Arginine-239 in the beta subunit is at or near the active site of bovine pyruvate dehydrogenase.

We have modified bovine pyruvate dehydrogenase (E1), the first catalytic component of the pyruvate dehydrogenase complex, with pyreneglyoxal. Treatment of E1 with pyreneglyoxal resulted in the loss of enzyme activity. Pyruvate plus thiamin pyrophosphate (TPP) afforded approximately 80% protection against this inactivation and protected two arginine residues per mol of E1 tetramer (alpha 2 beta 2) from modification. Circular dichroism spectral analysis indicated absence of any gross structural changes in the enzyme as a result of modification. Comparison of the peptide maps, monitored at 345 nm of unprotected and pyruvate plus TPP protected E1s after V8 digestion revealed that a peptide in the protected enzyme was labeled by pyreneglyoxal to a lesser extent than its counterpart in the unprotected enzyme. Sequence analysis of the peptide demonstrated that it corresponded precisely to amino-acid residues 235 to 246 in the human E1 beta sequence, with arginine residues at positions 239 and 242. Since Arg-239 is conserved in the beta-subunit of all presently known sequences of the pyruvate dehydrogenase complex and branched-chain alpha-keto acid dehydrogenase complex, it is strongly suggested that Arg-239 in the human E1 beta sequence is at or near the active site of bovine E1.

Structural characterization of the entire 1.3S subunit of transcarboxylase from Propionibacterium shermanii.

Transcarboxylase (TC) from Propionibacterium shermanii, a biotin-dependent enzyme, catalyzes the transfer of a carboxyl group from methylmalonyl-CoA to pyruvate in two partial reactions. Within the multisubunit enzyme complex, the 1.3S subunit functions as the carboxyl group carrier. The 1.3S is a 123-amino acid polypeptide (12.6 kDa), to which biotin is covalently attached at Lys 89. We have expressed 1.3S in Escherichia coli with uniform 15N labeling. The backbone structure and dynamics of the protein have been characterized in aqueous solution by three-dimensional heteronuclear nuclear magnetic resonance (NMR) spectroscopy. The secondary structure elements in the protein were identified based on NOE information, secondary chemical shifts, homonuclear 3J(HNHalpha) coupling constants, and amide proton exchange data. The protein contains a predominantly disordered N-terminal half, while the C-terminal half is folded into a compact domain comprising eight beta-strands connected by short loops and turns. The topology of the C-terminal domain is consistent with the fold found in both carboxyl carrier and lipoyl domains, to which this domain has approximately 26-30% sequence similarity.

Primary structure of the 5 S subunit of transcarboxylase as deduced from the genomic DNA sequence.

Transcarboxylase from Propionibacterium shermanii is a complex biotin-containing enzyme composed of 30 polypeptides of three different types. It is composed of six dimeric outer subunits associated with a central cylindrical hexameric subunit through 12 biotinyl subunits; three outer subunits on each face of the central hexamer. Each outer dimer is termed a 5 S subunit which associates with two biotinyl subunits. The enzyme catalyzes a two-step reaction in which methylmalonyl-CoA and pyruvate form propionyl-CoA and oxalacetate, the 5 S subunit specifically catalyzing one of these reactions. We report here the cloning, sequencing and expression of the monomer of the 5 S subunit. The gene was identified by matching amino acid sequences derived from isolated authentic 5 S peptides with the deduced sequence of an open reading frame present on a cloned P. shermanii genomic fragment known to contain the gene encoding the 1.3 S biotinyl subunit. The cloned 5 S gene encodes a protein of 519 amino acids, M(r) 57,793. The deduced sequence shows regions of extensive homology with that of pyruvate carboxylase and oxalacetate decarboxylase, two enzymes which catalyze the same or reverse reaction. A fragment was subcloned into pUC19 in an orientation such that the 5 S open reading frame could be expressed from the lac promoter of the vector. Crude extracts prepared from these cells contained an immunoreactive band on Western blots which co-migrated with authentic 5 S and were fully active in catalyzing the 5 S partial reaction. We conclude that we have cloned, sequenced and expressed the monomer of the 5 S subunit and that the expressed product is catalytically active.

