The active site of pyrophosphate-dependent phosphofructo-1-kinase based on site-directed mutagenesis and molecular modeling

Rampant horizontal gene transfer and phospho-donor change in the evolution of the phosphofructokinase

Previous work on the evolution of the phosphofructokinase (PFK) has shown that this key regulatory enzyme of glycolysis has undergone an intricate evolutionary history. Here, we have used a comprehensive data set to address the taxonomic distribution of the different types of PFK (ATP-dependent and PPi-dependent ones) and to estimate the frequency of horizontal gene transfer (HGT) events. Numerous HGT events appear to have occurred. In addition, we focused on the analysis of sites 104 and 124 (usually Gly(104)+Gly(124) or Asp(104)+Lys(124)), known to be involved in catalysis (J. Biol. Chem. 275 (2000) 35677). It revealed the existence of numerous sequences from distantly related species carrying atypical combinations of amino acids. Several adaptive changes of phospho-donors, probably requiring a single mutation at position 104, have likely occurred independently in many lineages. The analysis of this gene suggests the existence of a high rate of both HGT and substitution in its active sites. These rampant HGT events and flexibility in phospho-donor use illustrate the importance of tinkering in molecular evolution.

The primordial high energy compound: ATP or inorganic pyrophosphate?

The pyrophosphate-dependent phosphofructokinase (PP(i)-PFK) of Entamoeba histolytica displays a million fold preference for inorganic pyrophosphate (PP(i)) over ATP (calculated as the ratio of k(cat)/K(m)). The introduction of a single mutation by site-directed mutagenesis changes its preference from PP(i) to ATP. The single mutant has an 8-fold preference for ATP whereas a related double mutant shows a preference exceeding 10,000-fold. The results suggest the presence of a latent nucleotide binding site aligned for a catalytic role in PP(i)-PFK. It is proposed that the ancestral PFK was an ATP-dependent enzyme and that PP(i)-PFKs are a later evolving adaptation.

Site-directed mutagenesis of the fructose 6-phosphate binding site of the pyrophosphate-dependent phosphofructokinase of Entamoeba histolytica

Attempts to define the active site of pyrophosphate-dependent phosphofructokinase (PPi-PFK) using homology modeling based on the three-dimensional structure of the ATP-dependent PFKs from bacteria have been frustrated by low sequence identity between PPi- and ATP-PFKs in their carboxyl terminal halves. In the current study, alanine scanning mutagenesis of residues in the carboxyl terminal half of the PPi-PFK of Entamoeba histolytica coupled with comparative sequence analysis and computational modeling is used to identify residues that contribute to fructose 6-phosphate (fructose 6-P) binding. Of seven alanine mutants that were generated by site-directed mutagenesis, Arg377, Ser392, Arg405, Lys408, His415, His416, and Arg423, only the last mutant, Arg423Ala, was found to have dramatically lower affinity for fructose 6-P. Mutation of Arg 423 decreased k(cat) by 10,000-fold and decreased apparent affinity for fructose 6-P by 126-fold, while the K(m) for PPi increased only 4-fold. The second greatest effect was seen with Arg377Ala, which had a nearly 10-fold decrease in apparent affinity and an approximate 60-fold decrease in maximal activity. Another residue, Tyr420, was chosen for mutagenesis by its complete identity in all other PPi-PFK. This residue and its homologue in Escherichia coli ATP-PFK, His249, were mutated and shown to be very important for substrate binding in both enzymes.

Expression, characterization, and crystallization of the pyrophosphate-dependent phosphofructo-1-kinase of Borrelia burgdorferi

The two genes for the putative pyrophosphate-dependent phosphofructokinases (PPi-PFKs) of Borrelia burgdorferi were cloned by PCR and expressed in Escherichia coli, and their protein products were purified to near homogeneity. The larger of the two gene products, a 62-kDa protein, is an active PPi-PFK and exists in solution as a dimer. It has apparent K(m) values for fructose 6-P and PPi of 109 and 15 microM, respectively, and a pH optimum of 6.4 to 7.2. The 62-kDa protein was crystallized and subjected to preliminary diffraction analysis. The smaller gene product, a 48-kDa protein, exists in solution as a higher polymer and shows no ATP- or PPi-dependent activity, despite having a secondary structure as estimated by circular dichroism that is not significantly different from that of other PFKs.

Identification of residues of Escherichia coli phosphofructokinase that contribute to nucleotide binding and specificity

The apparent affinity of phosphofructo-1-kinase (PFK) of Escherichia coli for ATP is at least 10 times higher than for other nucleotides. Mutagenesis was directed toward five residues that may interact with ATP: Y41, F76, R77, R82, and R111. Alanine at position 41 or 76 increased the apparent Km by 49- and 62-fold, respectively. Position 41 requires the presence of a large hydrophobic residue and is not restricted to aromatic rings. Tryptophan and, to a lesser extent, phenylalanine could substitute at position 76. None of the mutants at 41 or 76 showed a change in the preference for alternative purines, although F76W used CTP 3 times better than the wild type enzyme. Mutations of R77 suggested that the interaction was hydrophobic with no influence on nucleotide preference. Mutation of R82 to alanine or glutamic acid increased the apparent Km for ATP by more than 20-fold and lowered the kcat/Km with ATP more than 30-fold. However, these mutants had a higher kcat/Km than wild type for both GTP and CTP, reflecting a loss of substrate preference. A loss in preference is seen as well with R111A where the kcat/Km for ATP decreases by only 68%, but the kcat/Km with GTP increases more than 10-fold. Activities with ITP, CTP, and UTP are also higher than with the wild type enzyme. Arginine residues at positions 82 and 111 are important dictators of nucleoside triphosphate preference.

An essential methionine residue involved in substrate binding by phosphofructokinases

An alignment of all PPi-dependent phosphofructokinases and all allosteric ATP-dependent PFKs shows relatively few residues that are fully conserved. One residue that is conserved is a methionine residue that appears from the crystal structure of Escherichia coli PFK to be interacting with fructose 6-P. Very conservative substitutions for this methionine with leucine or isoleucine by site-directed mutagenesis of E. coli ATP-PFK and Entamoeba histolytica PPi-PFK produced profound decreases either in the apparent affinity for fructose 6-P or in maximal velocity, or both. Methionine provides a highly specific interaction with fructose 6-P for binding and for transition state stabilization.