrine system, such as the hypothalamus and pituitary. It also affects the secretion of hormones and damages the target organs of these hormones; this can result in endocrine system dysfunction. However, the results have been equivocal and further research is needed.
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Affiliation(s)
- Jingjing Yang
- The Second Clinical Medical College, Lanzhou University, Lanzhou, 730030 Gansu, China
| | - Zhanjun Ma
- The Second Clinical Medical College, Lanzhou University, Lanzhou, 730030 Gansu, China; Department of Orthopedics, Lanzhou University Second Hospital, Lanzhou, 730030 Gansu, China.
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21
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Nickel as a virulence factor in the Class I bacterial carcinogen, Helicobacter pylori. Semin Cancer Biol 2021; 76:143-155. [PMID: 33865991 DOI: 10.1016/j.semcancer.2021.04.009] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Accepted: 04/12/2021] [Indexed: 01/16/2023]
Abstract
Helicobacter pylori is a human bacterial pathogen that causes peptic ulcers and has been designated a Class I carcinogen by the International Agency for Research on Cancer (IARC). Its ability to survive in the acid environment of the stomach, to colonize the stomach mucosa, and to cause cancer, are linked to two enzymes that require nickel-urease and hydrogenase. Thus, nickel is an important virulence factor and the proteins involved in nickel trafficking are potential antibiotic targets. This review summarizes the nickel biochemistry of H. pylori with a focus on the roles of nickel in virulence, nickel homeostasis, maturation of urease and hydrogenase, and the unique nickel trafficking that occurs between the hydrogenase maturation pathway and urease nickel incorporation that is mediated by the metallochaperone HypA and its partner, HypB.
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22
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Replacing the Z-phenyl Ring in Tamoxifen ® with a para-Connected NCN Pincer-Pt-Cl Grouping by Post-Modification †. Molecules 2021; 26:molecules26071888. [PMID: 33810499 PMCID: PMC8038112 DOI: 10.3390/molecules26071888] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Revised: 03/23/2021] [Accepted: 03/23/2021] [Indexed: 11/26/2022] Open
Abstract
Post-modification of a series of NCN-pincer platinum(II) complexes [PtX(NCN-R-4)] (NCN = [C6H2(CH2NMe2)2-2,6]–, R = C(O)H, C(O)Me and C(O)Et), X = Cl– or Br–) at the para-position using the McMurry reaction was studied. The synthetic route towards two new [PtCl(NCN-R-4)] (R = C(O)Me and C(O)Et) complexes used above is likewise described. The utility and limitations of the McMurry reaction involving these pincer complexes was systematically evaluated. The predicted “homo-coupling” reaction of [PtBr(NCN-C(O)H-4)] led to the unexpected formation of 3,3′,5,5′-tetra[(dimethylamino)methyl]-4,4′-bis(platinum halide)-benzophenone (halide = Br or Cl), referred to hereafter as the bispincer-benzophenone complex 13. This material was further characterized using X-ray crystal structure determination. The applicability of the pincer complexes in the McMurry reaction is shown to open a route towards the synthesis of tamoxifen-type derivatives of which one phenyl ring of Tamoxifen® itself is replaced by an NCN arylplatinum pincer fragment. The newly synthesized derivatives can be used as potential candidates in anti-cancer drug screening protocols. Two NCN-arylpincer platinum tamoxifen type derivatives, 5 and 6, were successfully synthesized and of 5 the separation of the diastereomeric E-/Z-forms was achieved. Compound 6, which is the pivaloyl protected NCN pincer platinum hydroxy-Tamoxifen® derivative, was obtained as a mixture of E-/Z-isomers. The new derivatives were further analyzed and characterized with 1H-, 13C{1H}- and 195Pt{1H}-NMR, IR, exact mass MS and elemental analysis.
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23
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Lau S, Gasperini D, Webster RL. Amine–Boranes as Transfer Hydrogenation and Hydrogenation Reagents: A Mechanistic Perspective. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202010835] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Affiliation(s)
- Samantha Lau
- Department of Chemistry University of Bath Claverton Down Bath UK
| | - Danila Gasperini
- Department of Chemistry University of Bath Claverton Down Bath UK
| | - Ruth L. Webster
- Department of Chemistry University of Bath Claverton Down Bath UK
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24
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Kisgeropoulos EC, Manesis AC, Shafaat HS. Ligand Field Inversion as a Mechanism to Gate Bioorganometallic Reactivity: Investigating a Biochemical Model of Acetyl CoA Synthase Using Spectroscopy and Computation. J Am Chem Soc 2021; 143:849-867. [PMID: 33415980 DOI: 10.1021/jacs.0c10135] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The biological global carbon cycle is largely regulated through microbial nickel enzymes, including carbon monoxide dehydrogenase (CODH), acetyl coenzyme A synthase (ACS), and methyl coenzyme M reductase (MCR). These systems are suggested to utilize organometallic intermediates during catalysis, though characterization of these species has remained challenging. We have established a mutant of nickel-substituted azurin as a scaffold upon which to develop protein-based models of enzymatic intermediates, including the organometallic states of ACS. In this work, we report the comprehensive investigation of the S = 1/2 Ni-CO and Ni-CH3 states using pulsed EPR spectroscopy and computational techniques. While the Ni-CO state shows conventional metal-ligand interactions and a classical ligand field, the Ni-CH3 hyperfine interactions between the methyl protons and the nickel indicate a closer distance than would be expected for an anionic methyl ligand. Structural analysis instead suggests a near-planar methyl ligand that can be best described as cationic. Consistent with this conclusion, the frontier molecular orbitals of the Ni-CH3 species indicate a ligand-centered LUMO, with a d9 population on the metal center, rather than the d7 population expected for a typical metal-alkyl species generated by oxidative addition. Collectively, these data support the presence of an inverted ligand field configuration for the Ni-CH3 Az species, in which the lowest unoccupied orbital is centered on the ligands rather than the more electropositive metal. These analyses provide the first evidence for an inverted ligand field within a biological system. The functional relevance of the electronic structures of both the Ni-CO and Ni-CH3 species are discussed in the context of native ACS, and an inverted ligand field is proposed as a mechanism by which to gate reactivity both within ACS and in other thiolate-containing metalloenzymes.
