Ribulose 1,5-bisphosphate carboxylase from the halophilic cyanobacterium Aphanothece halophytica

Various structural and functional properties of ribulose 1,5-bisphosphate carboxylase/ oxygenase (RuBisCO) isolated from the halophilic cyanobacterium (blue-green alga) Aphanothece halophytica were reexamined. The ready dissociation of this algal RuBisCO during sedimentation in a linear sucrose density gradient was observed. Low NaCl concentrations promote the dissociation of small subunit (B) from the original native enzyme molecule as evidenced by the sucrose density gradient centrifugation and sodium dodecyl sulfate-polyacrylamide gel electrophoresis. It is thus possible that the intracellular osmoticum of A. halophytica might influence the structural integrity and activity of RuBisCO. The low residual carboxylase activity ascribed to the catalytic core, an oligomer form of the large subunit (A) apparently deficient in small subunit (B), was found to be markedly stimulated by a protein component which appears identical to subunit B. The purification and structural characterization of the catalytic core and subunit B were attempted by step-wise column chromatography on DEAE-cellulose, Utrogel AcA 34, Sephadex G-75, and hydroxylapatite, and at the final stage each component was purified to near homogeneity, although the catalytic core is still associated with a small quantity of subunit B. The addition of subunit B to the catalytic core does not alter the K_m (HCO₃^?, RuBP) values, but V_max values are markedly enhanced. Sucrose density gradient centrifugation gave a value of 16 S for the catalytic core. The molecular weights of the monomeric forms of the catalytic core (subunit A) and subunit B were 5.0 × 10⁴ and 1.4 × 10⁴, respectively.     

Biosynthetic mechanism of ribulose-1,5-bisphosphate carboxylase in the purple photosynthetic bacterium,Chromatium vinosum: II. Biosynthesis of constituent subunits

[³⁵S]Methionine-labeled free subunits A and B of RuBP carboxylase were present in barely detectable amounts; the radioactivity in the free subunit B was approximately 1/150th of that in the subunit B contained in the holoenzyme of RuBP carboxylase. The turnover rates of subunits A and B in the holoenzyme were equal at each time during the incubation period. The ratio of subunit A to subunit B was constant throughout the incubation time both in quantity and in the level of [³H]leucine and [³⁵S]methionine incorporated. CO₂ contained in the incubation medium suppressed [³⁵S]methionine incorporation into both subunits A and B equally. These results suggest that the biosynthesis of subunits A and B is completely synchronized and may be regulated by identical mechanisms.     

Enzymic and physicochemical characterization of ribulose 1,5-bisphosphate carboxylase/oxygenase from diploid and tetraploid cultivars of perennial ryegrass

Homogeneous preparations of ribulose 1,5-bisphosphate carboxylase/oxygenase (EC 4.1.1.39) were isolated from several diploid and tetraploid cultivars of perennial ryegrass (Lolium perenne L.) by three different purification protocols. The apparent K_m values for substrate CO₂ were essentially identical for the fully $\text{CO}{}_2\text{Mg}{}^{\mathrm{2+}}$-activated diploid and tetraploid enzymes, as were the kinetics for deactivation and activation of the $\text{CO}{}_2\text{Mg}{}^{\mathrm{2+}}$ activated and -depleted carboxylases, respectively. Similarly, virtually indistinguishable electrophoretic properties were observed for both the native and dissociated diploid and tetraploid ryegrass proteins, including native and subunit molecular weights and the isoelectric points of the native proteins and the large and small subunit component polypeptides. The quantity of carboxylase protein or total soluble leaf protein did not differ significantly between the diploid and tetraploid cultivars. Contrary to a previous report (M. K. Garrett, 1978, Nature (London)274, 913–915), these results indicate that increased ploidy level (i.e., nuclear gene dosage) has had essentially no effect on the quantity or enzymic and physicochemical properties of ribulosebisphosphate carboxylase/ oxygenase in perennial ryegrass.     

