Effect of amines as activators on the alcohol-oxidizing activity of pyrroloquinoline quinone-dependent quinoprotein alcohol dehydrogenase

Pyrroloquinoline quinone-dependent quinoprotein alcohol dehydrogenases (PQQ-ADH) require ammonia or primary amines as activators in in vitro assays with artificial electron acceptors. We found that PQQ-ADH from Pseudomonas putida KT2440 (PpADH) was activated by various primary amines, di-methylamine, and tri-methylamine. The alcohol oxidation activity of PpADH was strongly enhanced and the affinity for substrates was also improved by pentylamine as an activator.     

Phenol Ethers and Terpenes of Six Heterotropa Species Distributed in the Ryukyu Islands and Formosa

A new intracellular peptidase, which we call “d-peptidase S,” was purified from Nocardia orientalis IFO 12806 (ISP 5040). The purified enzyme was homogeneous on disc gel electrophoresis. The molecular weight and the isoelectric point were estimated to be 52,000 and 4.9, respectively. The optimum pH for the hydrolysis of d-leucyl-d-leucine was 8.0 to 8.1, and the optimum temperature was 36°C. The purified enzyme usually hydrolyzed the peptide bonds preceding the hydrophobic D-amino acids of dipeptides. Tri- and tetra-peptides extending to the amino terminus of such peptides were also hydrolyzed. Therefore, the enzyme is a carboxylpeptidase-like peptidase specific to d-amino acid peptides. The Km values for d-leucyl-d-leucine and l-leucyl-d-leucine were 0.21 × 10^-3 and 0.44 × 10^-3 m respectively. The activity was inhibited by several sulfhydryl reagents and two chelators, 8-hydroxyquinoline and o-phenanthroline.     

Further Characterization of Aminopeptidase of Rabbit Skeletal Muscle

Further investigation on characterization was conducted on purified neutral aminopeptidase of 160,000 daltons from rabbit skeletal muscle. The enzyme possesses arylamidase activity. The greater part of leucine-β-naphthylamide hydrolyzing activity of the muscle extract was attributed to the enzyme. The Km value for Ala-Gly-Phe-Ala, the most cleavable substrate tested, was 0.25 mm. Substrate inhibition was observed for Val-Val-Val-Ala and Val-Val-Val. The enzyme was inhibited by puromycin in a non-competitive manner, Ki being 4 × 10^?6 m. The enzyme was also inhibited by insulin and the oxidized B-chain of insulin. The tetrapeptide with N-terminal residue of d configuration, tRNA, pyruvate and α-ketoglutarate had no effect on the enzyme. On the basis of all properties determined so far, this muscle aminopeptidase is concluded to be identical to none of the known aminopeptidases from other tissues.     

Construction and characterization of heterodimeric soluble quinoprotein glucose dehydrogenase

In order to study in greater detail the subunit interaction of the homodimeric soluble quinoprotein glucose dehydrogenase (PQQGDH-B), we developed an effective method of creating heterodimeric PQQGDH-B. Two different homodimers are combined, one of which has a polyarginine tail (Arg-tail), and subjected to a protein dissociation/redimerization procedure. Separation of the mixture by cation exchange chromatography results in three peaks showing GDH activity, eluting at 133, 231 and 273 mM NaCl concentration. These peaks were determined to correspond to the Arg-tailless homodimer, heterodimer, and Arg-tailed homodimer, respectively. To test this approach, we constructed and characterized heterodimeric PQQGDH-B composed of native (wild-type) and inactive mutant (His168Gln) subunits. The heterodimeric wild-type-His168Gln showed slightly decreased GDH activity and almost identical substrate specificity profile to the wild-type enzyme. Moreover, the Hill coefficient of the heterodimer was calculated as 1.13, indicating positive cooperativity.     

