Shigetarou Mori

Identification of ATP-NADH kinase isozymes and their contribution to supply of NADP(H) in Saccharomyces cerevisiae

ATP‐NAD kinase phosphorylates NAD to produce NADP by using ATP, whereas ATP‐NADH kinase phosphorylates both NAD and NADH. Three NAD kinase homologues, namely, ATP‐NAD kinase (Utr1p), ATP‐NADH kinase (Pos5p) and function‐unknown Yel041wp (Yef1p), are found in the yeast Saccharomyces cerevisiae. In this study, Yef1p was identified as an ATP‐NADH kinase. The ATP‐NADH kinase activity of Utr1p was also confirmed. Thus, the three NAD kinase homologues were biochemically identified as ATP‐NADH kinases. The phenotypic analysis of the single, double and triple mutants, which was unexpectedly found to be viable, for UTR1, YEF1 and POS5 demonstrated the critical contribution of Pos5p to mitochondrial function and survival at 37u2003°C and the critical contribution of Utr1p to growth in low iron medium. The contributions of the other two enzymes were also demonstrated; however, these were observed only in the absence of the critical contributor, which was supported by complementation for some pos5 phenotypes by the overexpression of UTR1 and YEF1. The viability of the triple mutant suggested that a ‘novel’ enzyme, whose primary structure is different from those of all known NAD and NADH kinases, probably catalyses the formation of cytosolic NADP in S.u2003cerevisiae. Finally, we found that LEU2 of Candida glabrata, encoding β‐isopropylmalate dehydrogenase and being used to construct the triple mutant, complemented some pos5 phenotypes; however, overexpression of LEU2 of S.u2003cerevisiae did not. The complementation was putatively attributed to an ability of Leu2p of C.u2003glabrata to use NADP as a coenzyme and to supply NADPH.

A Novel Bacterial ATP-Binding Cassette Transporter System That Allows Uptake of Macromolecules

A gram-negative bacterium, Sphingomonas sp. strain A1, isolated as a producer of alginate lyase, has a characteristic cell envelope structure and forms a mouth-like pit on its surface. The pit is produced only when the cells have to incorporate and assimilate alginate. An alginate uptake-deficient mutant was derived from cells of strain A1. One open reading frame, algS (1,089 bp), exhibiting homology to the bacterial ATP-binding domain of an ABC transporter, was cloned as a fragment complementing the mutation. algS was followed by two open reading frames, algM1 (972 bp) and algM2 (879 bp), which exhibit homology with the transmembrane permeases of ABC transporters. Disruption of algS of strain A1 resulted in the failure to incorporate alginate and to form a pit. Hexahistidine-tagged AlgS protein (AlgS(His6)) overexpressed in Escherichia coli and purified by Ni(2+) affinity column chromatography showed ATPase activity. Based on these results, we propose the occurrence of a novel pit-dependent ABC transporter system that allows the uptake of macromolecules.

Crystal Structure of Bacterial Inorganic Polyphosphate/ATP-glucomannokinase: INSIGHTS INTO KINASE EVOLUTION

Inorganic polyphosphate (poly(P)) is a biological high energy compound presumed to be an ancient energy carrier preceding ATP. Several poly(P)-dependent kinases that use poly(P) as a phosphoryl donor are known to function in bacteria, but crystal structures of these kinases have not been solved. Here we present the crystal structure of bacterial poly(P)/ATP-glucomannokinase, belonging to Gram-positive bacterial glucokinase, complexed with 1 glucose molecule and 2 phosphate molecules at 1.8 Å resolution, being the first among poly(P)-dependent kinases and bacterial glucokinases. The poly(P)/ATP-glucomannokinase structure enabled us to understand the structural relationship of bacterial glucokinase to eucaryotic hexokinase and ADP-glucokinase, which has remained a matter of debate. These comparisons also enabled us to propose putative binding sites for phosphoryl groups for ATP and especially for poly(P) and to obtain insights into the evolution of kinase, particularly from primordial poly(P)-specific to ubiquitous ATP-specific proteins.

Molecular Conversion of NAD Kinase to NADH Kinase through Single Amino Acid Residue Substitution

NAD kinase phosphorylates NAD+ to form NADP+ and is strictly specific to NAD+, whereas NADH kinase phosphorylates both NAD+ and NADH, thereby showing relaxed substrate specificity. Based on their primary and tertiary structures, the difference in the substrate specificities between NAD and NADH kinases was proposed to be caused by one aligned residue: Gly or polar amino acid (Gln or Thr) in five NADH kinases and a charged amino acid (Arg) in two NAD kinases. The substitution of Arg with Gly in the two NAD kinases relaxed the substrate specificity (i.e. converted the NAD kinases to NADH kinases). The substitution of Arg in one NAD kinase with polar amino acids also relaxed the substrate specificity, whereas substitution with charged and hydrophobic amino acids did not show a similar result. In contrast, the substitution of Gly with Arg in one NADH kinase failed to convert it to NAD kinase. These results suggest that a charged or hydrophobic amino acid residue in the position of interest is crucial for strict specificity of NAD kinases to NAD+, whereas Gly or polar amino acid residue is not the sole determinant for the relaxed substrate specificity of NADH kinases. The significance of the conservation of the residue at the position in 207 NAD kinase homologues is also discussed.

