Cofactor biosynthesis through protein post-translational modification

Gordonia hydrophobica Nitrile Hydratase for Amide Preparation from Nitriles

The active pharmaceutical ingredient levetiracetam has anticonvulsant properties and is used to treat epilepsies. Herein, we describe the enantioselective preparation of the levetiracetam precursor 2-(pyrrolidine-1-yl)butanamide by enzymatic dynamic kinetic resolution with a nitrile hydratase enzyme. A rare representative of the family of iron-dependent nitrile hydratases from Gordonia hydrophobica (GhNHase) was evaluated for its potential to form 2-(pyrrolidine-1-yl)butanamide in enantioenriched form from the three small, simple molecules, namely, propanal, pyrrolidine and cyanide. The yield and the enantiomeric excess (ee) of the product are determined most significantly by the substrate concentrations, the reaction pH and the biocatalyst amount. GhNHase is also active for the hydration of other nitriles, in particular for the formation of N-heterocyclic amides such as nicotinamide, and may therefore be a tool for the preparation of various APIs.

Functional and structural characterization of a flavoprotein monooxygenase essential for biogenesis of tryptophylquinone cofactor

Bioconversion of peptidyl amino acids into enzyme cofactors is an important post-translational modification. Here, we report a flavoprotein, essential for biosynthesis of a protein-derived quinone cofactor, cysteine tryptophylquinone, contained in a widely distributed bacterial enzyme, quinohemoprotein amine dehydrogenase. The purified flavoprotein catalyzes the single-turnover dihydroxylation of the tryptophylquinone-precursor, tryptophan, in the protein substrate containing triple intra-peptidyl crosslinks that are pre-formed by a radical S-adenosylmethionine enzyme within the ternary complex of these proteins. Crystal structure of the peptidyl tryptophan dihydroxylase reveals a large pocket that may dock the protein substrate with the bound flavin adenine dinucleotide situated close to the precursor tryptophan. Based on the enzyme-protein substrate docking model, we propose a chemical reaction mechanism of peptidyl tryptophan dihydroxylation catalyzed by the flavoprotein monooxygenase. The diversity of the tryptophylquinone-generating systems suggests convergent evolution of the peptidyl tryptophan-derived cofactors in different proteins.

Functional Expression and Characterization of a Panel of Cobalt and Iron-Dependent Nitrile Hydratases

Nitrile hydratases (NHase) catalyze the hydration of nitriles to the corresponding amides. We report on the heterologous expression of various nitrile hydratases. Some of these enzymes have been investigated by others and us before, but sixteen target proteins represent novel sequences. Of 21 target sequences, 4 iron and 16 cobalt containing proteins were functionally expressed from Escherichia coli BL21 (DE3) Gold. Cell free extracts were used for activity profiling and basic characterization of the NHases using the typical NHase substrate methacrylonitrile. Co-type NHases are more tolerant to high pH than Fe-type NHases. A screening for activity on three structurally diverse nitriles was carried out. Two novel Co-dependent NHases from Afipia broomeae and Roseobacter sp. and a new Fe-type NHase from Gordonia hydrophobica were very well expressed and hydrated methacrylonitrile, pyrazine-carbonitrile, and 3-amino-3-(p-toluoyl)propanenitrile. The Co-dependent NHases from Caballeronia jiangsuensis and Microvirga lotononidis, as well as two Fe-dependent NHases from Pseudomonades, were—in addition—able to produce the amide from cinnamonitrile. Summarizing, seven so far uncharacterized NHases are described to be promising biocatalysts.