Specificity of Enzyme System Producing C6-Aldehyde in Tea Chloroplasts

The substrate specificity of enzyme system producing C₆-aldehyde in Thea chloroplasts was clarified with an entire series of synthesized positional isomers, in which the position of cis-1, cis-4-pentadiene system varies from C-3 to C-13 in C₁₈ fatty acid and geometrical isomers of linoleic acid. The structural requirement for the substrate of enzyme system producing C₆-aldehyde is the presence of cis-1, cis-4-pentadiene system between ω-6 and ω-10.     

Quinate oxidation in Gluconobacter oxydans IFO3244: purification and characterization of quinoprotein quinate dehydrogenase

Quinoprotein quinate dehydrogenase (QDH) is a membrane-bound enzyme containing pyrroloquinoline quinone (PQQ) as the prosthetic group. QDH in Gluconobacter oxydans IFO3244 was found to be inducible by quinate and it is not constitutively expressed in the absence of quinate. The purification of holo-form of QDH to nearly homogeneity was achieved. The purified QDH appears to have two subunits of approximately 65 and 21 kDa, which could be the result of proteolysis of single polypeptide. Kinetic analysis indicated that the purified enzyme is much more specific to quinate than QDH from Acinetobacter calcoaceticus. The efficiency of the artificial electron acceptor was also determined.     

NAD-dependent, PQQ-containing methanol dehydrogenase: a bacterial dehydrogenase in a multienzyme complex

Cell-free extracts of methanol-grown Nocardia sp. 239 only show significant dye-linked methanol-oxidizing activity when NAD+ is added to the assay mixture. This activity resides in a multienzyme complex which could be resolved into 3 components, namely the methanol dehydrogenase, NAD-dependent aldehyde dehydrogenase and NADH dehydrogenase. In its dissociated form, the methanol dehydrogenase no longer shows dye reduction and although rises in the absorbance values around 340 nm are seen on addition of methanol plus NAD+ to the enzyme, this is not due to NADH production. However, dye reduction (NAD dependent) could be restored on incubating methanol dehydrogenase with the corresponding NADH dehydrogenase, obtained from the enzyme complex. It is concluded that this novel methanol dehydrogenase transfers the reducing equivalents, derived from methanol, directly to its associated NADH dehydrogenase via a mechanism in which NAD+ and PQQ are involved.     

Three-dimensional structure of the quinoprotein methylamine dehydrogenase from Paracoccus denitrificans determined by molecular replacement at 2.8 A resolution.

The three-dimensional structure of the quinoprotein methylamine dehydrogenase from Paracoccus dentrificans (PD-MADH) has been determined at 2.8 A resolution by the molecular replacement method combined with map averaging procedures, using data collected from an area detector. The structure of methylamine dehydrogenase from Thio-bacillus versutus, which contains an "X-ray" sequence, was used as the starting search model. MADH consists of 2 heavy (H) and 2 light (L) subunits related by a molecular 2-fold axis. The H subunit is folded into seven four-stranded beta segments, forming a disk-shaped structure, arranged with pseudo-7-fold symmetry. A 31-residue elongated tail exists at the N-terminus of the H subunit in MADH from T. versutus but is partially digested in this crystal form of MADH from P. denitrificans, leaving the H subunit about 18 residues shorter. Each L subunit contains 127 residues arranged into 10 beta-strands connected by turns. The active site of the enzyme is located in the L subunit and is accessible via a hydrophobic channel between the H and L subunits. The redox cofactor of MADH, tryptophan tryptophylquinone is highly unusual. It is formed from two covalently linked tryptophan side chains at positions 57 and 107 of the L subunit, one of which contains an orthoquinone.     

Stabilization of quaternary structure of water-soluble quinoprotein glucose dehydrogenase

Water-soluble quinoprotein glucose dehydrogease (PQQGDH-B) is a dimeric enzyme whose application for glucose sensing is the focus of much attention. We attempted to increase the thermal stability of PQQGDH-B by introducing a disulfide bond at the dimer interface. The Ser residue at position 415 was selected for substitution with Cys, as structural information revealed that its side chains face each other at the dimer interface of PQQGDH-B. PQQGDH-B with Ser415Cys showed 30-fold greater thermal stability at 55°C than did the wild-type enzyme without any decrease in catalytic activity. After incubation at 70°C for 10 min, Ser415Cys retained 90% of the GDH activity of the wild-type enzyme. Disulfide bond formation between the mutant subunits was confirmed by analyses with sodium dodecylsulfate-polyacrylamide gel electrophoresis in the presence and absence of reductants. Our results indicate that the introduction of one Cys residue in each monomer of PQQGDH-B resulted in formation of a disulfide bond at the dimer interface and thus achieved a large increase in the thermal stability of the enzyme.     