Establishment of a mass-production system for NADP using bacterial inorganic polyphosphate/ATP-NAD kinase

The inorganic polyphosphate/ATP-dependent NAD kinase (Ppnk) of Mycobacterium tuberculosis was applied to the mass-production of NADP from NAD and inorganic polyphosphate (metaphosphate). When Ppnk purified from recombinant Escherichia coli cells overexpressing the M. tuberculosis Ppnk was used, 30 mM (27 g/l) NADP was produced from 50 mM NAD and 100 mg/ml metaphosphate at 37 degrees C and pH 7.0. The recombinant E. coli cells were immobilized in polyacrylamide gel, and treated with acetone to render the cells permeable to substrates and products. When acetone-treated immobilized cells were used, 16 mM (14 g/l) NADP was produced from 50 mM NAD and 100 mg/ml metaphosphate at 37 degrees C and pH 7.0. The isolation of NADP formed in the reaction mixture was easy because of the absence of by-products (ATP degradation compounds), and this NADP production system using purified Ppnk or immobilized recombinant E. coli cells expressing Ppnk is thought to be feasible in the production of NADP on an industrial scale.

Crystallographic Studies of Mycobacterium tuberculosis Polyphosphate/ATP-NAD Kinase Complexed with NAD

NAD kinase from Mycobacterium tuberculosis (Ppnk) uses ATP or inorganic polyphosphate [poly(P)]. Ppnk overexpressed in Escherichia coli was purified and crystallized in the presence of NAD. Preliminary X-ray analysis of the resultant crystal indicate that the crystal belongs to hexagonal space group P6(2)22 and is holo-Ppnk complexed with NAD.

A novel member of glycoside hydrolase family 88: overexpression, purification, and characterization of unsaturated β-glucuronyl hydrolase of Bacillus sp. GL1

Unsaturated beta-glucuronyl hydrolase of Bacillus sp. GL1 catalyzes the hydrolytic release of unsaturated glucuronic acids from oligosaccharides produced through the reactions of polysaccharide lyases such as gellan, xanthan, hyaluronate, and chondroitin lyases. An overexpression system for the enzyme was constructed in Escherichia coli cells involving regulation of the enzyme gene under the T7 promoter and terminator. The expression level of the enzyme in E. coli cells was 250-fold higher than that in Bacillus sp. GL1 cells. The enzyme expressed in E. coli cells was purified and characterized. The optimal pH and temperature, and substrate specificity of the purified enzyme were similar to those of the native enzyme from Bacillus sp. GL1 cells, although the enzyme expressed in E. coli cells underwent self-assembly into polymeric forms through the formation of intermolecular disulfide bonds. Circular dichroism analysis indicated that the secondary structure of the enzyme was rich in alpha-helices. Genes showing high identity (over 40% identity) with that of the enzyme were found in the genomes of some pathogenic bacteria, such as Streptococcus pyogenes and Streptococcus pneumoniae, which cause serious diseases (e.g., meningitis and pneumonia). Therefore, the enzyme of Bacillus sp. GL1 and the streptococcal proteins form a new glycoside hydrolase family, 88.

Primary structure of inorganic polyphosphate/ATP-NAD kinase from Micrococcus flavus, and occurrence of substrate inorganic polyphosphate for the enzyme.

The gene encoding an inorganic polyphosphate/ATP-NAD kinase was cloned from Micrococcus flavus, and its primary structure was analyzed. Alignment of the primary structure with those of other characterized NAD kinases revealed candidate amino acid residues, mainly charged ones, that would be related to inorganic polyphosphate use. The alignment also showed that the primary structure found carried a protruding C-terminal polypeptide. Although the C-terminal polypeptide was demonstrated to be dispensable for the kinase activities, and was proposed to be removed in M. flavus, the entire primary structure including the C-terminal polypeptide was homologous with that of the ATP synthase β chain. The inorganic polyphosphate used by the inorganic polyphosphate/ATP-NAD kinase as a phosphoryl donor was isolated from cells of M. flavus, suggesting that the ability of the enzyme to use inorganic polyphosphate is of physiological significance and is not an evolutionary trait alone.

Crystallization and preliminary X-ray analysis of NAD kinase from Mycobacterium tuberculosis H37Rv.

NAD kinase from Mycobacterium tuberculosis H37Rv utilizes ATP or inorganic polyphosphate [poly(P)] as a phosphoryl donor for the phosphorylation of NAD. The enzyme overexpressed in Escherichia coli was purified and crystallized by means of the hanging-drop vapour-diffusion method with polyethylene glycol 4000 as the precipitant. Preliminary X-ray analysis of the resultant crystals revealed they belonged to the monoclinic space group C2 and had unit-cell parameters a = 140.0, b = 69.3, c = 106.3 A, beta = 130.1 degrees. The molecular weight of the NAD kinase is 35 kDa; assuming that a crystal contains two subunits of the NAD kinase in an asymmetric unit, the solvent content V(sol) is 0.62. X-ray diffraction data to 2.99 A have been collected from the native crystal.

Crystallization and preliminary X-ray analysis of a novel unsaturated glucuronyl hydrolase from Bacillus sp. GL1

Unsaturated glucuronyl hydrolase from Bacillus sp. GL1 catalyzes the hydrolytic release of unsaturated glucuronic acids from oligosaccharides produced by the reactions of polysaccharide lyases such as gellan, xanthan, hyaluronate and chondroitin lyases. The enzyme was crystallized at 293 K from a droplet containing 56% MPD, 0.1 M NaCl, 0.1 M glycine-NaOH pH 8.2 and 0.1 M dithiothreitol using the vapour-diffusion method. The crystals were hexagonal and belonged to space group P6(1)22 or P6(5)22, with unit-cell parameters a = b = 102.8, c = 223.4 A. Diffraction data to 2.4 A were collected from a single crystal.