A functional gltB gene is essential for utilization of acidic amino acids and expression of periplasmic glutaminase/asparaginase (PGA) by Pseudomonas putida KT2440.

Pseudomonas putida KT2440, a root-colonizing fluorescent pseudomonad, is capable of utilizing acidic amino acids (Asp and Glu) and their amides (Asn and Gln) as its sole source of carbon and nitrogen. The uptake of Gln and Asn is facilitated by a periplasmic glutaminase/asparaginase (PGA), which hydrolyses Asn and Gln to the respective dicarboxylates. Here, we describe transposon mutagenesis of P. putida KT2440 with a self-cloning promoter probe vector, Tn 5-OT182. Transconjugants defective in Glu-mediated PGA induction were selected for further studies. In most clones the transposon was found to have integrated into the gltB gene, which encodes the major subunit of the glutamate synthase (GOGAT). The transconjugants were nonmotile, no longer showed a chemotactic response towards amino acids, and could not survive prolonged periods of starvation. The acidic amino acids and their amides supported growth of the transconjugants only when supplied together with glucose, suggesting that the gltB-mutants had lost the ability to utilize amino acids as a carbon source. To confirm that gltB inactivation was the cause of this phenotype, we constructed a mutant with a targeted disruption of gltB. This strain behaved like the clones obtained by random mutagenesis, and failed to express not only PGA but also a number of other Glu-induced proteins. In contrast to wild-type cells, the gltB(-) strain accumulated considerable amounts of both Glu and Gln during long-term incubation.

Engineering the substrate specificity of Escherichia coli asparaginase. II. Selective reduction of glutaminase activity by amino acid replacements at position 248.

The use of Escherichia coli asparaginase II as a drug for the treatment of acute lymphoblastic leukemia is complicated by the significant glutaminase side activity of the enzyme. To develop enzyme forms with reduced glutaminase activity, a number of variants with amino acid replacements in the vicinity of the substrate binding site were constructed and assayed for their kinetic and stability properties. We found that replacements of Asp248 affected glutamine turnover much more strongly than asparagine hydrolysis. In the wild-type enzyme, N248 modulates substrate binding to a neighboring subunit by hydrogen bonding to side chains that directly interact with the substrate. In variant N248A, the loss of transition state stabilization caused by the mutation was 15 kJ mol(-1) for L-glutamine compared to 4 kJ mol(-1) for L-aspartic beta-hydroxamate and 7 kJ mol(-1) for L-asparagine. Smaller differences were seen with other N248 variants. Modeling studies suggested that the selective reduction of glutaminase activity is the result of small conformational changes that affect active-site residues and catalytically relevant water molecules.

Dynamics of a mobile loop at the active site of Escherichia coli asparaginase.

Asparaginase II from Escherichia coli is well-known member of the bacterial class II amidohydrolases. Enzymes of this family utilize a peculiar catalytic mechanism in which a pair of threonine residues play pivotal roles. Another common feature is a mobile surface loop that closes over the active site when the substrates is bound. We have studied the motion of the loop by stopped-flow experiments using the fluorescence of tryptophan residues as the spectroscopic probe. With wild-type enzyme the fluorescence of the only tryptophan, W66, was monitored. Here asparagine induced a rapid closure of the loop. The rate constants of the process (100-150 s(-1) at 4 degrees C) were considerably higher than those of the rate-limiting catalytic step. A more selective spectroscopic probe was generated by replacing W66 with tyrosine and Y25, a component of the loop, with tryptophan. In the resulting enzyme variant, k(cat) and the rate of loop movement were reduced by factors of 10(2) and >10(3), respectively, while substrate binding was unaffected. This indicates that the presence of tyrosine in position 25 is essential for both loop closure and catalysis. Numerical simulations of the observed transients are consistent with a model where loop closure is an absolute prerequisite for substrate turnover.

The distribution of aminoacylase I among mammalian species and localization of the enzyme in porcine kidney.

