An evolutionary non-conserved motif in Helicobacter pylori arginase mediates positioning of the loop containing the catalytic residue for catalysis

Abstract

The binuclear metalloenzyme Helicobacter pylori arginase is important for pathogenesis of the bacterium in the human stomach. Despite conservation of the catalytic residues, this single Trp enzyme has an insertion sequence (--153ESEEKAWQKLCSL165--) that is extremely crucial to function. This sequence contains the critical residues, which are conserved in the homologue of other Helicobacter gastric pathogens. However, the underlying basis for the role of this motif in catalytic function is not completely understood. Here, we used biochemical, biophysical and molecular dynamics simulations studies to determine that Glu155 of this stretch interacts with both Lys57 and Ser152. These interactions are essential for positioning of the motif through Trp159, which is located near Glu155 (His122-Trp159-Tyr125 contact is essential to tertiary structural integrity). The individual or double mutation of Lys57 and Ser152 to Ala considerably reduces catalytic activity with Lys57 to Ala being more significant, indicating they are crucial to function. Our data suggest that the Lys57-Glu155-Ser152 interaction influences the positioning of the loop containing the catalytic His133 so that this His can participate in catalysis, thereby providing a mechanistic understanding into the role of this motif in catalytic function. Lys57 was also found only in the arginases of other Helicobacter gastric pathogens. Based on the non-conserved motif, we found a new molecule, which specifically inhibits this enzyme. Thus, the present study not only provides a molecular basis into the role of this motif in function, but also offers an opportunity for the design of inhibitors with greater efficacy.

Illuminating the structure–function landscape of an evolutionary nonconserved motif in the arginases of Helicobacter gastric pathogens

“…It may be noted that these mutations did not impact the bimetallic centre as well as the substrate binding. 66 These observations indicate that this network of interactions is crucial to catalysis.…”

“…30 A number of studies reported later verified the importance of the motif residues in structure and function. 60,65,66…”

“…24,62,64 A notable difference was also observed in the H. pylori enzyme, where a 13-residue long nonconserved motif ( 153 ESEEKAWQKLCSL 165 ) was present in the middle of the protein sequence (Figure 2). 5,30,60,65,66 This review delivers a structural basis into the role of the nonconserved motif of this enzyme in function and the knowledge gained could be utilised to design small molecule inhibitors specific to the arginases of H. pylori and other Helicobacter gastric pathogens.…”

Differential role of Pax6 and its interaction with Shh–Gli1–IDH2 axis in regulation of glioma growth and chemoresistance

“…[ 55 ] Auto dock 4.2 software was used for MD with these protein receptors and protein complexes using the Lamarckian genetic algorithm. [ 56 ] During MD, the proteins were fixed, and TMZ was allowed to move in the conformational space. The population size, number of energy evaluations, and number of Lamarckian genetic algorithm runs were 750, 2,500,000, and 50 respectively.…”

“…[55] Auto dock 4.2 software was used for MD with these protein receptors and protein complexes using the Lamarckian genetic algorithm. [56] During MD, the proteins were fixed, and TMZ was allowed to move in the conformational space.…”