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Affiliation(s)
- Effie C Kisgeropoulos
- Department of Chemistry and Biochemistry and Ohio State Biochemistry Program, The Ohio State University, Columbus, Ohio 43210, United States
| | - Anastasia C Manesis
- Department of Chemistry and Biochemistry and Ohio State Biochemistry Program, The Ohio State University, Columbus, Ohio 43210, United States
| | - Hannah S Shafaat
- Department of Chemistry and Biochemistry and Ohio State Biochemistry Program, The Ohio State University, Columbus, Ohio 43210, United States
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25
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Affiliation(s)
- Gerard Koten
- Organic Chemistry and Catalysis Debye Institute for Materials Science Faculty of Science Utrecht University 3584CG Utrecht The Netherlands
| | - T. Keith Hollis
- Department of Chemistry Mississippi State University MS 39762 Mississippi State United States
| | - David Morales‐Morales
- Instituto de Química Universidad Nacional Autónoma de México Circuito Exterior, Ciudad Universitaria 04510 Ciudad de México Mexico
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26
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Desguin B, Urdiain-Arraiza J, Da Costa M, Fellner M, Hu J, Hausinger RP, Desmet T, Hols P, Soumillion P. Uncovering a superfamily of nickel-dependent hydroxyacid racemases and epimerases. Sci Rep 2020; 10:18123. [PMID: 33093595 PMCID: PMC7583248 DOI: 10.1038/s41598-020-74802-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Accepted: 10/06/2020] [Indexed: 12/13/2022] Open
Abstract
Isomerization reactions are fundamental in biology. Lactate racemase, which isomerizes L- and D-lactate, is composed of the LarA protein and a nickel-containing cofactor, the nickel-pincer nucleotide (NPN). In this study, we show that LarA is part of a superfamily containing many different enzymes. We overexpressed and purified 13 lactate racemase homologs, incorporated the NPN cofactor, and assayed the isomerization of different substrates guided by gene context analysis. We discovered two malate racemases, one phenyllactate racemase, one α-hydroxyglutarate racemase, two D-gluconate 2-epimerases, and one short-chain aliphatic α-hydroxyacid racemase among the tested enzymes. We solved the structure of a malate racemase apoprotein and used it, along with the previously described structures of lactate racemase holoprotein and D-gluconate epimerase apoprotein, to identify key residues involved in substrate binding. This study demonstrates that the NPN cofactor is used by a diverse superfamily of α-hydroxyacid racemases and epimerases, widely expanding the scope of NPN-dependent enzymes.
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Affiliation(s)
- Benoît Desguin
- Louvain Institute of Biomolecular Science and Technology, UCLouvain, 1348, Louvain-La-Neuve, Belgium.
| | - Julian Urdiain-Arraiza
- Louvain Institute of Biomolecular Science and Technology, UCLouvain, 1348, Louvain-La-Neuve, Belgium
| | | | - Matthias Fellner
- Biochemistry, University of Otago, PO Box 56, Dunedin, Otago, 9054, New Zealand.,Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, 48824, USA
| | - 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 Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, 48824, USA.,Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, 48824, USA
| | - Tom Desmet
- Department of Biotechnology, Ghent University, 9000, Ghent, Belgium
| | - Pascal Hols
- Louvain Institute of Biomolecular Science and Technology, UCLouvain, 1348, Louvain-La-Neuve, Belgium
| | - Patrice Soumillion
- Louvain Institute of Biomolecular Science and Technology, UCLouvain, 1348, Louvain-La-Neuve, Belgium
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27
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Swisher NA, Grubbs RH. Synthesis and Characterization of 3,5-Bis(di- tert-butylphosphinito)pyridine Pincer Complexes. Organometallics 2020. [DOI: 10.1021/acs.organomet.0c00270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Nicholas A. Swisher
- Arnold and Mabel Beckman Laboratory for Chemical Synthesis, California Institute of Technology, Pasadena, California 91125, United States
| | - Robert H. Grubbs
- Arnold and Mabel Beckman Laboratory for Chemical Synthesis, California Institute of Technology, Pasadena, California 91125, United States
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28
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Abstract
At least two types of pincer complexes are known to exist in biology. A metal-pyrroloquinolone quinone (PQQ) cofactor was first identified in bacterial methanol dehydrogenase, and later also found in selected short-chain alcohol dehydrogenases of other microorganisms. The PQQ-associated metal can be calcium, magnesium, or a rare earth element depending on the enzyme sequence. Synthesis of this organic ligand requires a series of accessory proteins acting on a small peptide, PqqA. Binding of metal to PQQ yields an ONO-type pincer complex. More recently, a nickel-pincer nucleotide (NPN) cofactor was discovered in lactate racemase, LarA. This cofactor derives from nicotinic acid adenine dinucleotide via action of a carboxylase/hydrolase, sulfur transferase, and nickel insertase, resulting in an SCS-type pincer complex. The NPN cofactor likely occurs in selected other racemases and epimerases of bacteria, archaea, and a few eukaryotes.