Different forms of quinoprotein aldose-(glucose-) dehydrogenase in Acinetobacter calcoaceticus

The ratios of the oxidation rates of aldose sugars, determined in cell-free extracts of Acinetobacter calcoaceticus, vary with the strain and growth conditions used. Three distinct forms of glucose dehydrogenase with different substrate specificities, occurring in variable proportions in these extracts, are responsible for this effect. One form is the already known soluble glucose dehydrogenase, the other two forms are complexes containing enzyme and components of the respiratory chain. The proportions in which the enzyme forms are found in the cell-free extract correlate with the oxidative behaviour of whole cells with respect to aldose sugars. It is concluded, therefore, that the enzyme forms are not an artefact of the isolation procedure but that they exist as such in vivo. Since the two complexes can be converted into the soluble enzyme form, aldose dehydrogenase can, probably, be integrated in three different ways into the respiratory chain.The presence of glucose during growth does not stimulate aldose dehydrogenase production. This is not surprising since the enzyme has no function in carbon metabolism, except perhaps in strains growing on pentoses at high pH. Therefore, the physiological role of quinoprotein aldose dehydrogenase in this organism may be primarily in energy generation.Non-standard abbreviations quinoproteins enzymes containing 2,7,9-tricarboxy-1 H-pyrrolo [2,3f] quinoline-4,5-dione (pyrrolo-quinoline quinone) as the coenzyme     

Bioelectrochemical fuel cell and sensor based on a quinoprotein,alcohol dehydrogenase

A biofuel cell, yielding a stable and continuous low-power output, based on the enzymatic oxidation of methanol to formic acid has been designed and investigated. The homogeneous kinetics of the electrochemically-coupled enzymatic oxidation reaction were investigated and optimized. The biofuel cell also functioned as a sensitive method for the detection of primary alcohols. A method for medium-scale preparation of the enzyme alcohol dehydrogenase [alcohol:(acceptor) oxidoreductase, EC 1.1.99.8] is described.     

High-performance liquid chromatography of phospholipids: quantitation by phosphate analysis

Quantitation of individual phospholipids separated by HPLC from tissue extracts by colorimetric analysis of phosphate was investigated. Elution of inorganic phosphate and breakthrough of lecithin were determined using radioisotopes. A substance which interfered with sample phosphate determinations was found in the column eluant, and a method to minimize its effect was developed. This method allows accurate quantitation of individual phospholipids present at a minimum of 20 nmol phosphate.     

Identification and properties of an inducible phenylacyl-CoA dehydrogenase in Pseudomonas putida KT2440

A novel acyl-CoA dehydrogenase that initiates beta-oxidation of the side chains of phenylacyl-CoA compounds by Pseudomonas putida was induced by growth with phenylhexanoate as carbon source. It was identified as the product of gene PP_0368, which was cloned and overexpressed in Escherichia coli. This phenylacyl-CoA dehydrogenase was found to be dimeric with a subunit molecular mass of 66 kDa, to contain FAD and to be active with phenylacyl-CoA substrates having side chains from four to at least 11 carbon atoms. The same enzyme was induced by the aliphatic alkanoate octanoate. The optimal aliphatic substrates for the enzyme were palmitoyl-CoA and stearoyl-CoA, a property shared with mammalian very-long-chain acyl-CoA dehydrogenases. The FAD in the enzyme was reduced by aromatic and aliphatic substrates, with changes to the oxidation-reduction potential. Chemical reduction by dithionite ion and oxidation by ferricyanide ion showed that the enzyme can accept four electrons: two to reduce the flavin and two to slowly reduce an unknown acceptor, which in its reduced form interacts with the oxidized flavin in a charge-transfer complex. The experiments identify for the first time an acyl-CoA dehydrogenase that oxidizes the activated forms of aromatic acids similar to those used to first demonstrate the biological beta-oxidation of fatty acids.     

