Structural Analysis of the Bacterial HPr Kinase/Phosphorylase V267F Mutant Gives Insights into the Allosteric Regulation Mechanism of This Bifunctional Enzyme

Abstract

The HPr kinase/phosphorylase (HPrK/P) is a bifunctional enzyme that controls the phosphorylation state of the phosphocarrier protein HPr, which regulates the utilization of carbon sources in Gram-positive bacteria. It uses ATP or pyrophosphate for the phosphorylation of serine 46 of HPr and inorganic phosphate for the dephosphorylation of Ser(P)-46-HPr via a phosphorolysis reaction. HPrK/P is a hexameric protein kinase of a new type with a catalytic core belonging to the family of nucleotide-binding protein with Walker A motif. It exhibits no structural similarity to eukaryotic protein kinases. So far, HPrK/P structures have shown the enzyme in its phosphorylase conformation. They permitted a detailed characterization of the phosphorolysis mechanism. In the absence of a structure with bound nucleotide, we used the V267F mutant enzyme to assess the kinase conformation. Indeed, the V267F replacement was found to cause an almost entire loss of the phosphorylase activity of Lactobacillus casei HPrK/P. In contrast, the kinase activity remained conserved. To elucidate the structural alterations leading to this drastic change of activity, the x-ray structure of the catalytic domain of L. casei HPrK/P-V267F was determined at 2.6 Å resolution. A comparison with the structure of the wild type enzyme showed that the mutation induces conformation changes compatible with the switch from phosphorylase to kinase function. Together with nucleotide binding fluorescence measurements, these results allowed us to decipher the cooperative behavior of the protein and to gain new insights into the allosteric regulation mechanism of HPrK/P.In Gram-positive bacteria, HPr kinase/phosphorylase (HPrK/P) 6 is the central regulator of carbon catabolite repression, the paradigm of signal transduction (1). In response to certain metabolites that change their concentration in the presence of rapidly metabolizable carbon sources, HPrK/P either phosphorylates or dephosphorylates Ser-46 of the histidine-containing protein HPr. In Gram-positive bacteria, Ser(P)-46-HPr functions as co-repressor for carbon catabolite repression by interacting with the transcriptional regulator CcpA (catabolite control protein A) that regulates the expression of many genes (2, 3) (for a review, see Ref. 4). In the Gram-negative Neisseria meningitidis devoid of CcpA-mediated carbon catabolite repression, Ser(P)-46-HPr is involved in the cell adhesion process (5), suggesting that HPrK/P might constitute a potential target for new antimicrobial agents in pathogenic bacteria. Finally, the formation of Ser(P)-46-HPr inhibits PrfA, a transcription activator of several virulence genes in Listeria monocytogenes (6).HPrK/P was first identified as a serine protein kinase, and this activity is enhanced in the presence of glycolytic intermediates such as fructose-1, 6-bisphosphate (FBP) and inhibited in the presence of inorganic phosphate (P i ) (7). Dephosphorylation of Ser(P)-46-HPr by HPrK/P was assumed to be hydrolytic. However, P i was also reported to stimulate the HPrK/P-c...

HPrK Regulates Succinate-Mediated Catabolite Repression in the Gram-Negative SymbiontSinorhizobium meliloti

“…In addition, S. meliloti appears to lack the regulator CcpA. Interestingly, an artificially truncated HPrK from Lactobacillus casei, which contained the same regions as the shorter S. meliloti HPrK, exhibited wild-type kinase and phosphatase activities toward HPr (9,18). This suggests that the S. meliloti HPrK may also have kinase and phosphatase activities toward HPr.…”

Transcriptional Activator YesS Is Stimulated by Histidine-phosphorylated HPr of the Bacillus subtilis Phosphotransferase System

“…The effects of the ATP- and PEP-dependent HPr kinases HprK/P and EI, respectively, on the protein interactions of their natural substrate HPr were investigated using the yeast tri-hybrid approach (see “Experimental Procedures”). Because HprK/P is a bifunctional enzyme that catalyzes phosphorylation and dephosphorylation of Ser(P)-HPr (3), we included in one set of our assays the B. subtilis HprK/P and in another the L. casei ΔHprK/PV267F mutant protein, which exhibits normal HPr kinase but drastically reduced Ser(P)-HPr phosphorylase activity (17). Phosphorylation-dependent interactions were revealed when the interaction phenotype appeared in response to the presence of a kinase, whereas binary interactions were detected independently of the presence of a third protein.…”

“…The ptsH S46A, ptsH H15A, and crh S46A mutant alleles were PCR-amplified from genomic DNA of the B. subtilis strains RHGR64 (16), GR11, 4 and QB7112 (7), respectively. The Δ hprK V267F mutant gene from Lactobacillus casei was PCR-amplified from pΔHPRKLCV267F (17). The various PCR products were cloned into the bait vector pGBDU (URA3), the prey vector pGAD (LEU2) (18), as well as in the p3H vector (TRP1) for tri-hybrid assays (19).…”

“…coli strain NM522 carrying plasmid pAG2, pAG3, and pQE30-ΔHprK/PV267F, respectively, as described previously (7, 17). …”

Effects of non‐catalytic, distal amino acid residues on activity of E. coli DinB (DNA polymerase IV)

“…Distal residues can have a variety of effects on the structure [Chalissery et al, 2007;Chaptal et al, 2007], substrate binding affinity [Heitman et al, 2006;Carpten et al, 2007;Chalissery et al, 2007;Mirza et al, 2007], stability [Hong et al, 2007], and function [El Omari et al, 2006;Dupre et al, 2007;Klyuyeva et al, 2008] of a wide variety of different enzymes [Lee et al, 2011]. The semantics of defining the ''shell'' to which a specific amino acid residue belongs can be challenging, in particular in enzymes with large substrates, such as DNA polymerases.…”