Lactate Racemase Nickel-Pincer Cofactor Operates by a Proton-Coupled Hydride Transfer Mechanism

Protein-derived cofactors: chemical innovations expanding enzyme catalysis

Protein-derived cofactors, formed through posttranslational modification of a single amino acid or covalent crosslinking of amino acid side chains, represent a rapidly expanding class of catalytic moieties that redefine enzyme functionality. Once considered rare, these cofactors are recognized across all domains of life, with their repertoire growing from 17 to 38 types in two decades in our survey. Their biosynthesis proceeds via diverse pathways, including oxidation, metal-assisted rearrangements, and enzymatic modifications, yielding intricate motifs that underpin distinctive catalytic strategies. These cofactors span paramagnetic and non-radical states, including both mono-radical and crosslinked radical forms, sometimes accompanied by additional modifications. While their discovery has accelerated, mechanistic understanding lags, as conventional mutagenesis disrupts cofactor assembly. Emerging approaches, such as site-specific incorporation of non-canonical amino acids, now enable precise interrogation of cofactor biogenesis and function, offering a viable and increasingly rigorous means to gain mechanistic insights. Beyond redox chemistry and electron transfer, these cofactors confer enzymes with expanded functionalities. Recent studies have unveiled new paradigms, such as long-range remote catalysis and redox-regulated crosslinks as molecular switches. Advances in structural biology, mass spectrometry, and biophysical spectroscopy continue to elucidate their mechanisms. Moreover, synthetic biology and biomimetic chemistry are increasingly leveraging these natural designs to engineer enzyme-inspired catalysts. This review integrates recent advances in cofactor biogenesis, reactivity, metabolic regulation, and synthetic applications, highlighting the expanding chemical landscape and growing diversity of protein-derived cofactors and their far-reaching implications for enzymology, biocatalysis, and biotechnology.

Structural Basis for the Catalysis and Substrate Specificity of a LarA Racemase with a Broad Substrate Spectrum

The LarA family consists of diverse racemases/epimerases that interconvert the diastereomers of α-hydroxyacids by using a nickel-pincer nucleotide (NPN) cofactor. The hidden redox reaction catalyzed by the NPN cofactor makes LarA enzymes attractive engineering targets for various applications. However, how a LarA enzyme binds its natural substrate and recognizes different α-hydroxyacids has not been elucidated. Here, we report three high-resolution structures of the enzyme-substrate complexes of a broad-spectrum LarA enzyme from Isosphaera pallida (LarA Ip ). The substrate binding mode reveals a near-optimal orientation and distance between the hydride donor and acceptor, consistent with an updated proton-coupled hydride transfer mechanism. The experimentally solved structures, together with the structural models of other LarA enzymes, lead to the identification of the residues/structural elements that are critically involved in the interactions with different α-hydroxyacids. Collectively, this work provides a structural basis for the catalysis and substrate specificity of the LarA enzymes.

Unveiling 14 novel 2-hydroxy acid racemization and epimerization reactions in the lactate racemase superfamily