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Affiliation(s)
- Jorge Nevarez
- Department of Chemistry, 578 South Shaw Lane, Michigan State University, East Lansing, Michigan 48824 (USA)
| | - Aiko Turmo
- Department of Biochemistry and Molecular Biology, 603 Wilson Road, Room 212, Michigan State University, East Lansing, Michigan 48824 (USA)
| | - Jian Hu
- Department of Chemistry, 578 South Shaw Lane, Michigan State University, East Lansing, Michigan 48824 (USA).,Department of Biochemistry and Molecular Biology, 603 Wilson Road, Room 212, Michigan State University, East Lansing, Michigan 48824 (USA)
| | - Robert P Hausinger
- Department of Biochemistry and Molecular Biology, 603 Wilson Road, Room 212, Michigan State University, East Lansing, Michigan 48824 (USA).,Department of Microbiology and Molecular Genetics, 567 Wilson Road, 2215 Biomedical Physical Sciences, Michigan State University, East Lansing, Michigan 48824 (USA)
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29
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Crystallographic characterization of a tri-Asp metal-binding site at the three-fold symmetry axis of LarE. Sci Rep 2020; 10:5830. [PMID: 32242052 PMCID: PMC7118094 DOI: 10.1038/s41598-020-62847-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Accepted: 03/20/2020] [Indexed: 11/16/2022] Open
Abstract
Detailed crystallographic characterization of a tri-aspartate metal-binding site previously identified on the three-fold symmetry axis of a hexameric enzyme, LarE from Lactobacillus plantarum, was conducted. By screening an array of monovalent, divalent, and trivalent metal ions, we demonstrated that this metal binding site stoichiometrically binds Ca2+, Mn2+, Fe2+/Fe3+, Co2+, Ni2+, Cu2+, Zn2+, and Cd2+, but not monovalent metal ions, Cr3+, Mg2+, Y3+, Sr2+ or Ba2+. Extensive database searches resulted in only 13 similar metal binding sites in other proteins, indicative of the rareness of tri-aspartate architectures, which allows for engineering such a selective multivalent metal ion binding site into target macromolecules for structural and biophysical characterization.
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30
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Bioinspired Design and Computational Prediction of SCS Nickel Pincer Complexes for Hydrogenation of Carbon Dioxide. Catalysts 2020. [DOI: 10.3390/catal10030319] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Inspired by the structures of the active site of lactate racemase and H2 activation mechanism of mono-iron hydrogenase, we proposed a series of sulphur–carbon–sulphur (SCS) nickel complexes and computationally predicted their potentials for catalytic hydrogenation of CO2. Density functional theory calculations reveal a metal–ligand cooperated mechanism with the participation of a sulfur atom in the SCS pincer ligand as a proton receiver for the heterolytic cleavage of H2. For all newly proposed complexes containing functional groups with different electron-donating and withdrawing abilities in the SCS ligand, the predicted free energy barriers for the hydrogenation of CO2 to formic acid are in a range of 22.2–25.5 kcal/mol in water. Such a small difference in energy barriers indicates limited contributions of those functional groups to the charge density of the metal center. We further explored the catalytic mechanism of the simplest model complex for hydrogenation of formic acid to formaldehyde and obtained a total free energy barrier of 34.6 kcal/mol for the hydrogenation of CO2 to methanol.
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31
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Alfano M, Cavazza C. Structure, function, and biosynthesis of nickel-dependent enzymes. Protein Sci 2020; 29:1071-1089. [PMID: 32022353 DOI: 10.1002/pro.3836] [Citation(s) in RCA: 66] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2020] [Revised: 01/23/2020] [Accepted: 01/23/2020] [Indexed: 12/17/2022]
Abstract
Nickel enzymes, present in archaea, bacteria, plants, and primitive eukaryotes are divided into redox and nonredox enzymes and play key functions in diverse metabolic processes, such as energy metabolism and virulence. They catalyze various reactions by using active sites of diverse complexities, such as mononuclear nickel in Ni-superoxide dismutase, glyoxylase I and acireductone dioxygenase, dinuclear nickel in urease, heteronuclear metalloclusters in [NiFe]-carbon monoxide dehydrogenase, acetyl-CoA decarbonylase/synthase and [NiFe]-hydrogenase, and even more complex cofactors in methyl-CoM reductase and lactate racemase. The presence of metalloenzymes in a cell necessitates a tight regulation of metal homeostasis, in order to maintain the appropriate intracellular concentration of nickel while avoiding its toxicity. As well, the biosynthesis and insertion of nickel active sites often require specific and elaborated maturation pathways, allowing the correct metal to be delivered and incorporated into the target enzyme. In this review, the phylogenetic distribution of nickel enzymes will be briefly described. Their tridimensional structures as well as the complexity of their active sites will be discussed. In view of the latest findings on these enzymes, a special focus will be put on the biosynthesis of their active sites and nickel activation of apo-enzymes.