Aminoacylase I (Acy-1, EC 3.5.1.14) is found in many mammalian tissues, with highest activities occurring in kidney. The enzyme hydrolyzes a variety of N-acylated amino acids; however, the physiological role and the exact cellular localization of Acy-1 are still a matter of debate. The comparison of Acy-1 activities in kidney and liver homogenates of 11 mammalian species showed that the enzyme is most abundant in true herbivores such as sheep and cattle as well as in omnivores, while activities were very low in both rodents and the cat. Acy-1 activity was not detected in livers of dogs of five different breeds. Using in situ hybridization of porcine kidney sections with DIG-labeled RNA probes, Acy-1 mRNA was shown to be evenly distributed throughout the tubular system, while glomeruli and the interstitium were free of stain. During subcellular fractionation, porcine Acy-1 behaved like a typical cytosolic enzyme. Commonly, Acy-1 is thought to catalyze hydrolytic reactions, i.e., the formation of free amino acids from acylated derivatives. Based on the present results and literature data, we propose a novel hypothesis, i.e., that Acy-1 catalyzes the synthesis (rather than the hydrolysis) of hippurate that is formed as a detoxification product of aromatic compounds.

Mutational analysis of two PWW sequence motifs in human aminoacylase 1.

Human and porcine aminoacylase 1 (Acy1) contain two peculiar sequence motifs located near the interface between the two major domains of the Acy1 subunit. Each motif consists of the sequence PWW preceded by four strongly polar residues. In order to examine the significance of these sequences for Acy1 stability and/or catalysis, we used site-directed mutagenesis of human Acy1 to replace the tryptophan residues in either motif with alanines. Both mutants showed unchanged zinc binding and normal substrate affinity. Modification in PWW motif 1 (residues 192 -194) and motif 2 (residues 321 - 323) resulted in markedly reduced specific activity in the first case and diminished stability in either mutant. Fluorescence quenching measurements showed that all four tryptophans of the PWW motifs are solvent-accessible. We conclude that PWW motif 1 maintains the native conformation of the active site by creating the proper spatial relationship between dimerization domains and catalytic domains, while motif PWW2 is necessary for the stability of the catalytic domain.

Preliminary crystallographic studies of Y25F mutant of periplasmic Escherichia coli L-asparaginase.

Periplasmic Escherichia coli L-asparaginase II with Y25F mutation in the active-site cavity has been obtained by recombinant techniques. The protein was crystallized in a new hexagonal form (P6(5)22). Single crystals of this polymorph, suitable for X-ray diffraction, were obtained by vapor diffusion using 2-methyl-2,4-pentanediol as precipitant (pH 4.8). The crystals are characterized by a = 81.0, c = 341.1 A and diffract to 2.45 A resolution. The asymmetric unit contains two protein molecules arranged into an AB dimer. The physiologically relevant ABA'B' homotetramer is generated by the action of the crystallographic 2-fold axis along [1, -1, 0]. Kinetic studies show that the loss of the phenolic hydroxyl group at position 25 brought about by the replacement of Y with F strongly impairs kcat without significantly affecting Km.

Cloning, sequence analysis, and expression of ansB from Pseudomonas fluorescens, encoding periplasmic glutaminase/asparaginase.

A gene (ansB) encoding a class II glutaminase/asparaginase has been cloned from Pseudomonas fluorescens and characterized by DNA sequencing, promoter analysis and heterologous expression in Escherichia coli. We show that ansB is monocistronic and depends on the alternate sigma factor sigma 54 for expression. A second open reading frame located downstream of ansB is highly homologous to a number of bacterial genes that encode secreted endonucleases of unknown function.

Human and porcine aminoacylase I overproduced in a baculovirus expression vector system: evidence for structural and functional identity with enzymes isolated from kidney.

