Heterodimeric deoxyguanosine kinase/deoxyadenosine kinase of Lactobacillus acidophilus R-26: heterotropic activation of deoxyadenosine kinase subunit implicated by limited proteolysis and affinity labeling

Mutations within the Putative Active Site of Heterodimeric Deoxyguanosine Kinase Block the Allosteric Activation of the Deoxyadenosine Kinase Subunit

Replacement of the Asp-84 residue of the deoxyguanosine kinase subunit of the tandem deoxyadenosine kinase/ deoxyguanosine kinase (dAK/dGK) from Lactobacillus acidophilus R-26 by Ala, Asn, or Glu produced increased Km values for deoxyguanosine on dGK. However, it did not seem to affect the binding of Mg-ATP. The Asp-84 dGK replacements had no apparent effect on the binding of deoxyadenosine by dAK. However, the mutant dGKs were no longer inhibited by dGTP, normally a potent distal endproduct inhibitor of dGK. Moreover, the allosteric activation of dAK activity by dGTP or dGuo was lost in the modified heterodimeric dAK/dGK enzyme. Therefore, it seems very likely that Asp-84 participates in dGuo binding at the active site of the dGK subunit of dAK/dGK from Lactobacillus acidophilus R-26.

Functional assignment by Chimera construction of the domain affecting heterotropic activation of deoxyadenosine kinase from Lactobacillus acidophilus R-26

The heterodimeric subunits of deoxyadenosine kinase (dAK)-deoxyguanosine kinase (dGK) from Lactobacillus acidophilus R-26 exhibit contrasting conformations manifested in the nearly unidirectional heterotropic activation of dAK when dGK binds deoxyguanosine. This is mediated, in part, by the conserved Ras switch I-like sequence (residues 153-161) [Guo et al. (1997) J. Biol. Chem. 272, 6890-6897]. In an attempt to identify domains differentiating the specificities of dAK and dGK, we constructed several chimeras splicing heterodimeric dAK within this region. In Chimera-III, dAK residues 120-170 were replaced by the homologous section of dGK. dAK activity was elevated 40%, but although it retained its original specificity and Km values, it could no longer be activated by deoxyguanosine. Moreover, both the activated dAK and the "dAK" of Chimera-III exhibited (i) an increased Ks for the leading substrate ATP-Mg2+, suggesting the formation of intermediate enzyme species along their respective kinetic pathways, and (ii) broadened and lower pH optima for the dAK activities. These observations further indicate the importance of dAK residues 120-170, including the Ras-like segment, in catalysis and heterotropic activation. The other conformational properties of dAK (e.g. self-inactivity and MgATP being the leading substrate) were unaltered by this substitution, thus localizing the responsible domains even further upstream.

Life on the salvage path: the deoxynucleoside kinase of Lactobacillus acidophilus R-26

In Lactobacillus acidophilus R-26, the synthesis of DNA precursor deoxynucleotides occurs exclusively by salvage of deoxynucleosides, beginning with phosphorylation by four deoxynucleoside kinases. Subunits bearing three of these activities are uniquely organized into two heterodimers, deoxyadenosine/deoxycytidine kinase (dAK/dCK) and deoxyadenosine/deoxyguanosine kinase (dAK/dGK), which, along with a distinct deoxythymidine kinase (TK), catalyze the parallel first committed steps of dNTP biosynthesis. Whereas TK is common to most prokaryotes (and eukaryotes), the other three activities that are the emphasis of this review are quite unusual in bacteria. Each activity is regulated in cis by its homologous end-product (dNTP) which is understood to act as a multisubstrate inhibitor capable of binding to both nucleoside and phosphate subsites. Conversely, the inactive dAK subunit is progressively activated by 1) association with a dGK or dCK subunit and 2) the conformationally driven heterotropic affect of dGuo or dCyd bound to the opposing subunit. Limited proteolysis has proven to be a powerful probe of conformational states. Further indication of conformational or structural differences between dAK and dGK (or dCK) is that the former follows an ordered kinetic path, while dGK or dCK exhibits rapid-equilibrium random kinetics. The multi-substrate behavior of end-product binding provides a convenient new diagnostic tool for distinguishing kinetic mechanisms. Tandem dak-dgk genes have been cloned from Lactobacillus DNA and expressed in Escherichia coli as dAK/dGK, utilizing the associated promoter. Sequence alignments reveal 65% identity in their DNA and 61% in their derived amino acid sequences. Encoded N-terminal sequences are identical for the first 18 residues, and both subunits share conserved sequences in common with adenylate kinase and viral TK. A more unusual conserved element, which appears to play a role in the activation of dAK, resembles the G2 loop of p21 ras. Remarkably, no homologous gene(s) for the dAK/dCK pair could be found. Comparisons of amino acid sequences, isoelectric pHs and subunit masses strongly indicated that native dCK and dGK are identical in sequence, except at their extreme N-termini (M-IVL for dCK and -TVIVL for dGK), suggesting that processing of a common precursor occurs in Lactobacillus. Accordingly, deletion of codons 2 and 3 from dgk resulted in the expression of dAK/dCK in the E. coli host; its kinetic properties are indistinguishable from those of native dAK/dCK. Subcloning the dgk or engineered dck gene resulted in expression of active dGK or dCK homodimers, each with a virtually unchanged Km toward its primary deoxynucleoside. However, in common with human dCK, dCK (or dGK) homodimer exhibits secondary activities with much larger Kms towards dAdo and dGuo (or dCyd). dCTP (or dGTP) is the best inhibitor of all three activities of the respective homodimer. Fully active heterodimers can be reconstituted simply by mixing a homodimer with independently expressed (inactive) dAK.