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Affiliation(s)
- Marila Alfano
- University of Grenoble Alpes, CEA, CNRS, IRIG, CBM, Grenoble, France
| | - Christine Cavazza
- University of Grenoble Alpes, CEA, CNRS, IRIG, CBM, Grenoble, France
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32
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Zambelli B, Mazzei L, Ciurli S. Intrinsic disorder in the nickel-dependent urease network. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2020; 174:307-330. [DOI: 10.1016/bs.pmbts.2020.05.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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33
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Shi R, Wodrich MD, Pan H, Tirani FF, Hu X. Functional Models of the Nickel Pincer Nucleotide Cofactor of Lactate Racemase. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201910490] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Renyi Shi
- Laboratory of Inorganic Synthesis and CatalysisInstitute of Chemical Sciences and EngineeringÉcole Polytechnique Fédérale de Lausanne (EPFL), ISIC-LSCI BCH 3305 Lausanne 1015 Switzerland
| | - Matthew D. Wodrich
- Laboratory of Inorganic Synthesis and CatalysisInstitute of Chemical Sciences and EngineeringÉcole Polytechnique Fédérale de Lausanne (EPFL), ISIC-LSCI BCH 3305 Lausanne 1015 Switzerland
- Laboratory for Computational Molecular DesignInstitute of Chemical Science and EngineeringEcole Polytechnique Fédérale de Lausanne (EPFL) Lausanne 1015 Switzerland
| | - Hui‐Jie Pan
- Laboratory of Inorganic Synthesis and CatalysisInstitute of Chemical Sciences and EngineeringÉcole Polytechnique Fédérale de Lausanne (EPFL), ISIC-LSCI BCH 3305 Lausanne 1015 Switzerland
| | - Farzaneh Fadaei Tirani
- Laboratory of Inorganic Synthesis and CatalysisInstitute of Chemical Sciences and EngineeringÉcole Polytechnique Fédérale de Lausanne (EPFL), ISIC-LSCI BCH 3305 Lausanne 1015 Switzerland
| | - Xile Hu
- Laboratory of Inorganic Synthesis and CatalysisInstitute of Chemical Sciences and EngineeringÉcole Polytechnique Fédérale de Lausanne (EPFL), ISIC-LSCI BCH 3305 Lausanne 1015 Switzerland
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34
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Desage‐El Murr M. Nature is the Cure: Engineering Natural Redox Cofactors for Biomimetic and Bioinspired Catalysis. ChemCatChem 2019. [DOI: 10.1002/cctc.201901642] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Affiliation(s)
- Marine Desage‐El Murr
- Institut de Chimie UMR 7177Université de Strasbourg 1 rue Blaise Pascal Strasbourg 67000 France
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35
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Shi R, Wodrich MD, Pan HJ, Tirani FF, Hu X. Functional Models of the Nickel Pincer Nucleotide Cofactor of Lactate Racemase. Angew Chem Int Ed Engl 2019; 58:16869-16872. [PMID: 31535787 DOI: 10.1002/anie.201910490] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Indexed: 11/06/2022]
Abstract
A novel nickel pincer cofactor was recently discovered in lactate racemase. Reported here are three synthetic nickel pincer complexes that are both structural and functional models of the pincer cofactor in lactate racemase. DFT computations suggest the ipso-carbon atom of the pyridinium pincer ligands act as a hydride acceptor for lactate isomerization, whereas an organometallic pathway involving nickel-mediated β-hydride elimination is less favored.
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Affiliation(s)
- Renyi Shi
- Laboratory of Inorganic Synthesis and Catalysis, Institute of Chemical Sciences and Engineering, École Polytechnique Fédérale de Lausanne (EPFL), ISIC-LSCI, BCH 3305, Lausanne, 1015, Switzerland
| | - Matthew D Wodrich
- Laboratory of Inorganic Synthesis and Catalysis, Institute of Chemical Sciences and Engineering, École Polytechnique Fédérale de Lausanne (EPFL), ISIC-LSCI, BCH 3305, Lausanne, 1015, Switzerland.,Laboratory for Computational Molecular Design, Institute of Chemical Science and Engineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, 1015, Switzerland
| | - Hui-Jie Pan
- Laboratory of Inorganic Synthesis and Catalysis, Institute of Chemical Sciences and Engineering, École Polytechnique Fédérale de Lausanne (EPFL), ISIC-LSCI, BCH 3305, Lausanne, 1015, Switzerland
| | - Farzaneh Fadaei Tirani
- Laboratory of Inorganic Synthesis and Catalysis, Institute of Chemical Sciences and Engineering, École Polytechnique Fédérale de Lausanne (EPFL), ISIC-LSCI, BCH 3305, Lausanne, 1015, Switzerland
| | - Xile Hu
- Laboratory of Inorganic Synthesis and Catalysis, Institute of Chemical Sciences and Engineering, École Polytechnique Fédérale de Lausanne (EPFL), ISIC-LSCI, BCH 3305, Lausanne, 1015, Switzerland
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36
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Qiu B, Wang W, Yang X. Computational Prediction of Ammonia-Borane Dehydrocoupling and Transfer Hydrogenation of Ketones and Imines Catalyzed by SCS Nickel Pincer Complexes. Front Chem 2019; 7:627. [PMID: 31572716 PMCID: PMC6753508 DOI: 10.3389/fchem.2019.00627] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2019] [Accepted: 08/30/2019] [Indexed: 11/22/2022] Open
Abstract
Inspired by the catalytic mechanism and active site structure of lactate racemase, three scorpion-like SCS nickel pincer complexes were proposed as potential catalysts for transfer hydrogenation of ketones and imines with ammonia-borane (AB) as the hydrogen source. Density functional theory calculations reveal a stepwise hydride and proton transfer mechanism for the dehydrocoupling of AB and hydrogenation of N-methylacetonimine, and a concerted proton-coupled hydride transfer process for hydrogenation of acetone, acetophenone, and 3-methyl-2-butanone. Among all proposed Ni complexes, the one with symmetric NH2 group on both arms of the SCS pincer ligand has the lowest free energy barrier of 15.0 kcal/mol for dehydrogenation of AB, as well as total free energy barriers of 17.8, 18.2, 18.0, and 18.6 kcal/mol for hydrogenation of acetone, N-methylacetonimine, acetophenone, and 3-methyl-2-butanone, respectively.