Evidence of a quinoprotein glucose dehydrogenase apoenzyme in several strains of Escherichia coli

Abstract When grown on glucose in K⁺-limited chemostat culture, or in batch culture with or without 2,4-dinitrophenol, several strains of Escherichia coli (including the type strain) were found to synthesize a quinoprotein glucose dehydrogenase apoenzyme. The pyridine nucleotides, NAD⁺ and NADP⁺, would not serve as cofactor, but activity could be demonstrated upon addition of 2,7,9-tricarboxy-1 H -pyrrolo(2,3- f )quinoline-4,5-dione (PQQ). Thus, in the presence of PQQ, but not in its absence, glucose was oxidized to gluconic acid. A mutant of E. coli PC 1000 was isolated that lacked Enzyme I of the phospho enol pyruvate phosphotransferase system (PTS) but still synthesized the glucose dehydrogenase apoenzyme. Whereas this mutant would not grow on glucose in the absence of PQQ, it would do so in the presence of low concentrations (1 μM) of this cofactor. On the basis of these observations, it is concluded that the protein (apoenzyme) formed is a genuine glucose dehydrogenase, but that it is not functional in growing cells due to their inability to synthesize the appropriate cofactor (PQQ), at least under these conditions.     

Construction and characterization of a linked-dimeric pyrroloquinoline quinone glucose dehydrogenase

Using the structural gene of a homo dimeric enzyme, the water-soluble pyrroloquinoline quinone glucose dehydrogenase (PQQGDH-B), a gene consisting of two identical subunits linked together by a DNA segment coding linker peptide region was constructed. Using the constructed gene, a linked-dimeric PQQGDH-B was produced in Escherichia coli as the active soluble enzyme. Linked-dimeric PQQGDH-B showed a larger increase in thermal stability than the native dimeric enzyme. During incubation over 45 °C, the residual activity of linked-dimeric PQQGDH-B was more than twice that of the native dimeric enzyme. The potential application of linked-dimeric PQQGDH-B for glucose enzyme sensor is also discussed.     

Crystal structure of formaldehyde dehydrogenase from Pseudomonas putida: the structural origin of the tightly bound cofactor in nicotinoprotein dehydrogenases

Formaldehyde dehydrogenase from Pseudomonas putida (PFDH) is a member of the zinc-containing medium-chain alcohol dehydrogenase family. The pyridine nucleotide NAD(H) in PFDH, which is distinct from the coenzyme (as cosubstrate) in typical alcohol dehydrogenases (ADHs), is tightly but not covalently bound to the protein and acts as a cofactor. PFDH can catalyze aldehyde dismutations without an external addition of NAD(H). The structural basis of the tightly bound cofactor of PFDH is unknown. The crystal structure of PFDH has been solved by the multiwavelength anomalous diffraction method using intrinsic zinc ions and has been refined at a 1.65 A resolution. The 170-kDa homotetrameric PFDH molecule shows 222 point group symmetry. Although the secondary structure arrangement and the binding mode of catalytic and structural zinc ions in PFDH are similar to those of typical ADHs, a number of loop structures that differ between PFDH and ADHs in their lengths and conformations are observed. A comparison of the present structure of PFDH with that of horse liver ADH, a typical example of an ADH, reveals that a long insertion loop of PFDH shields the adenine part of the bound NAD(+) molecule from the solvent, and a tight hydrogen bond network exists between the insertion loop and the adenine part of the cofactor, which is unique to PFDH. This insertion loop is conserved completely among the aldehyde-dismutating formaldehyde dehydrogenases, whereas it is replaced by a short turn among typical ADHs. Thus, the insertion loop specifically found among the aldehyde-dismutating formaldehyde dehydrogenases is responsible for the tight cofactor binding of these enzymes and explains why PFDH can effectively catalyze alternate oxidation and reduction of aldehydes without the release of cofactor molecule from the enzyme.     