Aminoacylase I (EC 3.5.1.14) is one of the most abundant enzymes in the cortical region of mammalian kidney. Both the porcine and the human enzyme were overexpressed using baculovirus expression vector systems and purified by hydrophobic interaction chromatography and anion-exchange chromatography. The resulting preparations were analyzed for structural and functional identity with the corresponding enzymes isolated from kidney. The dansyl method as well as mass spectroscopy confirmed N-terminal blocking. For the porcine enzyme, atomic absorption spectroscopy yielded the correct metal content (one zinc per subunit). Kinetic analyses showed identical Km values for the expression products and the enzymes isolated from kidney. By contrast, the porcine enzyme when overexpressed in Escherichia coli had a much lower specific activity. Comparative substrate specificity studies with natural and recombinant human aminoacylase and 16 different N-acetyl-L-amino acids showed that, among the derivatives of proteinogenic amino acids, N-acetyl-L-methionine was the best substrate, followed by acetylated glutamate, leucine, alanine, and valine. These amino acids are also the most abundant residues at the N-termini of acetylated proteins. This suggests that kidney aminoacylase may be involved in the salvage of amino acids by hydrolyzing acetyl amino acids released from proteins.

Crystal structure and amino acid sequence of Wolinella succinogenes L-asparaginase.

The amino acid sequence and tertiary structure of Wolinella succinogenes L-asparaginase were determined, and were compared with the structures of other type-II bacterial L-asparaginases. Each chain of this homotetrameric enzyme consists of 330 residues. The amino acid sequence is 40-50% identical to the sequences of related proteins from other bacterial sources, and all residues previously shown to be crucial for the catalytic action of these enzymes are identical. Differences between the amino acid sequence of W. succinogenes L-asparaginase and that of related enzymes are discussed in terms of the possible influence on the substrate specificity. The overall fold of the protein subunit is almost identical to that observed for other L-asparaginases. Two fragments in each subunit, a very highly flexible loop (approximately 20 amino acids) that forms part of the active site, and the N-terminus (two amino acids), are not defined in the structure. The orientation of Thr14, a residue probably involved in the catalytic activity, indicates the absence of ligand in the active-site pocket. The rigid part of the active site, which includes the asparaginase triad Thr93-Lys 166-Asp94, is structurally very highly conserved with equivalent regions found in other type-II bacterial L-asparaginases.

A covalently bound catalytic intermediate in Escherichia coli asparaginase: crystal structure of a Thr-89-Val mutant.

Escherichia coli asparaginase II catalyzes the hydrolysis of L-asparagine to L-aspartate via a threonine-bound acyl-enzyme intermediate. A nearly inactive mutant in which one of the active site threonines, Thr-89, was replaced by valine was constructed, expressed, and crystallized. Its structure, solved at 2.2 A resolution, shows high overall similarity to the wild-type enzyme, but an aspartyl moiety is covalently bound to Thr-12, resembling a reaction intermediate. Kinetic analysis confirms the deacylation deficiency, which is also explained on a structural basis. The previously identified oxyanion hole is described in more detail.

Thermostable aminoacylase from Bacillus stearothermophilus: significance of the metal center for catalysis and protein stability.

A thermostable aminoacylase (N-acylamino acid amidohydrolase, EC 3.5.1.14) from Bacillus stearothermophilus was overexpressed in E. coli and characterized with respect to metal content, metal dependence, heat stability, and quaternary structure. Like other enzymes of the aminoacylase family, native aminoacylase contains one Zn2+ ion per subunit. Several other transition metal ions (Co2+, Mn2+ and Cd2+) also sustain aminoacylase activity toward N-acetyl L-alanine with Cd2+ giving the highest turnover number. The stability constants of the respective metal complexes were estimated by activity measurements in metal buffer systems. Co2+ also acts as an activator mainly by lowering the Km for the substrate. These data and CD spectra obtained with the native and the metal-free enzyme suggest a predominantly structural role for the intrinsic metal ion of thermostable aminoacylase. In contrast to previous reports the enzyme behaved as a dimer in analytical gel filtration.

Aminoacylase I from porcine kidney: identification and characterization of two major protein domains.