Cell selective induction and transcriptional activation of immediate early genes by hypoxia.

c-fos and jun belong to the immediate early response genes (IERG) that initiate phenotypic changes in response to a variety of extracellular stimuli. In the present study, we examined whether hypoxia induces IERG expression in isolated cells. Experiments were performed on pheochromocytoma-12 (PC-12), hepatoblastoma (Hep3B), neuroblastoma and fibroblast cells that were exposed either to normoxia (21% O2) or to hypoxia (5% O2) for one hour. mRNAs for c-fos, c-jun, junB, junD were analyzed by northern blot assay. Increases in IERG mRNAs were seen in PC-12, Hep3B, and fibroblasts but not in neuroblastoma cells. Significant induction of c-fos mRNA was seen with hypoxic exposure as short as 15 min and the effects persisted at 10 h of low pO2 exposure. Hypoxia stimulated transcription from a 356 bp fragment of the c-fos promoter linked to a choloramphenicol acetyl transferase reporter in PC-12 but not in neuroblastoma cells. Fetal bovine serum, however, activated c-fos promoter both in PC-12 and neuroblastoma cells. These results demonstrate cell type selective mechanisms for c-fos promoter activation that require nucleic acid sequences with in the first 356 bp of the c-fos promoter. These observations suggest that increased IERG transcription is one of the early events in genomic adaptations to hypoxia.

Purification and properties of the synthetase catalyzing the biotination of the aposubunit of transcarboxylase from Propionibacterium shermanii.

The synthetase that attaches biotin to the aposubunit of transcarboxylase (biotin-[methylmalonyl-CoA-carboxyltransferase]ligase) (EC 6.3.4.9) was purified to homogeneity by ion-exchange chromatography on cellulose DE-52 and CM-cellulose. The synthetase is a monomer of molecular weight 30,000. The pH and temperature optima for the synthetase are 6.0 and 37 degrees C, respectively. The apparent Km for the substrates ATP, biotin, and apo 1.3 S subunit of apotranscarboxylase are 38, 2.0, and 0.9 microM, respectively. Ni2+, Co2+, Zn2+, or Mn2+ could replace Mg2+ in the reaction. The affinity of synthetase toward metals is as follows: Zn2+ greater than Ni2+ greater than Mn2+ greater than Co2+ greater than Mg2+, and the activity with Zn2+ was much greater than that with the other divalent metals. EDTA completely inactivates the enzyme. The metals are necessary not only for the catalytic activity but also for the storage stability of the enzyme. The synthetase shows absolute specificity toward ATP.

Identification and characterization of a factor which is essential for assembly of transcarboxylase.

Transcarboxylase (TC) from Propionibacterium shermanii is a biotin-containing enzyme which catalyzes the reversible transfer of a carboxyl group from methylmalonyl-CoA to pyruvate. It is composed of a central, hexameric 12S subunit with six outer, dimeric 5S subunits held in a stable 26S complex by twelve 1.3S biotinyl subunits. Each of these subunits has been cloned from the P. shermanii genome and expressed in Escherichia coli. The purified, expressed recombinant proteins are all indistinguishable from their authentic counterparts except for the recombinant 5S subunit (termed 5S WT), which does not form TC complexes or catalyze the overall transcarboxylase reaction. Circular dichroism and isoelectric focusing suggested differences existed between the authentic and E. coli-expressed 5S proteins. HPLC gel filtration was used to separate the authentic 5S dimer from additional components in the preparation. 5S dimer thus purified was unable to form TC complexes or catalyze the overall reaction, behaving identically to the recombinant 5S WT subunit. Fractions from the HPLC gel-filtration purification of authentic 5S were then added to 5S WT or 5S dimer, and one fraction was identified which catalyzed the assembly of TC complexes with either 5S preparation. This assembly activity was shown to be dependent on the concentration of this HPLC fraction. Assembly-promoting factor (APF) is heat-stable and probably a protein, on the basis of its protease susceptibility. Studies with APF and the other TC subunits demonstrate its ability to promote complex formation with 12S and 1.3S subunits. Since the APF was purified from crystals of 26S TC, we believe it to be a novel, previously unidentified subunit of transcarboxylase.