His-Cys and Trp-Cys cross-links generated by post-translational chemical modification

Galactose oxidase and amine oxidase contain a cofactor which is generated by post-translational chemical modification to the corresponding amino acid side chains near the copper active center. Such cofactors provide proteins unusual catalytic ability that canonical amino acids cannot exert as well as their structural stability, and thereby are called as protein-derived cofactors. These cofactors and modifications are mostly derived from aromatic amino acid residues, especially Tyr, Trp, and His. Current information about unusual cofactors derived from two of those, heteroaromatic residues (Trp and His) is summarized, especially chemical properties and maturation process of the cross-links between cysteine and heteroaromatic amino acids (His-Cys and Trp-Cys cross-links).Abbreviations: FMN: flavin mononucleotide; FAD: flavin adenine nucleotide; RNA: ribonucleic acid; PDC: protein-derived cofactor; GFP: green fluorescent protein; MIO: 3,5-dihydro-5-methylidene-4-imidazol-4-one; LTQ: lysyl tyrosylquinone; CTQ: cysteine tryptophylquinone; TTQ: tryptophan tryptophylquinone; E.coli: Escherichia coli; WT: wild type.

Overexpression and characterization of two types of nitrile hydratases from Rhodococcus rhodochrous J1

Nitrile hydratase (NHase) from Rhodococcus rhodochrous J1 is widely used for industrial production of acrylamide and nicotinamide. However, the two types of NHases (L-NHase and H-NHase) from R. rhodochrous J1 were only slightly expressed in E. coli by routine methods, which limits the comprehensive and systematic characterization of the enzyme properties. We successfully expressed the two types of recombinant NHases in E. coli by codon-optimization, engineering of Ribosome Binding Site (RBS) and spacer sequences. The specific activity of the purified L-NHase and H-NHase were 400 U/mg and 234 U/mg, respectively. The molecular mass of L-NHase and H-NHase was identified to be 94 kDa and 504 kDa, respectively, indicating that the quaternary structure of the two types of NHases was the same as those in R. rhodochrous J1. H-NHase exhibited higher substrate and product tolerance than L-NHase. Moreover, higher activity and shorter culture time were achieved in recombinant E. coli, and the whole cell catalyst of recombinant E. coli harboring H-NHase has equivalent efficiency in tolerance to the high-concentration product relative to that in R. rhodochrous J1. These results indicate that biotransformation of nitrile by R. rhodochrous J1 represents a potential alternative to NHase-producing E. coli.

Activation of dioxygen by copper metalloproteins and insights from model complexes

Nature uses dioxygen as a key oxidant in the transformation of biomolecules. Among the enzymes that are utilized for these reactions are copper-containing metalloenzymes, which are responsible for important biological functions such as the regulation of neurotransmitters, dioxygen transport, and cellular respiration. Enzymatic and model system studies work in tandem in order to gain an understanding of the fundamental reductive activation of dioxygen by copper complexes. This review covers the most recent advancements in the structures, spectroscopy, and reaction mechanisms for dioxygen-activating copper proteins and relevant synthetic models thereof. An emphasis has also been placed on cofactor biogenesis, a fundamentally important process whereby biomolecules are post-translationally modified by the pro-enzyme active site to generate cofactors which are essential for the catalytic enzymatic reaction. Significant questions remaining in copper-ion-mediated O2-activation in copper proteins are addressed.

Extending enzyme molecular recognition with an expanded amino acid alphabet

Natural enzymes are constructed from the 20 proteogenic amino acids, which may then require posttranslational modification or the recruitment of coenzymes or metal ions to achieve catalytic function. Here, we demonstrate that expansion of the alphabet of amino acids can also enable the properties of enzymes to be extended. A chemical mutagenesis strategy allowed a wide range of noncanonical amino acids to be systematically incorporated throughout an active site to alter enzymic substrate specificity. Specifically, 13 different noncanonical side chains were incorporated at 12 different positions within the active site of N-acetylneuraminic acid lyase (NAL), and the resulting chemically modified enzymes were screened for activity with a range of aldehyde substrates. A modified enzyme containing a 2,3-dihydroxypropyl cysteine at position 190 was identified that had significantly increased activity for the aldol reaction of erythrose with pyruvate compared with the wild-type enzyme. Kinetic investigation of a saturation library of the canonical amino acids at the same position showed that this increased activity was not achievable with any of the 20 proteogenic amino acids. Structural and modeling studies revealed that the unique shape and functionality of the noncanonical side chain enabled the active site to be remodeled to enable more efficient stabilization of the transition state of the reaction. The ability to exploit an expanded amino acid alphabet can thus heighten the ambitions of protein engineers wishing to develop enzymes with new catalytic properties.

