Chemistry and subunit structure of yeast hexokinase isoenzymes

Evidence from ultracentrifugation, sodium dodecyl sulfate electrophoresis, peptide mapping, and carboxypeptidase A digestion allows the conclusion that the two native hexokinases, P-I and P-II, consist of polypeptide chains having molecular weights slightly higher than 50,000. It was demonstrated that some preparations are contaminated with a protease, and that this impurity caused erroneous results in sodium dodecyl sulfate electrophoresis and carboxypeptidase A digestion.Amino acid analyses indicated that both P-I and P-II contain four cysteine, four tryptophan, and eleven methionine residues per mole. In contrast, P-I contains eight, and P-II five, histidine residues per mole. Many of the differences in amino acid composition are small, but reproducible.Peptide mapping indicated that many segments of P-I and P-II have identical sequences. There were about 27 common tryptic peptides, and about 16–19 unique to each form. In addition, both isozymes were found to have the same amino terminus, valine, and the same carboxy terminus, alanine; some evidence for a difference in the penultimate residue at the carboxy terminus was indicated.     

Three-dimensional structure of the complex of guanylate kinase from yeast with its substrate GMP

The enzyme guanylate kinase was isolated from baker's yeast and crystallized as a complex with its substrate GMP. The crystal structure was solved by multiple isomorphous replacement, solvent-flattening, restrained least-squares refinement, and simulated annealing. The current R-factor is 28.9% at a resolution of 2.0 A. The model is given as a backbone tracing, the GMP binding site is shown in atomic detail. In its major domain (residues 1 to 32 and 82 to 186), the chain fold is closely similar to the adenylate kinases, while the minor domain (residues 33 to 81) differs grossly from the 3-helix fold of the adenylate kinases. Structural homology and mechanistical similarity allow us to assign the AMP site of the adenylate kinases on the basis of the GMP site.     

Genetics of yeast hexokinase

Two independent isolates of Saccharomyces cerevisiae lacking hexokinase activity (EC 2.7.1.1) are described. Both mutant strains grow on glucose but are unable to grow on fructose, and contain two mutant genes hxk1 and hxk2 each. The mutations are recessive and noncomplementing. Genetic analysis suggests that these two unlinked genes hxk1 and hxk2 determine, independently of each other, the synthesis of hexokinase isozymes P1 and P2, respectively. hxk1 is located on chromosome VIR distal to met10, and hxk2 is on chromosome IIIR distal to MAL2. Of four hexokinase-positive spontaneous reversions, one is very tightly linked to hxk1 and the other three to the hxk2 locus. The reverted enzymes are considerably more thermolabile than the respective wild-type enzymes, and in one case show altered immunological properties. Data are presented which suggest that the hxk1 and hxk2 mutations are missense mutations in the structural genes of hexokinase P1 and hexokinase P2, respectively. These are presumably the only enzymes that allow S. cerevisiae to grow on fructose.     

The interaction of nucleotides and yeast hexokinase

The kinetics of ethenoadenosine triphosphate (?ATP) as the phosphate donor in the phosphoryl transfer reaction of hexokinase were examined to obtain the K_m′s, V's, and K_α's for the nucleotide and sugar. Dissociation constants for eATP and ?ADP with hexokinase were obtained from fluorometric measurements and compared with similar constants obtained kinetically. Other selected nucleoside triphosphates were used as phosphate donors in the hexokinase reaction and their kinetic constants were obtained. Reactions were also performed using two nucleotides simultaneously as phosphorylating substrates for the hexokinase reaction in an attempt to find the individual dissociation constants, K_m′s and K_i′s. These were compared with the K_m′s obtained from using the nucleotides separately in the hexokinase reaction. From these kinetic and fluorescence binding studies, evidence is presented supporting the postulate that the K_m′s are primarily dissociation constants in a random bi-bi mechanism. Analysis of the K_m values provides additional evidence to support the importance of the amino group in position 6 on the purine ring as a hydrogen-bond acceptor during binding. It was found that ?CTP was a much better hexokinase substrate than CTP. These observations suggest that the V for this reaction is highly dependent upon the size of the nucleotide.     

Thermally induced changes in the structure and activity of yeast hexokinase B

Yeast hexokinase has been poorly characterized in regard with its stability. In the present study, various spectroscopic techniques were employed to investigate thermal stability of the monomeric form of yeast hexokinase B (YHB). The enzyme underwent a conformational transition with a T(m) of about 41.9 degrees C. The structural transition proved to be significantly reversible below 55 degrees C and irreversible at higher temperatures. Thermoinactivation studies revealed that enzymatic activity diminished significantly at high temperatures, with greater loss of activity observed above 55 degrees C. Release of ammonia upon deamidation of YHB obeyed a similar temperature-dependence pattern. Dynamic light scattering and size exclusion-HPLC indicated formation of stable aggregates. Taking various findings on the influence of osmolytes and chaperone-like agents on YHB thermal denaturation together, it is proposed that the purely conformational transition of YHB is reversible, and irreversibility is due to aggregation, as a major cause. Deamidation of a critical Asn or Gln residue(s) may also play an important role.     