The conserved methionines of the 1.3 S biotinyl subunit of transcarboxylase: effect of mutations on conformation and activity.

Transcarboxylase from Propionibacterium shermanii is a biotin-containing enzyme which catalyzes the reversible transfer of a carboxyl group from methylmalonyl-CoA to pyruvate. Transcarboxylase 26 S complexes consist of a central, hexameric 12 S subunit with 6 outer, 5 S subunits attached by 12 1.3 S biotinyl subunits. Each of the subunits has been cloned and expressed in Escherichia coli in active form. We have used the cloned genes in mutagenic studies of the structure-function interactions of these subunits. One particular target of our studies has been the evolutionarily conserved tetrapeptide Ala-Met-Bct-Met which surrounds the biotinyl lysine. We have investigated the properties of subunits containing leucine substitutions at each methionine (1.3 S M88L and 1.3 S M90L) by assaying their activity in the two partial reactions in which this subunit participates. Partial reaction assays demonstrate that leucine substitution at either position has a greater effect on the 12 S partial reaction than on the 5 S reaction and Met 88 is more significant catalytically than Met 90. To determine whether structural alterations in the 1.3 S mutants were responsible for the effects on activity, the conformations of these mutants were investigated. In vitro hydrolysis studies with trypsin and V8 protease demonstrated differences in the susceptibility of 1.3 S M88L relative to 1.3 S WT and 1.3 S M90L. Complexes of avidin with 1.3 S WT or mutant subunits, as monitored by fluorescence properties, indicated that the microenvironment of the biocytin of 1.3 S M88L was different from those of 1.3 S WT and 1.3 S M90L. By contrast, substrate binding (oxalacetate for 5 S and methylmalonyl-CoA for 12 S) was unaffected by any of the 1.3 S mutants. Taken together, these results indicate that the conserved tetrapeptide of the 1.3 S biotinyl subunit, particularly Met 88, is required to provide an essential conformation and proper binding properties for catalysis of the partial reactions and the overall reaction.

Isolation and characterization of a novel haemoprotein b-559 from Bengal gram (Cicer arietinum).

A haemoprotein was purified to apparent homogeneity from Bengal-gram seeds. The purified protein exhibited an absorption maximum at 412 nm (Soret band) that upon reduction with dithionite gave rise to a shift in the Soret band to 426 nm with concomitant appearance of an alpha-band at 559 nm and a beta-band at 530 nm. In the reduced state the Bengal-gram haemoprotein showed reactivity towards CO, nitrite and hydroxylamine. SDS/polyacrylamide-slab-gel electrophoresis showed that the haemoprotein has Mr 78,000. Gel-filtration and ultracentrifugal analyses suggest that the Bengal-gram haemoprotein is oligomeric in nature. Since it differs from photosynthetic membrane cytochrome b-559 in solubility in buffer, in reactivity towards CO and in molecular size, it appears to be a novel haemoprotein b-559.

Fungal glucoamylases.