Interaction of constituent subunits in ribulose 1,5-bisphosphate carboxylase from Aphanothece halophytica

Ribulose 1,5-bisphosphate carboxylase-oxygenase (RuBisCO) from the halophilic cyanobacterium, Aphanothece halophytica, dissociates into catalytic core (large subunit A oligomer) and small subunit B under low ionic strength during sucrose density gradient centrifugation. Supplementation of KCl, NaCl, or K2SO4 ( [I] = 0.3 M) partly prevents the dissociation, the preventive effect of divalent cation salts such as MgCl2 and CaCl2 being more effective than monovalent cation salts. RuBisCO with its higher-plant-type molecular form can be isolated from the cyanobacterial extracts using gradient medium containing 0.3 M KCl, 20 mM MgCl2, and 10 mM CaCl2. The isolated enzyme contains large subunit A and small subunit B in a molar ratio of approximately 1:1, estimated from the densitometric scanning of Coomassie blue-stained gels. During the second sucrose density gradient centrifugation to remove minor contaminants, a small amount of subunit B is depleted from the holoenzyme. Determination of the molecular weight by equilibrium centrifugation and electron microscopic observation have confirmed that the cyanobacterial RuBisCO has an A8B8-type structure. The enzyme activity per se is found to be sensitive to concentrations of salts, and small subunit B is obligatory for the enzyme catalysis. It has been shown that the more the enzyme activity is inhibited by salts, the tighter the association of subunit B becomes. It is likely that the active enzyme retains the loose conformational structure to such an extent that the dissociable release of subunit B from the holoenzyme in vivo is not allowed.     

Complete primary structure of ribulosebisphosphate carboxylase/oxygenase from Rhodospirillum rubrum

Of the 14 cyanogen bromide fragments derived from Rhodospirillum rubrum ribulosebisphosphate carboxylase/oxygenase, four are too large to permit complete sequencing by direct means [F. C. Hartman, C. D. Stringer, J. Omnaas, M. I. Donnelly, and B. Fraij (1982) Arch. Biochem. Biophys. 219, 422-437]. These have now been digested with proteases, and the resultant peptides have been purified and sequenced, thereby providing the complete sequences of the original fragments. With the determination of these sequences, the total primary structure of the enzyme is provided. The polypeptide chain consists of 466 residues, 144 (31%) of which are identical to those at corresponding positions of the large subunit of spinach ribulosebisphosphate carboxylase/oxygenase. Despite the low overall homology, striking homology between the two species of enzyme is observed in those regions previously implicated at the catalytic and activator sites.     

Biosynthetic mechanism of ribulose-1,5-bisphosphate carboxylase in the purple photosynthetic bacterium, Chromatium vinosum. III. Absence of extrachromosomal DNA

Inducible formation of ribulose-1,5-bisphosphate (RuBP) carboxylase in the cells of Chromatium vinosum under autotrophic conditions was not affected by six different inhibitors of DNA synthesis. Photosynthetic CO2 fixation and RuBP carboxylase activities were not influenced by seven reagents known to eliminate plasmids. Plasmids were not detectable by agarose gel electrophoresis employing either the cleared lysate or alkaline sodium dodecyl sulfate method, nor were they detected by ethidium bromide-CsCl density gradient centrifugation. Overall experimental results tend to indicate that plasmids are absent in the Chromatium cells and that the induction of RuBP carboxylase is presumably not regulated in the DNA replication process.     

Analysis of catalytic subunit microheterogeneity in ribulosebisphosphate carboxylase/oxygenase from Nicotiana tabacum

Urea isoelectric focusing of dissociated, carboxymethylated Nicotiana tabacum ribulose-1,5-bisphosphate carboxylase/oxygenase reveals catalytic subunit microheterogeneity. Aggregated or nonaggregated sucrose gradient-purified preparations and the crystalline protein displayed essentially identical large subunit multiple polypeptide patterns. Various pretreatments which fully dissociate the holoenzyme did not alter catalytic subunit microheterogeneity. Direct comparison of the carboxymethylated and noncarboxymethylated crystalline and sucrose gradient-purified proteins demonstrated that the large subunit multiple polypeptide pattern was not an artifact of carboxymethylation. The inclusion of the seryl protease inhibitor phenylmethylsulfonyl fluoride during purification of the holoenzyme did not affect the large subunit multiplicity. However, the addition of leupeptin, a potent thiol proteinase inhibitor, to all solutions during purification of the native protein markedly reduced large subunit polypeptide L₃ and increased the staining of polypeptide L₂, suggesting that L₃ is a leupeptin-sensitive proteinase degradation product of L₂. Polypeptide L₁ also appeared to be a purification-related artifact, but derived from a modification of L₂ other than that which yielded L₃. We conclude that polypeptide L₂ is the single, native isoelectric form of the catalytic subunit of tobacco ribulosebisphosphate carboxylase/oxygenase.     