Structure at 1.9 A resolution of a quinohemoprotein alcohol dehydrogenase from Pseudomonas putida HK5

The type II quinohemoprotein alcohol dehydrogenase of Pseudomonas putida is a periplasmic enzyme that oxidizes substrate alcohols to the aldehyde and transfers electrons first to pyrroloquinoline quinone (PQQ) and then to an internal heme group. The 1.9 A resolution crystal structure reveals that the enzyme contains a large N-terminal eight-stranded beta propeller domain (approximately 60 kDa) similar to methanol dehydrogenase and a small C-terminal c-type cytochrome domain (approximately 10 kDa) similar to the cytochrome subunit of p-cresol methylhydoxylase. The PQQ is bound near the axis of the propeller domain about 14 A from the heme. A molecule of acetone, the product of the oxidation of isopropanol present during crystallization, appears to be bound in the active site cavity.     

Characterization of a group of pyrroloquinoline quinone‐dependent dehydrogenases that are involved in the conversion of L‐sorbose to 2‐Keto‐L‐gulonic acid in Ketogulonicigenium vulgare WSH‐001

Ketogulonicigenium vulgare WSH‐001 is an industrial strain used for vitamin C production. Based on genome sequencing and pathway analysis of the bacterium, some of its potential pyrroloquinoline quinone (PQQ)‐dependent dehydrogenases were predicted, including KVU_pmdA_0245, KVU_2142, KVU_2159, KVU_1366, KVU_0203, KVU_0095, and KVU_pmdB_0115. BLAST and function domain searches showed that enzymes encoded by these genes may act as putative PQQ‐dependent L ‐sorbose dehydrogenases (SDH) or L ‐sorbosone dehydrogenases (SNDH). To validate whether these dehydrogenases are PQQ‐dependent or not, these seven putative dehyrogenases were overexpressed in Escherichia coli BL21 (DE3) and purified for characterization. Biochemical and kinetic characterization of the purified proteins have led to the identification of seven enzymes that possess the ability to oxidize L ‐sorbose or L ‐sorbosone to varying degrees. In addition, the dehydrogenation of sorbose in K. vulgare is validated to be PQQ dependent, identification of these PQQ‐dependent dehydrogenases expanded the PQQ‐dependent dehydrogenase family. Besides, the optimal combination of enzymes that could more efficiently catalyze the conversion of sorbose to gulonic acid was proposed. These are important in supporting the development of metabolic engineering strategies and engineering of efficient strains for one‐step production of vitamin C in the future. © 2013 American Institute of Chemical Engineers Biotechnol. Prog., 29:1398–1404, 2013     

Catalytic properties and crystal structure of quinoprotein aldose sugar dehydrogenase from hyperthermophilic archaeon Pyrobaculum aerophilum

We identified a gene encoding a soluble quinoprotein glucose dehydrogenase homologue in the hyperthermophilic archaeon Pyrobaculum aerophilum. The gene was overexpressed in Escherichia coli, after which its product was purified and characterized. The enzyme was extremely thermostable, and the activity of the pyrroloquinoline quinone (PQQ)-bound holoenzyme was not lost after incubation at 100 °C for 10 min. The crystal structure of the enzyme was determined in both the apoform and as the PQQ-bound holoenzyme. The overall fold of the P. aerophilum enzyme showed significant similarity to that of soluble quinoprotein aldose sugar dehydrogenase (Asd) from E. coli. However, clear topological differences were observed in the two long loops around the PQQ-binding sites of the two enzymes. Structural comparison revealed that the hyperthermostability of the P. aerophilum enzyme is likely attributable to the presence of an extensive aromatic pair network located around a β-sheet involving N- and C-terminal β-strands.