Glucoamylase (alpha-1,4-glucan glucohydrolase, EC 3.2.1.3) from fungal sources is one of the microbial glycoproteins that has received considerable attention particularly because it is used in the commercial production of dextrose. Several investigators have isolated glucoamylase from various fungal sources. In many instances the presence of more than one form of enzyme is common. The enzymes from most sources have pH optima between 4 and 5 and exhibit maximum activity between 40 and 60 degrees C. The enzyme does not require any cofactors for activity or for stability. The enzyme has an Mr between 48,000 and 80,000 and usually has no subunit structure. The amino acid composition of multiple forms of glucoamylases differ in general, but all of them are glycoproteins. The carbohydrate content of the enzyme ranges from 3 to 30% containing mainly mannose, but glucose, galactose, and in some instances glucosamine and xylose are also present. In the enzyme from Aspergillus the carbohydrate structures are present as mono-, di-, tri-, and tetrasaccharide units linked O-glycosidically through mannose to the hydroxyl groups of serine and threonine. In the enzyme from Rhizopus part of the carbohydrate is present as disaccharide (Man-Man-) units linked O-glycosidically and the remainder is present as large heterosaccharide structures attached by N-glycosidic linkages involving aspargine and glucosamine. Carbohydrate moieties seem to have no influence on the enzyme activity or antigenicity but appear to stabilize the enzyme by preserving the three-dimensional structure.

Dissection of the biotinyl subunit of transcarboxylase into regions essential for activity and assembly.

Transcarboxylase, a multisubunit enzyme containing 12 S, 5 S, and 1.3 S subunits, catalyzes the transfer of a carboxyl group from methylmalonyl-CoA to pyruvate (overall reaction) via two partial reactions. In the first partial reaction, a carboxyl group from methylmalonyl-CoA bound to the 12 S subunit is transferred to the biotin of the 1.3 S subunit, and, in the second partial reaction, the carboxylated biotin transfers its carboxyl group from biotin to pyruvate, bound to the 5 S subunit. Previously we have shown that the region around the biotinyl lysine of the 1.3 S subunit is critical for catalysis, that peptides in the amino-terminal region of 1.3 S are capable of forming complexes with 12 S and 5 S, and that amino acids in the carboxyl terminus of the 1.3 S subunit form part of the recognition site for holocarboxylase synthetase. In order to further examine the role of the sequences in this subunit, we generated 8 shortened forms of the 1.3 S biotinyl subunits missing either one or both termini. Truncated 1.3 S subunits were active in both partial reactions until deletion reached amino acid 59. None of the truncated subunits was able to support stable complex formation with the 12 S and 5 S subunits or catalyze the overall reaction. The results suggest that the region between 59 and 78 is required for activity and the sequence 1-18 is required for enzyme assembly. Activity in the partial reactions correlated with intrinsic fluorescence enhancement of tryptophan residues in either the 12 S or 5 S subunit. Fluorescence enhancement was observed with the shortened 1.3 S subunits until truncation reached amino acid 59 implying either 1) that the internal sequence, 59-78, transiently associates with the other subunits to properly orient the biotin for catalysis or 2) that the sequence 59-78 contributes to the folded conformation of the 1.3 S subunit so that subunit interactions can take place.

Purification of polyphosphate and ATP glucose phosphotransferase from Mycobacterium tuberculosis H37Ra: evidence that poly(P) and ATP glucokinase activities are catalyzed by the same enzyme.

Polyphosphate [poly(P)n]:D-(+)-glucose-6-phosphotransferase (EC 2.7.1.63) from Mycobacterium tuberculosis H37Ra was purified to homogeneity using an improved method which yielded a 634-fold purification with higher recovery. The purified enzyme migrated as a single band with M(r) 33 kDa on sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE). The native enzyme was shown to be a dimer by gel filtration using high-performance liquid chromatography (HPLC). The purified enzyme fractionated as a single peak on a C8 reverse-phase HPLC column and was found to display both polyphosphate- and ATP-dependent glucokinase activities. Further evidence that a single protein was responsible for both activities was shown by nondenaturing PAGE, in which the two activities (as determined by an activity stain in dual experiments) were found to comigrate. The C-terminal analysis yielded a single sequence while the N-terminus which was blocked also yielded a single sequence after deblocking. The two activities were found to have the same temperature optimum of 50 degrees C. The pH optima were 9.5 and 8.6-9.5 with poly(P)32 and ATP as the phosphoryl donors, respectively. The apparent Km for poly(P)32 was 18.4 microM while the Km for ATP was 1.46 mM. In addition, the nucleotide analogue, Reactive Blue 4, was found to be a competitive inhibitor with ATP in the ATP-dependent glucokinase reaction, while it displayed noncompetitive inhibition patterns with poly(P) in the poly(P)-dependent glucokinase reaction. It is concluded that the poly(P) and ATP glucokinase activities are catalyzed by the same enzyme but that the two substrates may have different binding sites.

