A Novel Nickel Pincer Complex in the Active Site of Lactate Racemase

Metal-Ligand Proton Tautomerism, Electron Transfer, and C(sp3)-H Activation by a 4-Pyridinyl-Pincer Iridium Hydride Complex

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.

Functional Models of the Nickel Pincer Nucleotide Cofactor of Lactate Racemase

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.

Theoretical Studies of Nickel-Dependent Enzymes

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.

From NAD+ to Nickel Pincer Complex: A Significant Cofactor Evolution Presented by Lactate Racemase

Lactate racemase (LarA), a new nickel enzyme discovered recently, catalyzes the racemization between d- and l-lactates with a novel nickel pincer cofactor (Ni-PTTMN) derived from nicotinic acid. In this study, by using DFT and a 200-atom active-site model, LarA is revealed to employ a modified proton-coupled hydride-transfer mechanism in which a hydride is transferred to a cofactor pyridine carbon from the substrate α-carbon along with proton transfer from the substrate hydroxy group to a histidine, and then moved back from the opposite side. Tyr294 and Lys298 provide significant acceleration effects by orientating substrates and stabilizing the negative charge developing at the substrate hydroxy oxygen. The barrier was determined to be 12.0 kcal mol^-1 , which reveals enhanced racemase activity relative to the LarA reaction using NAD⁺ -like cofactors. Compared with NAD⁺ , Ni-PTTMN has a stronger hydride-addition reactivity in moderate and high environmental polarity and may fit perfectly the moderately polar active site of LarA.

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

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.

A bio-inspired design and computational prediction of scorpion-like SCS nickel pincer complexes for lactate racemization

Computationally predicted scorpion-like SCS nickel pincer complexes are promising for the catalysis of lactate racemization under mild conditions.

Nickel-pincer cofactor biosynthesis involves LarB-catalyzed pyridinium carboxylation and LarE-dependent sacrificial sulfur insertion

The lactate racemase enzyme (LarA) of Lactobacillus plantarum harbors a (SCS)Ni(II) pincer complex derived from nicotinic acid. Synthesis of the enzyme-bound cofactor requires LarB, LarC, and LarE, which are widely distributed in microorganisms. The functions of the accessory proteins are unknown, but the LarB C terminus resembles aminoimidazole ribonucleotide carboxylase/mutase, LarC binds Ni and could act in Ni delivery or storage, and LarE is a putative ATP-using enzyme of the pyrophosphatase-loop superfamily. Here, we show that LarB carboxylates the pyridinium ring of nicotinic acid adenine dinucleotide (NaAD) and cleaves the phosphoanhydride bond to release AMP. The resulting biscarboxylic acid intermediate is transformed into a bisthiocarboxylic acid species by two single-turnover reactions in which sacrificial desulfurization of LarE converts its conserved Cys176 into dehydroalanine. Our results identify a previously unidentified metabolic pathway from NaAD using unprecedented carboxylase and sulfur transferase reactions to form the organic component of the (SCS)Ni(II) pincer cofactor of LarA. In species where larA is absent, this pathway could be used to generate a pincer complex in other enzymes.