Sequences of tryptic peptides containing the five cysteinyl residues of ribulosebisphosphate carboxylase/oxygenase from Rhodospirillum rubrum

Tryptic peptides which account for all five cysteinyl residues in ribulosebisphosphate carboxylase/oxygenase from Rhodospirillum rubrum have been purified and sequenced. Collectively, these peptides contain 94 of the approximately 500 amino acid residues per molecule of subunit. Due to one incomplete cleavage at a site for trypsin and two incomplete chymotryptic-like cleavages, eight major radioactive peptides (rather than five as predicted) were recovered from tryptic digests of the enzyme that had been carboxymethylated with [³H]iodoacetate. The established sequences are: GlyTyrThrAlaPheValHisCys¹Lys TyrValAspLeuAlaLeuLysGluGluAspLeuIleAla GlyGlyGluHisValLeuCys¹AlaTyr AlaGlyTyrGlyTyrValAlaThrAlaAlaHisPheAla AlaGluSerSerThrGlyThrAspValGluValCys¹ ThrThrAsxAsxPheThrArg AlaCys¹ThrProIleIleSerGlyGlyMetAsnAla LeuArg ProPheAlaGluAlaCys¹HisAlaPheTrpLeuGly GlyAsnPheIleLys In these peptides, radioactive carboxymethylcysteinyl residues are denoted with asterisks and the sites of incomplete cleavage with vertical wavy lines. None of the peptides appear homologous with either of two cysteinyl-containing, active-site peptides previously isolated from spinach ribulosebisphosphate carboxylase/oxygenase.     

Purification and sequencing of cyanogen bromide fragments from ribulosebisphosphate carboxylase/oxygenase from Rhodospirillum rubrum

As a part of the goal to determine the total sequence of Rhodospirillum rubrum ribulosebisphosphate carboxylase/oxygenase, the cyanogen bromide fragments were fractionated and sequenced (or partially sequenced). Twelve of the anticipated 14 peptides were obtained in highly purified form. The other two peptides were located, respectively, within a trytophanyl cleavage product (which overlapped with four CNBr fragments) and within an active-site peptide characterized earlier (which overlapped with three CNBr fragments). These overlaps coupled with amino and carboxyl terminal sequence information of the intact subunit and the availability of the sequence of the corresponding enzyme from higher plants permitted alignment of all fragments. Eight CNBr peptides were sequenced completely; four of the CNBr peptides consisted of more than 80 residues and were only partially sequenced as permitted by direct Edman degradation. Of the approximate 475 residues per subunit, 339 were placed in sequence. The lack of extensive conservation of primary structure between R. rubrum and higher plant carboxylases permits the tentative identifications of those regions likely to be functionally important.     

myo-Inositol-1-phosphate synthase from pine pollen: sulfhydryl involvement at the active site

myo-Inositol-1-phosphate synthase [EC 5.5.1.4; 1L-myo-inositol-1-phosphate lyase, (isomerizing)] from Pinus ponderosa pollen has been partially purified and characterized. It has a pH optimum between 7.25 and 7.75. The km for D-glucose 6-phosphate (NAD+ constant at 1 mM) is 0.33 mM. Inhibition by p-chloromercuribenzoate and N-ethylmaleimide, and partial protection against this inhibition by D-glucose 6-phosphate in the presence of NAD+, suggests that there is sulfhydryl group involvement at the substrate binding site.     

R- and S-alkylidene acetals of adenosine: Stereochemical probes for the active site of adenosine deaminase

Condensation of adenosine with unsymmetrical ketones leads to 2′,3′-O-alkylidene acetals with a new chiral center. The diastereoisomers were separated chromatographically, and the ratio of products was found to be 3:1. The configuration of the new chiral centers was determined by nmr spectrosopy. The diastereoisomers were used as stereochemical probes for the active site of adenosine deaminase. By determination of the K_m values it was shown that the binding of the S-diastereoisomers is strongly decreased in comparison with the R-compounds. The data imply a close proximity of the 2′,3′-site of the ribose moiety to the active site of adenosine deaminase.     