Location in the yeast hexokinase structure of residues related to the enzyme activity

Seven residues implicated as acting directly in substrate binding in yeast hexokinase B have been identified in the crystallographic structure by chemical sequencing. The cysteine which is regarded as a residue critically maintaining the active conformation of yeast hexokinase has been selectively labelled and likewise located in the structure. In some parts of the amino acid sequence predicted from the high-resolution electron density map it is found that alignments of chemically sequenced peptides can be made unambiguously; however, the extent of matching to the predicted sequence varies considerably along the chain.     

The primary structure of the yeast hexokinase PII gene (HXK2) which is responsible for glucose repression

The nucleotide sequence of the Saccharomyces cerevisiae gene encoding the glycolytic isoenzyme hexokinase PII (HXK2), which is responsible for triggering glucose repression, has been determined. The reading frame was identified by comparison with the N-terminal undecameric amino acid (aa) sequence, determined previously [Schmidt and Colowick, Arch. Biochem. Biophys. 158 (1973) 458-470]. The codon sequence was not random, with 82.1% of the aa specified by only 25 codons. The structural gene sequence corresponded to 1455 bp, coding for 485 aa residues, corresponding to the Mr of 53 800 for the HXK2 monomer. Five initiation regions spanning 162 bp and three termination sites spanning 29 bp were detected. Sequences with similarities to a 5'-TATAAA-3' sequence were located 24-39 bp upstream of each initiation region. The most pronounced initiation region corresponded to the 5'-TATAAA-3' sequence at position -152. Two of the minor initiation sites were inside the coding sequence in front of two ATG codons.     

Autophosphorylation of yeast hexokinase PII

Autophosphorylation of hexokinase PII was studied using an enzyme purified from Saccharomyces cerevisiae. Incubation of this enzyme preparation with [gamma-32P]ATP and Mn2+ or Mg2+ gave a phosphoprotein of molecular mass 58,000 which corresponded to hexokinase PII. D-Xylose stimulated autophosphorylation of hexokinase PII. Dilution of hexokinase PII over a 10-fold concentration range did not change the specific activity of hexokinase PII autophosphorylation suggesting that it may occur by an intramolecular mechanism.     

Crystal structure of yeast hexokinase PI in complex with glucose: A classical "induced fit" example revised

Hexokinase is the first enzyme in the glycolytic pathway that catalyzes the transfer of a phosphoryl group from ATP to glucose to form glucose-6-phosphate and ADP. Two yeast hexokinase isozymes are known, namely PI and PII. Here we redetermined the crystal structure of yeast hexokinase PI from Saccharomyces cerevisiae as a complex with its substrate, glucose, and refined it at 2.95 A resolution. Comparison of the holo-PI yeast hexokinase and apo-hexokinase structures shows in detail the rigid body domain closure and specific loop movements as glucose binds and sheds more light on structural basis of the "induced fit" mechanism of reaction in the HK enzymatic action. We also performed statistical coupling analysis of the hexokinase family, which reveals two co-evolved continuous clusters of amino acid residues and shows that the evolutionary coupled amino acid residues are mostly confined to the active site and the hinge region, further supporting the importance of these parts of the protein for the enzymatic catalysis.     

The kinetics of reduction of yeast complex III by a substrate analog

The kinetics of reduction of the cytochrome and quinone constituents of yeast complex III by the substrate homolog Q1H2 have been measured under a variety of conditions. The maximum rates of reduction of cytochromes b and c1 and of the endogenous Q6 by Q1H2 were sufficiently fast to support the Vmax for the reduction of cytochrome c by this substrate. The absorbance at 562 nm showed an initial increase which was subsequently followed by a decrease. This decrease was synchronous with the appearance of reduced cytochrome c1 and is interpreted as reflecting the absorbance contribution of c1 at 562 nm under conditions where the steady state level of the b cytochromes is constant. Prereduction of c1 and the Fe/S cluster did not affect the initial very rapid reduction of b, but the second phase was eliminated. Antimycin abolished the very rapid rate of reduction of cytochrome b in untreated complex III and completely inhibited the reduction of cytochrome b in complex III in which c1 and the Fe/S cluster had been prereduced. However, the reduction of the endogenous quinone was essentially unaffected by these treatments. Antimycin had no effect on the reduction of c1. Funiculosin also suppressed the very rapid reduction of b while both myxothiazol and 5-n-undecyl-6-hydroxy-4,7-dioxobenzothiazole did not modify this phase of the reaction; no secondary decrease in absorbance was observed in the presence of any of these inhibitors. Most of the observed kinetic changes could be reproduced by simulation of the Q-cycle; simple linear and branched schemes were unable to reproduce the data.     

The substrate specificity of yeast hexokinase: reaction with D-arabinose oxime

By chromatography, electrophoresis, n.m.r. spectroscopy, and spectrophotometric assay, it has been shown that D-arabinose oxime acts as a weak substrate for yeast hexokinase. The enzyme-catalysed phosphorylation of the oxime, which exists as a mixture of E (80%) and Z (20%) acyclic forms in solution at equilibrium, is proposed to proceed via the transient formation of a furanoid species. Weak substrate-activity was also observed with 4-deoxy-D-xylo-hexose, but not with 5-deoxy-D-xylo-hexose. The relation of these and previous results concerning the carbohydrate-substrate specificity of yeast hexokinase in solution to X-ray crystallographic studies is discussed.