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Affiliation(s)
- Bing Qiu
- Beijing National Laboratory for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Wan Wang
- Beijing National Laboratory for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Xinzheng Yang
- Beijing National Laboratory for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
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37
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Zhuo Q, Zhang H, Ding L, Lin J, Zhou X, Hua Y, Zhu J, Xia H. Rhodapentalenes: Pincer Complexes with Internal Aromaticity. iScience 2019; 19:1214-1224. [PMID: 31551198 PMCID: PMC6831826 DOI: 10.1016/j.isci.2019.08.027] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Revised: 08/08/2019] [Accepted: 08/16/2019] [Indexed: 11/15/2022] Open
Abstract
Pincer complexes are a remarkably versatile family benefited from their stability, diversity, and tunability. Many of them contain aromatic organic rings at the periphery, and aromaticity plays an important role in their stability and properties, whereas their metallacyclic cores are not aromatic. Herein, we report rhodapentalenes, which can be viewed as pincer complexes in which the metallacyclic cores exhibit considerable aromatic character. Rhodapentalenes show good thermal stability, although the rhodium-carbon bonds in such compounds are fragile. Experimental and computational studies suggest that the stabilization of rigid CCC pincer architectures together with an intrinsic aromaticity is vital for these metallacyclic rhodium species. Dearomatization-aromatization reactions, corresponding to metal-ligand cooperation of classical aromatic pincer complexes, were observed in this system. These findings suggest a new concept for pincer chemistry, the internal aromaticity involving metal d-orbitals, which would be useful for exploiting the nature of construction motif and inspire further applications.
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Affiliation(s)
- Qingde Zhuo
- State Key Laboratory of Physical Chemistry of Solid Surfaces and Collaborative Innovation Center of Chemistry for Energy Materials (iChEM), College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Hong Zhang
- State Key Laboratory of Physical Chemistry of Solid Surfaces and Collaborative Innovation Center of Chemistry for Energy Materials (iChEM), College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Linting Ding
- State Key Laboratory of Physical Chemistry of Solid Surfaces and Collaborative Innovation Center of Chemistry for Energy Materials (iChEM), College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Jianfeng Lin
- State Key Laboratory of Physical Chemistry of Solid Surfaces and Collaborative Innovation Center of Chemistry for Energy Materials (iChEM), College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Xiaoxi Zhou
- State Key Laboratory of Physical Chemistry of Solid Surfaces and Collaborative Innovation Center of Chemistry for Energy Materials (iChEM), College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Yuhui Hua
- State Key Laboratory of Physical Chemistry of Solid Surfaces and Collaborative Innovation Center of Chemistry for Energy Materials (iChEM), College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Jun Zhu
- State Key Laboratory of Physical Chemistry of Solid Surfaces and Collaborative Innovation Center of Chemistry for Energy Materials (iChEM), College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Haiping Xia
- State Key Laboratory of Physical Chemistry of Solid Surfaces and Collaborative Innovation Center of Chemistry for Energy Materials (iChEM), College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China; Department of Chemistry, Shenzhen Grubbs Institute, Southern University of Science and Technology, Shenzhen 518055, China.
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38
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Abstract
The advancements of quantum chemical methods and computer power allow detailed mechanistic investigations of metalloenzymes. In particular, both quantum chemical cluster and combined QM/MM approaches have been used, which have been proven to successfully complement experimental studies. This review starts with a brief introduction of nickel-dependent enzymes and then summarizes theoretical studies on the reaction mechanisms of these enzymes, including NiFe hydrogenase, methyl-coenzyme M reductase, nickel CO dehydrogenase, acetyl CoA synthase, acireductone dioxygenase, quercetin 2,4-dioxygenase, urease, lactate racemase, and superoxide dismutase.
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39
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Zhou X, Pang X, Nie L, Zhu C, Zhuo K, Zhuo Q, Chen Z, Liu G, Zhang H, Lin Z, Xia H. Successive modification of polydentate complexes gives access to planar carbon- and nitrogen-based ligands. Nat Commun 2019; 10:1488. [PMID: 30940808 PMCID: PMC6445293 DOI: 10.1038/s41467-019-09367-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Accepted: 03/08/2019] [Indexed: 11/15/2022] Open
Abstract
Polydentate complexes containing combinations of nitrogen and carbon (N and C) ligating atoms are among the most fundamental and ubiquitous molecules in coordination chemistry, yet the formation of such complexes with planar high-coordinate N/C sites remains challenging. Herein, we demonstrate an efficient route to access related complexes with tetradentate CCCN and pentadentate CCCCN and NCCCN cores by successive modification of the coordinating atoms in complexes with a CCCC core. Combined experimental and computational studies reveal that the rich reactivity of metal-carbon bonds and the inherent aromaticity of the metallacyclic skeletons play key roles in these transformations. This strategy addresses the paucity of synthetic approaches to mixed N/C planar pentadentate chelating species and provides valuable insights into the synthesis of carbon-based high-coordinate complexes. Furthermore, the resulting complexes are the examples of organometallic species with combined photoacoustic, photothermal, and sonodynamic properties, which makes them promising for application in related areas.
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Affiliation(s)
- Xiaoxi Zhou
- State Key Laboratory of Physical Chemistry of Solid Surfaces and Collaborative Innovation Centre of Chemistry for Energy Materials (iChEM), College of Chemistry and Chemical Engineering, Xiamen University, 361005, Xiamen, China
| | - Xin Pang
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, Centre for Molecular Imaging and Translational Medicine, School of Public Health, Xiamen University, 361102, Xiamen, China
| | - Liming Nie
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, Centre for Molecular Imaging and Translational Medicine, School of Public Health, Xiamen University, 361102, Xiamen, China
| | - Congqing Zhu
- State Key Laboratory of Physical Chemistry of Solid Surfaces and Collaborative Innovation Centre of Chemistry for Energy Materials (iChEM), College of Chemistry and Chemical Engineering, Xiamen University, 361005, Xiamen, China
- State Key Laboratory of Coordination Chemistry, Jiangsu Key Laboratory of Advanced Organic Materials, School of Chemistry and Chemical Engineering, Nanjing University, 210023, Nanjing, China
| | - Kaiyue Zhuo
- State Key Laboratory of Physical Chemistry of Solid Surfaces and Collaborative Innovation Centre of Chemistry for Energy Materials (iChEM), College of Chemistry and Chemical Engineering, Xiamen University, 361005, Xiamen, China
| | - Qingde Zhuo
- State Key Laboratory of Physical Chemistry of Solid Surfaces and Collaborative Innovation Centre of Chemistry for Energy Materials (iChEM), College of Chemistry and Chemical Engineering, Xiamen University, 361005, Xiamen, China
| | - Zhixin Chen
- State Key Laboratory of Physical Chemistry of Solid Surfaces and Collaborative Innovation Centre of Chemistry for Energy Materials (iChEM), College of Chemistry and Chemical Engineering, Xiamen University, 361005, Xiamen, China
| | - Gang Liu
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, Centre for Molecular Imaging and Translational Medicine, School of Public Health, Xiamen University, 361102, Xiamen, China
| | - Hong Zhang
- State Key Laboratory of Physical Chemistry of Solid Surfaces and Collaborative Innovation Centre of Chemistry for Energy Materials (iChEM), College of Chemistry and Chemical Engineering, Xiamen University, 361005, Xiamen, China.