Characterization of guanosine kinase from Brevibacterium acetylicum ATCC 953

Guanosine kinase (GKase) activity was identified in a cell-free extract of Brevibacterium acetylicum ATCC 953. We have purified the enzyme 4000-fold from the cell-free extract to apparent homogeneity. Molecular weight of 71,300 and 36,300 determined by gel filtration and sodium dodecyl sulfate gel electrophoresis, respectively, revealed that the enzyme is a dimer molecule. Maximum activity of the GKase was attained when the magnesium/ATP concentration ratio was close to 1. The GKase activity was dependent on the presence of a divalent cation. The Km values for guanosine, inosine, and 2'-deoxyguanosine as phosphate acceptors were determined to be 0.022, 0.87, and 2.83 mM, respectively. In addition to ATP and dATP, GTP and dGTP were shown to be effective phosphate donors for the GKase. The optimal pH seemed to be around pH 8.3, although relatively high activity was observed in the alkaline pH range of 7.5-9.8. The addition of 0.1 mM pyrimidine nucleotides, especially CMP and CTP, activated the GKase activity. On the other hand, the addition of 1 mM AMP, ADP, and GMP inhibited the GKase activity. It is thus likely that the GKase activity might be regulated in vivo by nucleotide concentrations and may control the nucleoside monophosphate level by efficiently recycling guanosine.

cis-Active Ras G2-like sequence implicated in the heterotropic activation of the deoxyadenosine kinase of Lactobacillus acidophilus R-26

Deoxyadenosine kinase (dAK) forms a heterodimer with either deoxyguanosine kinase (dGK) or deoxycytidine kinase (dCK), and is heterotropically activated 3-5 times by dGuo or dCyd. Expressed alone, dAK is inactive and exhibits no response to dGuo or dCyd; activity and heterotropic response are fully restored upon reassociation with dGK or dCK. However, turnover of independently expressed dGK or dCK is nearly maximal, being further activated only 50-100% upon reassociation with dAK. In neither case is the heterotropic activation due to ligand-induced heterodimer formation. A proline/alanine substitution within a dAK segment homologous to loop G2 of Ras proteins yielded a heterodimer with dAK permanently cis-activated 2-fold, with a corresponding reduction in heterotropic activation by dGuo. A chimeric dAK, with 25% of its C terminus substituted by the homologous sequence from dGK, was inactive alone, and its characteristics were unchanged in the reconstituted heterodimer. Superimposing the Pro/Ala substitution on this chimera also reduced heterotropic activation by half. Cross-linking the dimer by 1,5-difluoro-2,4-dinitrobenzene was inhibited by ATP, dATP, dGTP, and dAdo, suggesting the proximity of the active site(s) to the interface. These data suggest that dAK depends on dGK or dCK in a manner resembling the reliance of Ras upon GTPase activating protein.

Deoxycytidine kinase and deoxyguanosine kinase of Lactobacillus acidophilus R-26 are colinear products of a single gene

Three of the four deoxynucleoside kinases required for growth of Lactobacillus acidophilus R-26 exist as heterodimeric pairs specific for deoxyadenosine (dAK) and deoxycytidine (dCK) or dAK and deoxyguanosine (dGK). However, only two tandem genes, dak/dgk, are found, and are expressed only as dAK/dGK in transformed Escherichia coli. Sequencing peptides spanning 63% of the native dCK subunit revealed a sequence identical to that deduced from dgk (beginning MTVIVL...), except that dCK lacks residues 2 and 3 (dCK is M..IVL; dGK is .TVIVL). Also, mass spectrometry indicates that native dCK and dGK subunits are identical in mass adjusted for the first three residues. Furthermore, the native enzymes have identical isoelectric pH values, indicating an equal number of charged residues. To enable E. coli to express peptide having the native dCK sequence, codons 2 and 3 were deleted from the dgk portion of the tandem genes, resulting in expression of protein having the specificities and regulatory properties of native dAK/dCK, including heterotropic stimulation of dAK activity by deoxycytidine or dCTP (not deoxyguanosine or dGTP) and end-product inhibition of the respective activities by dATP and dCTP. Subcloning normal and mutant dgk yielded homodimeric dGK and dCK, respectively. The dCK homodimer strongly resembles human dCK, with a low K(m) for deoxycytidine, the ability to phosphorylate deoxyadenosine and deoxyguanosine at much higher K(m) values, and end-product inhibition by dCTP. Thus two distinct and specific enzymes evidently are derived from a single Lactobacillus gene. The mechanism by which this occurs in vivo has yet to be elucidated.