Purification and characterization of the recombinant 5 S subunit of transcarboxylase from Escherichia coli.

Transcarboxylase from Propionibacterium shermanii is a biotin-containing enzyme which catalyzes the reversible transfer of a carboxyl group from methylmalonyl-CoA to pyruvate. It is composed of a central, hexameric 12 S subunit, 6 outer dimeric 5 S subunits which are held in a complex by 12 1.3 S biotinyl subunits. The transcarboxylase reaction requires two partial reactions, one of which is specific to 5 S. The cloning and expression of each of these subunits in Escherichia coli have been reported. We have designed a method for the purification of the 5 S subunit from an E. coli expression system. Protein purified to homogeneity by this method was shown to be active in the 5 S partial reaction, but unable to catalyze the overall transcarboxylase reaction. This protein was characterized as to its ability to form stable dimers, associate with the 1.3 S subunit in stable complexes referred to as 6 S, and assemble whole TC. The latter activity was shown to be lacking. The purified protein has a native molecular weight of 120 kDa and a subunit molecular weight of 60 kDa, consistent with the 5 S dimer. Plasma emission analysis of the metal content of the recombinant protein demonstrated the presence of both Co and Zn, comparable to the authentic protein. Fluorescence analysis verified the ability of the purified protein to bind substrates and 1.3 S subunits appropriately. Sequencing of the amino terminus and determination of the amino acid composition of the recombinant protein relative to that of the authentic subunit further verified the identity of the purified protein.(ABSTRACT TRUNCATED AT 250 WORDS)

Chemical modification of the functional arginine residues of carbon monoxide dehydrogenase from Clostridium thermoaceticum.

Carbon monoxide dehydrogenase (CODH) is the key enzyme of autotrophic growth with CO or CO2 and H2 by the acetyl-CoA pathway. The enzyme from Clostridium thermoaceticum catalyzes the formation of acetyl-CoA from the methyl, carbonyl, and CoA groups and has separate binding sites for these moieties. In this study, we have determined the role of arginine residues in binding of CoA by CODH. Phenylglyoxal, an arginine-specific reagent, inactivated CODH, and CoA afforded about 80-85% protection against this inactivation. The other ligands, such as the carbonyl and the methyl groups, gave no protection. By circular dichroism, it was shown that the loss of activity is not due to extensive structural changes in CODH. Earlier, we showed that tryptophan residues are located at the CoA binding site of CODH [Shanmugasundaram, T., Kumar, G. K., & Wood, H. G. (1988) Biochemistry 27, 6499-6503]. A comparison of the fluorescence spectra of the native and phenylglyoxal-modified enzymes indicates that the reactive arginine residues appear to be located close to fluorescing tryptophans. Fluorescence spectral studies with CoA analogues or its components showed that CoA interacts with the tryptophan(s) of CODH through its adenine moiety. In addition, evidence is presented that the arginines interact with the pyrophosphate moiety of CoA.

Absence of observable biotin-protein interactions in the 1.3S subunit of transcarboxylase: an NMR study.