| | - Zhenyang Lin
- Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, HK, Hong Kong
| | - Haiping Xia
- State Key Laboratory of Physical Chemistry of Solid Surfaces and Collaborative Innovation Centre of Chemistry for Energy Materials (iChEM), College of Chemistry and Chemical Engineering, Xiamen University, 361005, Xiamen, China
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40
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New metal cofactors and recent metallocofactor insights. Curr Opin Struct Biol 2019; 59:1-8. [PMID: 30711735 DOI: 10.1016/j.sbi.2018.12.008] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Accepted: 12/20/2018] [Indexed: 11/23/2022]
Abstract
A vast array of metal cofactors are associated with the active sites of metalloenzymes. This Opinion describes the most recently discovered metal cofactor, a nickel-pincer nucleotide (NPN) coenzyme that is covalently tethered to lactate racemase from Lactobacillus plantarum. The enzymatic function of the NPN cofactor and its pathway for biosynthesis are reviewed. Furthermore, insights are summarized from recent advances involving other selected organometallic and inorganic-cluster cofactors including the lanthanide-pyrroloquinoline quinone found in certain alcohol dehydrogenases, tungsten-pyranopterins or molybdenum-pyranopterins in chosen enzymes, the iron-guanylylpyridinol cofactor of [Fe] hydrogenase, the nickel-tetrapyrrole coenzyme F430 of methyl coenzyme M reductase, the vanadium-iron cofactor of nitrogenase, redox-dependent rearrangements of the nickel-iron-sulfur C-cluster in carbon monoxide dehydrogenase, and light-dependent changes in the multi-manganese cluster of the oxygen-evolving complex.
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41
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Computational Design of SCS Nickel Pincer Complexes for the Asymmetric Transfer Hydrogenation of 1-Acetonaphthone. Catalysts 2019. [DOI: 10.3390/catal9010101] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Inspired by the active site structures of lactate racemase and recently reported sulphur–carbon–sulphur (SCS) nickel pincer complexes, a series of scorpion-like SCS nickel pincer complexes with an imidazole tail and asymmetric claws was proposed and examined computationally as potential catalysts for the asymmetric transfer hydrogenation of 1-acetonaphthone. Density functional theory calculations reveal a proton-coupled hydride transfer mechanism for the dehydrogenation of (R)-(+)-1-phenyl-ethanol and the hydrogenation of 1-acetonaphthone to produce (R)-(+)-1-(2-naphthyl)ethanol and (S)-(−)-1-(2-naphthyl)ethanol. Among all proposed Ni complexes, 1Ph is the most active one with a rather low free energy barrier of 24 kcal/mol and high enantioselectivity of near 99% enantiomeric excess (ee) for the hydrogenation of prochiral ketones to chiral alcohols.
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42
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Zhang RK, Huang X, Arnold FH. Selective CH bond functionalization with engineered heme proteins: new tools to generate complexity. Curr Opin Chem Biol 2018; 49:67-75. [PMID: 30343008 DOI: 10.1016/j.cbpa.2018.10.004] [Citation(s) in RCA: 98] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2018] [Revised: 09/27/2018] [Accepted: 10/02/2018] [Indexed: 12/13/2022]
Abstract
CH functionalization is an attractive strategy to construct and diversify molecules. Heme proteins, predominantly cytochromes P450, are responsible for an array of CH oxidations in biology. Recent work has coupled concepts from synthetic chemistry, computation, and natural product biosynthesis to engineer heme protein systems to deliver products with tailored oxidation patterns. Heme protein catalysis has been shown to go well beyond these native reactions and now accesses new-to-nature CH transformations, including CN and CC bond forming processes. Emerging work with these systems moves us along the ambitious path of building complexity from the ubiquitous CH bond.
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Affiliation(s)
- Ruijie K Zhang
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 East California Boulevard, MC 210-41, Pasadena, CA 91125, United States
| | - Xiongyi Huang
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 East California Boulevard, MC 210-41, Pasadena, CA 91125, United States
| | - Frances H Arnold
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 East California Boulevard, MC 210-41, Pasadena, CA 91125, United States.