Construction of a subunit-fusion nitrile hydratase and discovery of an innovative metal ion transfer pattern

Metallochaperones are metal-binding proteins designed to deliver the appropriate metal to a target protein. The metal is usually transferred between different proteins. In this study, we discovered that metal was transferred between the same subunit of a mutant nitrile hydratase (NHase). Various “activator proteins” mediate the trafficking of metal ions into NHases. We constructed fusion NHases by fusing the β- and α-subunits and/or the “activator proteins” of the NHase from Pseudomonas putida. The fusion NHases exhibited higher thermostability and tolerance to high concentrations of the product amide. The mechanism of the cobalt incorporation changed from a self-subunit swapping pattern to an apoprotein-specific molecular chaperone pattern in vivo and a metallochaperone pattern in vitro. Notably, the cobalt transfer occurred between the same α-subunit in the metallochaperone pattern. These results not only demonstrated the superiority of fusion-type NHases, but also revealed an innovative metal ion transfer pattern in metalloprotein biosynthesis.

Cobalt and Nickel

Cobalt and nickel play key roles in biological systems as cofactors in a small number of important enzymes. The majority of these are found in microbes. Evidence for direct roles for Ni(II) and Co(II) enzymes in higher organisms is limited, with the exception of the well-known requirement for the cobalt-containing vitamin B12 cofactor and the Ni-dependent urease in plants. Nonetheless, nickel in particular plays a key role in human health because of its essential role in microbes that inhabit various growth niches within the body. These roles can be beneficial, as can be seen with the anaerobic production and consumption of H2 in the digestive tract by bacteria and archaea that results in increased yields of short-chain fatty acids. In other cases, nickel has an established role in the establishment of pathogenic infection (Helicobacter pylori urease and colonization of the stomach). The synthesis of Co- and Ni-containing enzymes requires metal import from the extracellular milieu followed by the targeting of these metals to the appropriate protein and enzymes involved in metallocluster or cofactor biosynthesis. These metals are toxic in excess so their levels must be regulated carefully. This complex pathway of metalloenzyme synthesis and intracellular homeostasis requires proteins that can specifically recognize these metals in a hierarchical manner. This chapter focuses on quantitative and structural details of the cobalt and nickel binding sites in transport, trafficking and regulatory proteins involved in cobalt and nickel metabolism in microbes.

Remote conformational control of a molecular switch via methylation and deprotonation

Methylation and deprotonation at remote sites of a diphenylacetylene-based molecular switch exert global conformational changes through subtle tuning of a hydrogen-bonding network.

MauG: a di-heme enzyme required for methylamine dehydrogenase maturation

Methylamine dehydrogenase (MADH) requires the cofactor tryptophan tryptophylquinone (TTQ) for activity. TTQ is a posttranslational modification that results from an 8-electron oxidation of two specific tryptophans in the MADH β-subunit. The final 6-electron oxidation is catalyzed by an unusual c-type di-heme enzyme, MauG. The di-ferric enzyme can react with H(2)O(2), but atypically for c-type hemes the di-ferrous enzyme can react with O(2) as well. In both cases, an unprecedented bis-Fe(IV) redox state is formed, composed of a ferryl heme (Fe(IV)=O) with the second heme as Fe(IV) stabilized by His-Tyr axial ligation. Bis-Fe(IV) MauG acts as a potent 2-electron oxidant. Catalysis is long-range and requires a hole hopping electron transfer mechanism. This review highlights the current knowledge and focus of research into this fascinating system.