The domain structure of hog-kidney aminoacylase I was studied by limited proteolytic digestion with trypsin and characterization of the resulting fragments. In the native enzyme, the sequences from residue 6 to 196 and 307 to 406 are resistant to trypsin and remain tightly bound in nondenaturing solvents, while the intervening sequence (197-306) is efficiently degraded by trypsin. We conclude that the N-terminal half of the molecule and its C-terminal fourth form two independently folded domains. Both contain a peculiar PWW(A,L) sequence motif preceded by several strongly polar residues. We propose that these sequences form surface loops that mediate the membrane association of aminoacyclase I. We further show that the three free cysteine residues and the essential Zn2+ ion reside in the trypsin-resistant domains, while the intervening sequence contains the only disulfide H bond of the protein.

States and functions of tyrosine residues in Escherichia coli asparaginase II.

The importance of five tyrosine residues of Escherichia coli asparaginase II (EcA2) for catalysis and protein stability was examined by site-directed mutagenesis, chemical modification of wild-type and variant enzymes, and by thermodynamic studies of protein denaturation. While the tyrosine residue Y25 is directly involved in catalysis, the hydroxyl groups of residues Y181, Y250, Y289 and Y326 are not necessary for EcA2 activity. However, residues Y181 and Y326 are crucial for stabilization of the native EcA2 tetramer. pH titration curves showed that the active-site residue Y25 has a normal pKa while the C-terminal Y326 is unusually acidic. 1H-NMR signals of a peculiar ligand-sensitive tyrosine residue were assigned to Y25. These and other data suggest that a peptide loop (residues 14-27) which shields the active site during catalysis is highly flexible in the free enzyme.

Ferricytochrome c induces monophasic kinetics of ferrocytochrome c oxidation in cytochrome c oxidase.

The kinetics of ferrocytochrome c oxidation by reconstituted cytochrome c oxidase (COX) from bovine heart was followed by a spectrophotometric method, using on-line data collection and subsequent calculation of reaction rates from a function fitted to the progress curve. When reaction rates were calculated at increasing reaction times, the multiphasic kinetics of ferrocytochrome c oxidation gradually changed into monophasic Michaelis-Menten kinetics. The same phenomenon was observed when ferrocytochrome c oxidation was followed in the presence of increasing amounts of ferricytochrome c. From these results we conclude that ferricytochrome c shifts the multiphasic kinetics of ferrocytochrome c oxidation by COX into monophasic kinetics, comparable to high ionic strength conditions. Furthermore, we show that ferricytochrome c inhibits the "high affinity phase" of ferrocytochrome c oxidation in an apparently competitive way, while inhibition of the "low affinity phase" is noncompetitive. These findings are consistent with a "regulatory site model" where both the catalytic and the regulatory site bind ferro- as well as ferricytochrome c.

Probing the role of threonine and serine residues of E. coli asparaginase II by site-specific mutagenesis.

Site-specific mutagenesis has been used to probe amino acid residues proposed to be critical in catalysis by Escherichia coli asparaginase II. Thr12 is conserved in all known asparaginases. The catalytic constant of a T12A mutant towards L-aspartic acid beta-hydroxamate was reduced to 0.04% of wild type activity, while its Km and stability against urea denaturation were unchanged. The mutant enzyme T12S exhibited almost normal activity but altered substrate specificity. Replacement of Thr119 with Ala led to a 90% decrease of activity without markedly affecting substrate binding. The mutant enzyme S122A showed normal catalytic function but impaired stability in urea solutions. These data indicate that the hydroxyl group of Thr12 is directly involved in catalysis, probably by favorably interacting with a transition state or intermediate. By contrast, Thr119 and Ser122, both putative target sites of the inactivator DONV, are functionally less important.

Cloning and sequence analyses of cDNAs encoding aminoacylase I from porcine kidney.

cDNAs encoding L-aminoacylase (EC 3.5.1.14) were isolated from a lambda gt10 cDNA library derived from porcine kidney mRNA. The clones were identified by hybridization with a synthetic oligonucleotide probe based on partial peptide sequences, or with a DNA probe encoding human aminoacylase I. Several cDNA clones isolated from the library had a length of about 1.3 kbp. They contained an open reading frame of 1218 bp encoding a polypeptide of 406 amino acids. The deduced amino-acid sequence contains the known peptide sequences; in addition, M(r) (45.3 kDa) and amino-acid composition of the predicted polypeptide match those of purified aminoacylase I. Data base searches did not reveal significant sequence homologies of aminoacylase I with other well-known amidases.