Transcarboxylase (TC) is a biotin-containing enzyme catalyzing the transfer of a carboxyl group from methylmalonyl-CoA to pyruvate to form propionyl-CoA and oxalacetate. The transfer is achieved via carboxylated biotin bound to a 1.3S subunit within the multisubunit enzyme complex. The 1.3S subunit of TC is a 123 amino acid polypeptide, to which biotin is covalently attached at Lys 89. We have overexpressed 1.3S in Escherichia coli and characterized the biotinylated and apo-forms by 1D- and 2D-NMR spectroscopy. To search for protein-biotin interactions, which could modulate the reactivity of the biotin ring on the 1.3S subunit, we have compared the chemical shifts, relaxation parameters, and NH exchange rates of the ureido ring protons of free and 1.3S-bound biotin. These properties are similar for both forms of the biotin. Further, NOE experiments on 1.3S revealed no detectable cross peaks between biotin and the protein. Consistent with these findings, the 2D NMR data for holo- and apo-1.3S are essentially identical indicating little or no changes in conformation between the two forms of the protein. The conclusion that strong protein-biotin interactions do not exist in 1.3S contrasts with the findings for the biotin carboxylase carrier protein from E. coli acetyl-CoA carboxylase, which reveal significant biotin-protein contacts [Athappilly, F. K., and Hendrickson, W. A. (1995) Structure 3, 1407-1419]. Further, the biotin NH1' exchange rates determined for 1.3S show that in the region of optimal activity for TC (pH 5.5-6.5) acid-catalyzed exchange predominates. In this pH range the base-catalyzed rate is too small (< 1 s-1) to account for the turnover rate of the enzyme. Thus, the means by which the N1' atom is activated for nucleophilic attack of the carboxyl group in methylmalonyl-CoA does not appear to depend on interactions within the 1.3S subunit alone; rather activation must occur at the interfaces of the subunits in the holoenzyme.

High resolution solution structure of the 1.3S subunit of transcarboxylase from Propionibacterium shermanii.

Transcarboxylase (TC) from Propionibacterium shermanii, a biotin-dependent enzyme, catalyzes the transfer of a carboxyl group from methylmalonyl-CoA to pyruvate to form propionyl-CoA and oxalacetate. Within the multi-subunit enzyme complex, the 1.3S subunit functions as the carboxyl group carrier and also binds the other two subunits to assist in the overall assembly of the enzyme. The 1.3S subunit is a 123 amino acid polypeptide (12.6 kDa) to which biotin is covalently attached at Lys 89. The three-dimensional solution structure of the full-length holo-1.3S subunit of TC has been solved by multidimensional heteronuclear NMR spectroscopy. The C-terminal half of the protein (51-123) is folded into a compact all-beta-domain comprising of two four-stranded antiparallel beta-sheets connected by short loops and turns. The fold exhibits a high 2-fold internal symmetry and is similar to that of the biotin carboxyl carrier protein (BCCP) of acetyl-CoA carboxylase, but lacks an extension that has been termed "protruding thumb" in BCCP. The first 50 residues, which have been shown to be involved in intersubunit interactions in the intact enzyme, appear to be disordered in the isolated 1.3S subunit. The molecular surface of the folded domain has two distinct surfaces: one side is highly charged, while the other comprises mainly hydrophobic, highly conserved residues.

Cloning, expression, and characterization of polyphosphate glucokinase from Mycobacterium tuberculosis.

Polyphosphate glucokinase from Mycobacterium tuberculosis catalyzes the phosphorylation of glucose using polyphosphate or ATP as the phosphoryl donor. The M. tuberculosis H37Rv gene encoding this enzyme has been cloned, sequenced, and expressed in Escherichia coli. The gene contains an open reading frame for 265 amino acids with a calculated mass of 27,400 daltons. The recombinant polyphosphate glucokinase was purified 189-fold to homogeneity and shown to contain dual enzymatic activities, similar to the native enzyme from H37Ra strain. The high G+C content in the codon usage (64.5%) of the gene and the absence of an E. coli-like promoter consensus sequence are consistent with other mycobacterial genes. Two phosphate binding domains conserved in the eukaryotic hexokinase family were identified in the polyphosphate glucokinase sequence, however, "adenosine" and "glucose" binding motifs were not apparent. In addition, a putative polyphosphate binding region is also proposed for the polyphosphate glucokinase enzyme.