Homologies in the active site regions of lactate dehydrogenases

Peptides isolated from several lactate dehydrogenases (EC 1.1.1.27) have been characterized and sequenced. These peptides include much of the substrate binding site as well as the loop of polypeptide chain which shows major conformational changes following coenzyme binding. Despite significant differences in catalytic properties, the amino acid sequence in these two active site regions of the molecule is highly conserved in most cases. A noteable exception is cysteine 165 which at one time was thought to be essential for enzymatic activity. The lactate dehydrogenases investigated were isolated from rabbit muscle, chicken heart, beef heart, and lobster tail.     

Activation of ribulose-1, 5-bisphosphate oxygenase, The role of Mg2+, CO2, and pH.

Ribulose-1,5-bisphosphate oxygenase was activated by incubation with CO₂ and Mg²⁺ and inactivated upon removal of CO₂ and Mg²⁺ by gel filtration. The activity of the enzyme was dependent upon the preincubation concentrations of CO₂ and Mg²⁺ and upon the preincubation pH. This indicated that activation involved the reversible formation of an equilibrium complex of enzyme-CO₂-Mg. The kinetics of the activation process were the same as those described by G. H. Lorimer et al. ((1976) Biochemistry15, 529–536), for ribulose bisphosphate carboxylase and are consistent with the ordered reversible reaction sequence:

The activity of the enzyme, after preincubation at constant concentrations of CO₂ and Mg²⁺, increased as the pH was raised, suggesting that CO₂ reacted with an enzyme group having an alkaline pK. Since CO₂ and O₂ interact competitively at the catalytic site, the activation of ribulose bisphosphate oxygenase by CO₂ and Mg²⁺ indicates that the CO₂ molecule which takes part in the activation process is not the same as that which becomes fixed during the carboxylase reaction. These results also indicate that the oxygenase and carboxylase functions of the catalytic site are tightly coupled rather than independent of one another.     

Modification of alpha-crystallin subunit chains and formation of alpha-neoprotein molecules: role of SH groups

Immunoadsorbents with bound antibodies restricted to determinants dependent on alpha-crystallin's quaternary structure permitted the fractionation of the population of 125I-labeled alpha-crystallin molecules, treated by iodoacetic acid, into molecules in which the native structure was still preserved and molecules with a completely different quaternary structure than the native protein. Parallel experiments with [14C]iodoacetic acid yielded information on the percentage of blocked SH groups in each of the above two fractions. The presence of molecules formed by A with B-chain association was established by sequential binding first to an immunoadsorbent with antibodies restricted to determinants located on alpha-crystallin's A-subunit chains as ligand and second, after desorption, to an immunoadsorbent with antibodies to B chains as ligand. With the aid of these techniques, it was established that (i) The modified alpha-crystallin molecules with quaternary determinants of the native protein contained a maximum of 23% blocked SH groups, indicating that the carboxymethylation involved only the fast-reacting surface SH groups. (ii) The modified alpha-crystallin molecules without the native protein's quaternary structure were built by a different association between A and B subunits than in alpha-crystallin, indicating formation of alpha-neoprotein molecules. (iii) Monomeric A chains with all SH groups carboxymethylated, and monomeric B chains in a ratio of 1A:5B, 2A:1B, and 5A:1B in urea solution, associate on dialysis, forming alpha-neoprotein molecules.     

Location of lysyl residues at the allosteric site of fructose 1,6-bisphosphatase

Various flavin analogs were used as alternate substrates or competitive inhibitors to characterize the FMN binding sites of the NADH- and NADPH-specific FMN oxidoreductases from Beneckea harveyi. Several polyhydroxyl compounds were found to be poor competitive inhibitors for the FMN sites of these enzymes. The FMN binding sites of the two enzymes were found to be quite similar. The NADH:FMN oxidoreductase binds FMN exclusively through the isoalloxazine ring. The methyl groups at positions 7 and 8 contribute significantly to this binding. Utilizing lumichrome as a competitive inhibitor of the FMN binding site and AMP as a competitive inhibitor of the NADH binding site, we were able to determine that the NADH:FMN oxidoreductase forms an active ternary complex with NADH binding first in an ordered mechanism. The NADPH oxidoreductase also binds FMN primarily through the isoalloxazine ring. Unlike their participation in reaction with the NADH-specfic enzyme, the methyl groups at positions 7 and 8 are not involved in binding. There was no significant binding of the ribityl phosphate moiety with either enzyme. Both enzymes have lower K_m values for lumiflavin than FMN.