2-hydroxy acids are organic carboxylic acids ubiquitous in the living world and are important building blocks in organic synthesis. Recently, the lactate racemase (LarA) superfamily, a diverse superfamily of 2-hydroxy acid racemases and epimerases using the nickel-pincer nucleotide (NPN) cofactor, has been uncovered. In this study, we performed a taxonomic analysis of the LarA superfamily, showing the distribution of lactate racemase homologs (LarAHs) sequences across the three domains of life. Subsequently, we overexpressed and purified nine LarAHs and investigated their biochemical properties and substrate specificities. We show that LarAHs from the lactate racemases group are more promiscuous than previously thought, with some members showing high specificity towards glycerate or 2-hydroxybutyrate. In other phylogenetic groups, we identified a new malate racemase and 2-hydroxyglutarate racemase, as well as a new 2-gluconate epimerase from an eukaryotic organism. We show that some LarAHs are able to isomerize up to 16 different substrates, mostly 2-hydroxy acids with hydrophobic side chains, thereby identifying 14 novel 2-hydroxy acid racemization and epimerization reactions catalyzed by LarAHs. These include the racemization of glycerate, 2-hydroxybutyrate, 2,4-dihydroxybutyrate, 2-hydroxyvalerate, 2-hydroxycaproate, 2,3-dihydroxyisovalérate, 2-hydroxy-3,3-dimethylbutyrate, 3-(4-hydroxyphenyl)lactate, 2-hydroxy-4-phenylbutyrate, and 2-hydroxy-4-oxo-4-phenylbutyrate. Additionally, we observed the C2-epimerization of all 2,3-dihydroxybutyrate stereoisomers (4-deoxy-DL-threonate and 4-deoxy-DL-erythronate) and the C2-epimerization of D-arabinarate epimers. Finally, through comparative analysis of Alphafold structural predictions, we identified key residues likely involved in substrate specificity and predicted the function of half of the LarAHs from the LarA superfamily. In conclusion, this study widely expands the scope of substrates isomerized by NPN-dependent enzymes.

Chemo-enzymatic synthesis of NPN cofactor taking advantage of ADP-ribosyl cyclase and LarC cyclometallase promiscuous activities

The nickel-pincer nucleotide cofactor (NPN) is a widespread organometallic cofactor required for lactate racemase (LarA) and for α-hydroxy acid racemases and epimerases of the LarA superfamily. Its biosynthesis, which starts with nicotinic acid adenine dinucleotide (NaAD), requires three enzymes: LarB, LarC, and LarE, and can be performed in vitro with purified enzymes. Nevertheless, as LarE and LarC are single turnover enzymes, the in vitro NPN biosynthesis requires huge amounts of enzymes (particularly 2 equivalents of LarE), which hampers the study of NPN and of NPN-dependent enzymes. By using adenosine diphosphate (ADP)-ribosyl cyclase (ARC), we exchanged the nicotinamide moiety in NAD+ with synthetic pyridine-3,5-bisthiocarboxylic acid in order to synthesize the novel intermediate pyridinium-3,5-bisthiocarboxylic acid adenine dinucleotide (P2TAD). The latter could be produced at a multimilligram scale allowing its characterization by Nuclear Magnetic Resonance (NMR) and mass spectrometry. Interestingly, P2TAD could directly be used by LarC in order to generate the NPN cofactor, bypassing both LarB and LarE. Globally, a new chemoenzymatic route towards NPN was developed via the intermediate P2TAD, which should facilitate the biochemical and biotechnological investigations on NPN binding enzymes.

A structural view of nickel-pincer nucleotide cofactor-related biochemistry

The nickel-pincer nucleotide (NPN) is an organometallic cofactor that was first discovered in lactate racemase from Lactiplantibacillus plantarum. In this review, we provide an overview on the structure-function relationships of enzymes that utilize or are involved in the biosynthesis of the NPN cofactor. Recent structural advances have greatly extended our understanding of the biological role of the NPN cofactor in a diverse family of 2-hydroxyacid racemases and epimerases. Moreover, structural studies of the accessory proteins LarB (a combined carboxylase/hydrolase), two distinct forms of LarE (an ATP-dependent sulfur transferase), and LarC (a CTP-dependent nickel insertase) have elucidated key features in the biosynthetic pathway for the NPN cofactor. Finally, we discuss the potential of future structural investigations to uncover additional enzymes that synthesize and use the NPN cofactor to catalyze new reactions.