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43
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Fellner M, Rankin JA, Desguin B, Hu J, Hausinger RP. Analysis of the Active Site Cysteine Residue of the Sacrificial Sulfur Insertase LarE from Lactobacillus plantarum. Biochemistry 2018; 57:5513-5523. [PMID: 30157639 DOI: 10.1021/acs.biochem.8b00601] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
LarE from Lactobacillus plantarum is an ATP-dependent sulfur transferase that sacrifices its Cys176 sulfur atom to form a dehydroalanine (Dha) side chain during biosynthesis of the covalently linked nickel-pincer nucleotide (NPN) cofactor (pyridinium 3-thioamide-5-thiocarboxylic acid mononucleotide) of lactate racemase. Coenzyme A (CoA) stabilizes LarE and forms a CoA-Cys176 mixed disulfide with the protein. This study presents the crystal structure of the LarE/CoA complex, revealing protein interactions with CoA that mimic those for binding ATP. CoA weakly inhibits LarE activity, and the persulfide of CoA is capable of partially regenerating functional LarE from the Dha176 form of the protein. The physiological relevance of this cycling reaction is unclear. A new form of LarE was discovered, an NPN-LarE covalent adduct, explaining prior results in which activation of the lactate racemase apoprotein required only the isolated LarE. The crystal structure of the inactive C176A variant revealed a fold essentially identical to that of wild-type LarE. Additional active site variants of LarE were created and their activities characterized, with all LarE variants analyzed in terms of the structure. Finally, the L. plantarum LarE structure was compared to a homology model of Thermoanaerobacterium thermosaccharolyticum LarE, predicted to contain three cysteine residues at the active site, and to other proteins with a similar fold and multiple active site cysteine residues. These findings suggest that some LarE orthologs may not be sacrificial but instead may catalyze sulfur transfer by using a persulfide mechanism or from a labile site on a [4Fe-4S] cluster at this position.
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Affiliation(s)
- Matthias Fellner
- Department of Biochemistry and Molecular Biology , Michigan State University , East Lansing , Michigan 48824 , United States
| | - Joel A Rankin
- Department of Biochemistry and Molecular Biology , Michigan State University , East Lansing , Michigan 48824 , United States
| | - Benoît Desguin
- 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 , Michigan 48824 , United States.,Department of Chemistry , Michigan State University , East Lansing , Michigan 48824 , United States
| | - Robert P Hausinger
- Department of Biochemistry and Molecular Biology , Michigan State University , East Lansing , Michigan 48824 , United States.,Department of Microbiology and Molecular Genetics , Michigan State University , East Lansing , Michigan 48824 , United States
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44
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Hausinger RP, Desguin B, Fellner M, Rankin JA, Hu J. Nickel-pincer nucleotide cofactor. Curr Opin Chem Biol 2018; 47:18-23. [PMID: 30015232 DOI: 10.1016/j.cbpa.2018.06.019] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2018] [Revised: 06/15/2018] [Accepted: 06/19/2018] [Indexed: 10/28/2022]
Abstract
A novel organometallic cofactor, nickel pyridinium-3,5-dithiocarboxylic acid mononucleotide, was recently discovered in lactate racemase (LarA) of Lactobacillus plantarum. This review summarizes the substantial progress made in uncovering the function of this cofactor as a transient hydride acceptor in the LarA mechanism. The latest developments related to cofactor biosynthesis reveal insights into a pathway in which LarB serves as a nicotinic acid adenine dinucleotide hydrolase/carboxylase, LarE acts as a sacrificial sulfur transferase, and LarC functions as a nickel insertase, forming the nickel-pincer nucleotide cofactor that becomes covalently tethered to LarA in some bacteria. Bioinformatic studies reveal a widespread occurrence of larA, larB, larC, and larE orthologs in microorganisms, and additional roles for the cofactor are considered.
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Affiliation(s)
- 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.
| | - Benoît Desguin
- Institute of Life Sciences, Université catholique de Louvain, B-1348 Louvain-La-Neuve, Belgium
| | - Matthias Fellner
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
| | - Joel A Rankin
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
| | - 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
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45
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Desguin B, Fellner M, Riant O, Hu J, Hausinger RP, Hols P, Soumillion P. Biosynthesis of the nickel-pincer nucleotide cofactor of lactate racemase requires a CTP-dependent cyclometallase. J Biol Chem 2018; 293:12303-12317. [PMID: 29887527 DOI: 10.1074/jbc.ra118.003741] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Revised: 05/29/2018] [Indexed: 11/06/2022] Open
Abstract
Bacterial lactate racemase is a nickel-dependent enzyme that contains a cofactor, nickel pyridinium-3,5-bisthiocarboxylic acid mononucleotide, hereafter named nickel-pincer nucleotide (NPN). The LarC enzyme from the bacterium Lactobacillus plantarum participates in NPN biosynthesis by inserting nickel ion into pyridinium-3,5-bisthiocarboxylic acid mononucleotide. This reaction, known in organometallic chemistry as a cyclometalation, is characterized by the formation of new metal-carbon and metal-sulfur σ bonds. LarC is therefore the first cyclometallase identified in nature, but the molecular mechanism of LarC-catalyzed cyclometalation is unknown. Here, we show that LarC activity requires Mn2+-dependent CTP hydrolysis. The crystal structure of the C-terminal domain of LarC at 1.85 Å resolution revealed a hexameric ferredoxin-like fold and an unprecedented CTP-binding pocket. The loss-of-function of LarC variants with alanine variants of acidic residues leads us to propose a carboxylate-assisted mechanism for nickel insertion. This work also demonstrates the in vitro synthesis and purification of the NPN cofactor, opening new opportunities for the study of this intriguing cofactor and of NPN-utilizing enzymes.