Effect of mutations at Met-88 and Met-90 on the biotination of Lys-89 of the apo 1.3S subunit of transcarboxylase.

The apo 1.3S subunit of transcarboxylase contains the sequence Ala-87-Met-88-Lys-89-Met-90, and it is Lys-89 that is biotinated. This sequence is highly conserved in all the biotin enzymes that have been sequenced (with the exception of acetyl-CoA carboxylase from chicken liver, which has Val in place of Ala). The role of Met-88 and Met-90 in specifying Lys-89 for biotination by synthetase was examined by site-directed mutagenesis. Genes of the 1.3S subunit coding for Thr-88, Leu-88, or Leu-90 were generated by oligonucleotide-directed in vitro mutagenesis and expressed in Escherichia coli. The mutated apo 1.3S subunits were isolated and the biotination by homogeneous synthetase from Propionibacterium shermanii was compared with that of the apo wild-type subunit. The Vmax for the apo mutants was the same as that for the apo wild type, but when Leu was substituted for Met-88 or Met-90, the Km for the mutant was lower than that of the wild-type or mutant Thr-88. The activity of the synthetase of E. coli was determined by an in vivo assay. During the early log phase of growth, a smaller portion of mutants Thr-88 and Leu-90 was biotinated than with the wild-type or mutant Leu-88. When the cultures progressed to stationary phase, mutants and the wild type were biotinated to the same extent. The overall results show that Met-88 and Met-90 are not required for biotination of the apo 1.3S subunit by the synthetases.

Involvement of tryptophan(s) at the active site of polyphosphate/ATP glucokinase from Mycobacterium tuberculosis.

The glucokinase (EC 2.7.1.63) from Mycobacterium tuberculosis catalyzes the phosphorylation of glucose using inorganic polyphosphate (poly(P)) or ATP as the phosphoryl donor. The nature of the poly(P) and ATP sites was investigated by using N-bromosuccinimide (NBS) as a probe for the involvement of tryptophan in substrate binding and/or catalysis. NBS oxidation of the tryptophan(s) resulted in fluorescence quenching with concomitant loss of both the poly(P)- and ATP-dependent glucokinase activities. The inactivation by NBS was not due to extensive structural changes, as evidenced by similar circular dichroism spectra and fluorescence emission maxima for the native and NBS-inactivated enzyme. Both phosphoryl donor substrates in the presence of xylose afforded approximately 65% protection against inactivation by NBS. The Km values of poly(P) and ATP were not altered due to the modification by NBS, while the catalytic efficiency of the enzyme was decreased, suggesting that the essential tryptophan(s) are involved in the catalysis of the substrates. Acrylamide quenching studies indicated that the tryptophan residue(s) were partially shielded by the substrates against quenching. The Stern-Volmer quenching constant (KSV) of the tryptophans in unliganded glucokinase was 3.55 M-1, while KSV values of 2.48 and 2.57 M-1 were obtained in the presence of xylose+poly(P)5 and xylose+ATP, respectively. When the tryptophan-containing peptides were analyzed by peptide mapping, the same peptide was found to be protected by xylose+poly(P)5 and xylose+ATP against oxidation by NBS. The two protected peptides were determined to be identical by N-terminal sequence analysis and amino acid composition.(ABSTRACT TRUNCATED AT 250 WORDS)

The importance of methionine residues for the catalysis of the biotin enzyme, transcarboxylase. Analysis by site-directed mutagenesis.