Site-specific mutagenesis of Escherichia coli asparaginase II. None of the three histidine residues is required for catalysis.

Site-specific mutagenesis was used to replace the three histidine residues of Escherichia coli asparaginase II (EcA2) with other amino acids. The following enzyme variants were studied: [H87A]EcA2, [H87L]EcA2, [H87K]EcA2, [H183L]EcA2 and [H197L]EcA2. None of the mutations substantially affected the Km for L-aspartic acid beta-hydroxamate or impaired aspartate binding. The relative activities towards L-Asn, L-Gln, and l-aspartic acid beta-hydroxamate were reduced to the same extent, with residual activities exceeding 10% of the wild-type values. These data do not support a number of previous reports suggesting that histidine residues are essential for catalysis. Spectroscopic characterization of the modified enzymes allowed the unequivocal assignment of the histidine resonances in 1H-NMR spectra of asparaginase II. A histidine signal previously shown to disappear upon aspartate binding is due to His183, not to the highly conserved His87. The fact that [H183L]EcA2 has normal activity but greatly reduced stability in the presence of urea suggests that His183 is important for the stabilization of the native asparaginase tetramer. 1H-NMR and fluorescence spectroscopy indicate that His87 is located in the interior of the protein, possibly adjacent to the active site.

A catalytic role for threonine-12 of E. coli asparaginase II as established by site-directed mutagenesis.

A threonine-12 to alanine mutant of E. coli asparaginase II (EC 3.5.1.1) has less than 0.01% of the activity of wild-type enzyme. Both tertiary and quaternary structure of the enzyme are essentially unaffected by the mutation; thus the activity loss seems to be the result of a direct impairment of catalytic function. As aspartate is still bound by the mutant enzyme, Thr-12 appears not be involved in substrate binding.

Construction of expression systems for Escherichia coli asparaginase II and two-step purification of the recombinant enzyme from periplasmic extracts.

Isoenzyme II of Escherichia coli L-asparaginase (L-asparagine amidohydrolase, EC 3.5.1.1) is among the few enzymes of major therapeutic importance, being used in the treatment of acute lymphoblastic leukemia. We have constructed several inducible expression systems that overproduce asparaginase II from recombinant plasmids. The most efficient of these systems consists of plasmid pTWE1, a derivative of pT7-7, and an ansB- strain of E. coli, CU1783. These cells produce and secrete amounts of asparaginase II that account for 10-15% of the total cellular protein. Most of the active recombinant enzyme can be released from the periplasmic space by a simple osmotic shock procedure. From the resulting material homogeneous asparaginase II was obtained by a two-step procedure. Overall yields of purified asparaginase were 10-15 mg asparaginase II per liter of E. coli culture. The recombinant enzyme appeared identical to conventionally purified preparations.

Carbon-13 labelled biotin--a new probe for the study of enzyme catalyzed carboxylation and decarboxylation reactions.

[2'-13C]Biotin was incorporated into avidin (egg white), glutaconyl-CoA decarboxylase (EC 4.1.1.70) from Acidaminococcus fermentans and the biotin carrier of transcarboxylase from Propionibacterium freudenreichii (EC 2.1.3.1). 13C-NMR measurements showed an upfield shift of the carbonyl carbon of 3.1 and 2.0 ppm for both enzymes, whereas binding to avidin induced no significant change of the chemical shift as compared to free biotin. The data indicate that the enzymes provide an electronic environment for the covalently bound biotin which favours carboxylation. In addition it was demonstrated by NMR-measurements that glutaconyl-CoA decarboxylase, from which the hydrophobic carboxy-lyase subunit (beta) was removed, could carboxylate free biotin.