A tethered niacin-derived pincer complex with a nickel-carbon bond in lactate racemase

Desguin, Benoît; Zhang, Tuo; Soumillion, Patrice; Hols, Pascal; Hu, Jian; Hausinger, Robert P.

doi:10.1126/science.aab2272

Cited by 94 publications

(108 citation statements)

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“…S1). The spectrum of 7, but not 4-6, resembles that of lactate racemase, which exhibits two strong absorption peaks at about 380 and 450 nm (5). The spectra of 4-7 suggest that the absorption at about 380 nm is due to the pyridinium moiety, whereas the absorption at about 450 nm is due to the nickel ion.…”

Section: Resultsmentioning

confidence: 83%

“…1). The nickel center is coordinated by an SCS pincer ligand derived from a nicotinic acid mononucleotide, in addition to histidine (200) (5,6). Based on the structure of this active site, it was proposed that the pincer ligand could reversibly capture a hydride from lactate at the carbon atom coordinated to nickel, in a manner similar to nicotinamide adenine dinucleotide in hydride transfer enzymes (Fig.…”

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confidence: 99%

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Nickel pincer model of the active site of lactate racemase involves ligand participation in hydride transfer

Wodrich

Scopelliti

et al. 2017

Proc. Natl. Acad. Sci. U.S.A.

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Lactate racemase is the first enzyme known to possess a metal pincer active site. The enzyme interconverts D-and L-lactic acid, which is important for the assembly of cell walls in many microorganisms. Here, we report a synthetic model of the active site of lactate racemase, which features a pyridinium-based SCS pincer ligand framework bound to nickel. The model complex mediates the dehydrogenation of alcohols, a reaction relevant to lactate racemization. Experimental and computational data indicate ligand participation in the dehydrogenation reaction.biomimetic chemistry | lactate racemase | nickel | pincer ligands | hydride transfer P incer complexes are widely applied in homogeneous catalysis thanks to their stability, diversity, and tunability (1-4). However, only very recently has the first pincer complex been discovered in the active site of a metalloenzyme (5-7). It was reported that lactate racemase, an enzyme responsible for the racemization of lactic acid and hence important for cell wall assembly in many microorganisms, hosts a nickel pincer cofactor (Fig. 1). The nickel center is coordinated by an SCS pincer ligand derived from a nicotinic acid mononucleotide, in addition to histidine (200) (5, 6). Based on the structure of this active site, it was proposed that the pincer ligand could reversibly capture a hydride from lactate at the carbon atom coordinated to nickel, in a manner similar to nicotinamide adenine dinucleotide in hydride transfer enzymes (Fig. 1). Nevertheless, evidence for this mechanism is still lacking.Although several nickel SCS pincer complexes have previously been reported (8-10), none exhibited an essential feature present in the active site of lactate racemase, namely a pyridinium-based pincer backbone. According to the proposed enzyme mechanism, the pyridinium group enables ligand participation in the hydride transfer reaction, which is likely impossible for a more conventional pyridine group. This hypothesis might be tested using model complexes containing either a pyridinium or a pyridine backbone. A further motivation for synthetic models of this unusual active site is the perspective of developing a new, bioinspired pincer ligand platform that enables metal ligand cooperation in catalysis (11,12). With these considerations in mind, we began investigating the biomimetic chemistry of lactate racemase. Here, we report the synthesis and characterization of a synthetic mimic of lactate racemase. Using dehydrogenation of alcohols as a model reaction, we show that the pyridinium functionality indeed facilitates hydride transfer by ligand participation. ResultsSynthesis. The pyridine-based ligand precursor (4) was synthesized from 4-chloro-3,5-dimethyl pyridine (1, Fig. 2). Oxidation of 1 by KMnO 4 gave 4-chloropyridine-3,5-dicarboxylic acid (2), which was converted to a dicarboxamide (3) by amidation. Reaction of 3 with Lawesson's reagent [2,4-bis(4-methoxyphenyl)-2,4-dithioxo-1,3,2,4-dithiadiphosphetane] yielded the ligand precursor 4 containing thioamides (13). Upon treatment o...

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Section: Resultsmentioning

confidence: 83%

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confidence: 99%

Nickel pincer model of the active site of lactate racemase involves ligand participation in hydride transfer

Wodrich

Scopelliti

et al. 2017

Proc. Natl. Acad. Sci. U.S.A.