Almost all biotin enzymes contain the conserved tetrapeptide Ala-Met-Bct-Met (Bct, N epsilon-biotinyl-L-lysine). In the 1.3 S biotinyl subunit of transcarboxylase (TC), this sequence is present between positions 87 and 90. The conserved nature of these amino acids implies a critical role in the function of biotin enzymes. In order to examine the role of these conserved amino acids, point mutations in the gene encoding the 1.3 S subunit have been made by site-directed mutagenesis to generate A87G, M88L, M90L, M88T, M88C, M88A, and a double mutant A87M, M88A in the 1.3 S subunit. TC, a multisubunit enzyme containing 12 S, 5 S, and 1.3 S subunits, catalyzes the transfer of a carboxyl group from methylmalonyl-CoA to pyruvate (overall reaction). TC can be dissociated into individual subunits and also reconstituted by assembling isolated subunits to a fully active form. The mutants of the 1.3 S subunit have been reconstituted with native 5 S and 12 S subunits from Propionibacterium shermanii. The effects of mutations on the activity of TC were compared with that of TC-1.3 S wild type (WT) prepared in a similar manner. The results show that any substitution of a residue in the conserved tetrapeptide causes impairment of the rate of TC activity. Comparison of gel filtration profiles, sodium dodecyl sulfate-polyacrylamide gel electrophoresis and electron micrographs of the TC assembled with mutant 1.3 S and with wild type 1.3 S subunits showed that the impairment of the overall activity was not due to a failure of the subunits to assemble into complexes. Steady state kinetic analysis using the mutant 1.3 S subunits indicated that the Km for methylmalonyl-CoA or pyruvate did not change significantly indicating that the binding of substrates is not altered. However, the kcat values were significantly lower for mutants at positions 87 and 88 than for those at position 90. The replacement of methionine at position 88 either by hydrophobic or hydrophilic residues significantly altered the activity in the overall reaction, while similar substitution at position 90 did not dramatically alter the kcat. These results suggest that Ala-87 and Met-88 are catalytically critical in the conserved tetrapeptide.

Identification of the tryptophan residue in the thiamin pyrophosphate binding site of mammalian pyruvate dehydrogenase.

The pyruvate dehydrogenase (E1) component of the mammalian pyruvate dehydrogenase complex catalyzes the oxidative decarboxylation of pyruvate with the formation of an acetyl residue and reducing equivalents, which are transferred sequentially to the dihydrolipoyl acetyltransferase and dihydrolipoamide dehydrogenase components. To examine the role of tryptophanyl residue(s) in the active site of E1, the enzyme was modified with the tryptophan-specific reagent N-bromosuccinimide. Modification of 2 tryptophan residues/mol of bovine E1 (out of 12 in a tetramer alpha 2 beta 2) resulted in complete inactivation of the enzyme. The inactivation was prevented by preincubation with thiamin pyrophosphate (TPP), indicating that the modified tryptophan residue(s) is part of the active site of this enzyme. Fluorescence studies showed that thiamin pyrophosphate interacts with tryptophan residue(s) of E1. The magnetic circular dichroism (MCD) spectral intensity at approximately 292 nm was decreased by approximately 15% for E1 + TPP relative to the intensity for E1 alone. Because this MCD band is uniquely sensitive to and quantitative for tryptophan, the simplest interpretation is that 1 out of 6 tryptophan residues present in E1 (alpha beta dimer) interacts with TPP. The natural circular dichroism (CD) spectrum of E1 is dramatically altered upon binding TPP, with concomitant induction of optical activity at approximately 263 nm for the nonchiral TPP macrocycle. From CD studies, it is also inferred that loss of activity following N-bromosuccinimide treatment occurred without significant changes in the overall secondary structure of the protein. A single peptide was isolated by differential peptide mapping in the presence and absence of thiamin pyrophosphate following modification with N-bromosuccinimide. This peptide generated from human E1 was found to correspond to amino acid residues 116-143 in the deduced sequence of human E1 beta, suggesting that the tryptophan residue 135 in the beta subunit of human E1 functions in the active site of E1. The amino acid sequence surrounding this tryptophan residue are conserved in E1 beta from several species, suggesting that this region may constitute a structurally and/or functionally essential part of the enzyme.