Structural Basis for Catalysis and Substrate Specificity of a LarA Racemase with a Broad Substrate Spectrum

The LarA family consists of diverse racemases/epimerases that interconvert the diastereomers of a variety of α-hydroxyacids by using a nickel-pincer nucleotide (NPN) cofactor. The hidden redox reaction catalyzed by the NPN cofactor makes LarA enzymes attractive engineering targets for applications. However, how a LarA enzyme binds its natural substrate and recognizes different α-hydroxyacids has not been elucidated. Here, we report three high-resolution structures of the enzyme-substrate complexes of a broad-spectrum LarA enzyme from Isosphaera pallida (LarA Ip ). The substrate binding mode reveals an optimal orientation and distance between the hydride donor and acceptor, strongly supporting the proposed proton-coupled hydride transfer mechanism. The experimentally solved structures, together with the structural models of other LarA enzymes, allow us to identify the residues/structural elements critically involved in the interactions with different α-hydroxyacid substrates. Collectively, this work provides a critical structural basis for catalysis and substrate recognition of the diverse enzymes in the LarA family, thus building a foundation for enzyme engineering.

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.

Intramolecular Proton-Coupled Hydride Transfers with Relatively Low Activation Barriers

We report that bifunctional molecules containing hydroxyl and carbonyl functional groups can undergo an effective transfer hydrogenation via an intramolecular proton-coupled hydride transfer (PCHT) mechanism. In this reaction mechanism, a hydride transfer between two carbon atoms is coupled with a proton transfer between two oxygen atoms via a cyclic bond rearrangement transition structure. The coupled transfer of the two hydrogens as H^δ+ and H^δ- is supported by atomic polar tensor charges. The activation energy for the PCHT reaction is strongly dependent on the length of the alkyl chain between the hydroxyl and carbonyl functional groups but relatively weakly dependent on the functional groups attached to the hydroxyl and carbonyl carbons. We investigate the PCHT reaction mechanism using the Gaussian-4 thermochemical protocol and obtain high activation energy barriers (ΔH^‡₂₉₈) of 210.5-228.3 kJ mol^-1 for chain lengths of one carbon atom and 160.2-163.9 kJ mol^-1 for chain lengths of two carbon atoms. However, for longer chain lengths containing 3-4 carbon atoms, we obtain ΔH^‡₂₉₈ values as low as 101.9 kJ mol^-1. Importantly, the hydride transfer between two carbon atoms proceeds without the need for a catalyst or hydride transfer activating agent. These results indicate that the intramolecular PCHT reaction provides an effective avenue for uncatalyzed, metal-free hydride transfers at ambient temperatures.

The nickel-pincer coenzyme of lactate racemase: A case study of uncovering cofactor structure and biosynthesis

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.

Structural and mutational characterization of a malate racemase from the LarA superfamily

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.

Five decades of metalloenzymology

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.

Irreversible inactivation of lactate racemase by sodium borohydride reveals reactivity of the nickel-pincer nucleotide cofactor

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.

Unveiling the mechanisms and biosynthesis of a novel nickel-pincer enzyme

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.

Racemases and epimerases operating through a 1,1-proton transfer mechanism: reactivity, mechanism and inhibition

Racemases and epimerases catalyse changes in the stereochemical configurations of chiral centres and are of interest as model enzymes and as biotechnological tools. They also occupy pivotal positions within metabolic pathways and, hence, many of them are important drug targets. This review summarises the catalytic mechanisms of PLP-dependent, enolase family and cofactor-independent racemases and epimerases operating by a deprotonation/reprotonation (1,1-proton transfer) mechanism and methods for measuring their catalytic activity. Strategies for inhibiting these enzymes are reviewed, as are specific examples of inhibitors. Rational design of inhibitors based on substrates has been extensively explored but there is considerable scope for development of transition-state mimics and covalent inhibitors and for the identification of inhibitors by high-throughput, fragment and virtual screening approaches. The increasing availability of enzyme structures obtained using X-ray crystallography will facilitate development of inhibitors by rational design and fragment screening, whilst protein models will facilitate development of transition-state mimics.

Uncovering a superfamily of nickel-dependent hydroxyacid racemases and epimerases

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.

Biological pincer complexes

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.

Crystallographic characterization of a tri-Asp metal-binding site at the three-fold symmetry axis of LarE

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.

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.

New metal cofactors and recent metallocofactor insights

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.

Nickel-pincer nucleotide cofactor

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.