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“…Certain bacteria possess the ability to interconvert the two enantiomers by using lactate racemase, which was only recently described in genetic (1), structural (2), synthetic modeling (3), and computational studies (4,5).…”

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confidence: 99%

“…This Ni-dependent enzyme (1) contains a newly identified cofactor, pyridinium-3,5-bisthiocarboxylic acid mononucleotide (P2TMN), that is covalently attached to an active-site lysine residue (2). Most interestingly, P2TMN binds an Ni atom using sulfur, carbon, and sulfur atoms of an SCS-pincer complex (2), making LarA the ninth discovered Ni-dependent enzyme (6).…”

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confidence: 99%

Structural insights into the catalytic mechanism of a sacrificial sulfur insertase of the N-type ATP pyrophosphatase family, LarE

Fellner

Desguin

Hausinger

et al. 2017

Proc. Natl. Acad. Sci. U.S.A.

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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.actic acid, composed of both L-and D-isomers, is a widespread organic compound produced during microbial fermentations via stereospecific lactate dehydrogenases. Certain bacteria possess the ability to interconvert the two enantiomers by using lactate racemase, which was only recently described in genetic (1), structural (2), synthetic modeling (3), and computational studies (4, 5).LarA from Lactobacillus plantarum is responsible for lactate racemase activity. This Ni-dependent enzyme (1) contains a newly identified cofactor, pyridinium-3,5-bisthiocarboxylic acid mononucleotide (P2TMN), that is covalently attached to an active-site lysine residue (2). Most interestingly, P2TMN binds an Ni atom using sulfur, carbon, and sulfur atoms of an SCS-pincer complex (2), making LarA the ninth discovered Ni-dependent enzyme (6).Synthesis of Ni-bound P2TMN occurs through a pathway involving three proteins encoded in the lar operon (i.e., LarB, LarC, LarE) (1). LarB is a carboxylase/hydrolase that produces pyridinium-3,5-biscarboxylic acid mononucleotide (P2CMN) from nicotinic acid adenine dinucleotide (7). LarE then converts P2CMN into P2TMN through two successive sulfur transfer reactions. Finally LarC is thought to provide the Ni atom to generate the active form of the pincer cofactor of LarA (7) (Fig. 1).The amino acid sequence of LarE suggests it has two domains. The N-terminal domain is homologous to N-type ATP pyrophosphatase (PPase) domains (8), containing a conserved SGGxDS motif that binds and hydrolyzes ATP to form AMP and pyrophosphate. Examples of enzymes with this domain are guanine monophosphate (GMP) synthetase, nicotinamide mononucleotide (NMN) synthetase, and nicotinamide adenine dinucleotide (NAD) synthetase. These enzymes activate substrate carboxyl or carbonyl groups by adenylylation (AMPylation) (9). The C-terminal domain of LarE has no homology to any member of the N-type ATP PPase family, which use their C-terminal domains to recognize specific substrates and catalyze their versatile reactions. We theref...

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“…[3] Very recently,Desguin et al characterized the structure of the active site of LarA [4] by using ac ombination of mass spectrometry,isotopic labeling,and X-ray crystallography,w hich revealed many unusual features of LarA that have not been seen before in nature. [4,5] As shown in Figure 1b,c, an icotinic acid mononucleotide derivative is tailored to engage in ac omplex with the nickel cofactor to form atridentate pincer complex, with aNi À Cbond and aS À Ni À Sb onding situation. This metal pincer complex with ametal-carbon bond is the first such example found in nature.…”

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The Nickel‐Pincer Complex in Lactate Racemase Is an Electron Relay and Sink that acts through Proton‐Coupled Electron Transfer

Wang

Shaik

2017

Angewandte Chemie

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QM/MM calculations reveal that the nickel pincer complex in lactate racemase functions as ar eversible "singlecenter electrode" that accepts and donates back an electron. In this way,i tc atalyzest he isomerization process d-lactateÐllactate through successive proton-coupled electron-transfer steps.Supportinginformation and the ORCID identification number(s) for the author(s) of this article can be found under: http://dx.

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A tethered niacin-derived pincer complex with a nickel-carbon bond in lactate racemase

Cited by 94 publications

References 30 publications

Nickel pincer model of the active site of lactate racemase involves ligand participation in hydride transfer

Nickel pincer model of the active site of lactate racemase involves ligand participation in hydride transfer

Structural insights into the catalytic mechanism of a sacrificial sulfur insertase of the N-type ATP pyrophosphatase family, LarE

The Nickel‐Pincer Complex in Lactate Racemase Is an Electron Relay and Sink that acts through Proton‐Coupled Electron Transfer

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