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Affiliation(s)
| | | | - Olivier Riant
- Institute of Condensed Matter and Nanosciences, Université Catholique de Louvain, B-1348 Louvain-La-Neuve, Belgium and
| | - Jian Hu
- the Departments of Biochemistry and Molecular Genetics.,Chemistry, and
| | - Robert P Hausinger
- the Departments of Biochemistry and Molecular Genetics.,Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan 48824
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46
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Zhang T, Zhang X, Chung LW. Computational Insights into the Reaction Mechanisms of Nickel-Catalyzed Hydrofunctionalizations and Nickel-Dependent Enzymes. ASIAN J ORG CHEM 2018. [DOI: 10.1002/ajoc.201700645] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Tonghuan Zhang
- Department of Chemistry; South University of Science and Technology of China (SUSTech); Shenzhen 518055 China
- Lab of Computational Chemistry and Drug Design; Key Laboratory of Chemical Genomics; Peking University Shenzhen Graduate School; Shenzhen 518055 China
| | - Xiaoyong Zhang
- Department of Chemistry; South University of Science and Technology of China (SUSTech); Shenzhen 518055 China
| | - Lung Wa Chung
- Department of Chemistry; South University of Science and Technology of China (SUSTech); Shenzhen 518055 China
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Rankin JA, Mauban RC, Fellner M, Desguin B, McCracken J, Hu J, Varganov SA, Hausinger RP. Lactate Racemase Nickel-Pincer Cofactor Operates by a Proton-Coupled Hydride Transfer Mechanism. Biochemistry 2018; 57:3244-3251. [PMID: 29489337 DOI: 10.1021/acs.biochem.8b00100] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Lactate racemase (LarA) of Lactobacillus plantarum contains a novel organometallic cofactor with nickel coordinated to a covalently tethered pincer ligand, pyridinium-3-thioamide-5-thiocarboxylic acid mononucleotide, but its function in the enzyme mechanism has not been elucidated. This study presents direct evidence that the nickel-pincer cofactor facilitates a proton-coupled hydride transfer (PCHT) mechanism during LarA-catalyzed lactate racemization. No signal was detected by electron paramagnetic resonance spectroscopy for LarA in the absence or presence of substrate, consistent with a +2 metal oxidation state and inconsistent with a previously proposed proton-coupled electron transfer mechanism. Pyruvate, the predicted intermediate for a PCHT mechanism, was observed in quenched solutions of LarA. A normal substrate kinetic isotope effect ( kH/ kD of 3.11 ± 0.17) was established using 2-α-2H-lactate, further supporting a PCHT mechanism. UV-visible spectroscopy revealed a lactate-induced perturbation of the cofactor spectrum, notably increasing the absorbance at 340 nm, and demonstrated an interaction of the cofactor with the inhibitor sulfite. A crystal structure of LarA provided greater resolution (2.4 Å) than previously reported and revealed sulfite binding to the pyridinium C4 atom of the reduced pincer cofactor, mimicking hydride reduction during a PCHT catalytic cycle. Finally, computational modeling supports hydride transfer to the cofactor at the C4 position or to the nickel atom, but with formation of a nickel-hydride species requiring dissociation of the His200 metal ligand. In aggregate, these studies provide compelling evidence that the nickel-pincer cofactor acts by a PCHT mechanism.
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Affiliation(s)
| | - Robert C Mauban
- Department of Chemistry , University of Nevada , Reno , Nevada 89557 , United States
| | | | - Benoît Desguin
- Institute of Life Sciences , Université catholique de Louvain , B-1348 Louvain-La-Neuve , Belgium
| | | | | | - Sergey A Varganov
- Department of Chemistry , University of Nevada , Reno , Nevada 89557 , United States
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Wang WJ, Wei WJ, Liao RZ. Deciphering the chemoselectivity of nickel-dependent quercetin 2,4-dioxygenase. Phys Chem Chem Phys 2018; 20:15784-15794. [DOI: 10.1039/c8cp02683a] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
QM/MM calculations were performed to elucidate the reaction mechanism and chemoselectivity of 2,4-QueD. The protonation state of the first-shell ligand Glu74 plays an important role in dictating the selectivity.
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Affiliation(s)
- Wen-Juan Wang
- Key Laboratory of Material Chemistry for Energy Conversion and Storage
- Ministry of Education
- Hubei Key Laboratory of Bioinorganic Chemistry and Materia Medica
- Hubei Key Laboratory of Materials Chemistry and Service Failure
- School of Chemistry and Chemical Engineering
| | - Wen-Jie Wei
- Key Laboratory of Material Chemistry for Energy Conversion and Storage
- Ministry of Education
- Hubei Key Laboratory of Bioinorganic Chemistry and Materia Medica
- Hubei Key Laboratory of Materials Chemistry and Service Failure
- School of Chemistry and Chemical Engineering
| | - Rong-Zhen Liao
- Key Laboratory of Material Chemistry for Energy Conversion and Storage
- Ministry of Education
- Hubei Key Laboratory of Bioinorganic Chemistry and Materia Medica
- Hubei Key Laboratory of Materials Chemistry and Service Failure
- School of Chemistry and Chemical Engineering
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Structural insights into the catalytic mechanism of a sacrificial sulfur insertase of the N-type ATP pyrophosphatase family, LarE. Proc Natl Acad Sci U S A 2017; 114:9074-9079. [PMID: 28784764 DOI: 10.1073/pnas.1704967114] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
The lar operon in Lactobacillus plantarum encodes five Lar proteins (LarA/B/C/D/E) that collaboratively synthesize and incorporate a niacin-derived Ni-containing cofactor into LarA, an Ni-dependent lactate racemase. Previous studies have established that two molecules of LarE catalyze successive thiolation reactions by donating the sulfur atom of their exclusive cysteine residues to the substrate. However, the catalytic mechanism of this very unusual sulfur-sacrificing reaction remains elusive. In this work, we present the crystal structures of LarE in ligand-free and several ligand-bound forms, demonstrating that LarE is a member of the N-type ATP pyrophosphatase (PPase) family with a conserved N-terminal ATP PPase domain and a unique C-terminal domain harboring the putative catalytic site. Structural analysis, combined with structure-guided mutagenesis, leads us to propose a catalytic mechanism that establishes LarE as a paradigm for sulfur transfer through sacrificing its catalytic cysteine residue.
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