Arginase is a bimetallic enzyme that utilizes mainly Mn 2+ or Co 2+ for catalytic function. In human homolog, the substitution of Mn 2+ with Co 2+ significantly reduces the K m value without affecting the k cat . However, in the Helicobacter pylori counterpart (important for pathogenesis), the k cat increases nearly 4-fold with Co 2+ ions both in the recombinant holoenzyme and arginase isolated from H. pylori grown with Co 2+ or Mn 2+ . This suggests that the active site of arginase in the two homologs is modulated differently by these two metal ions. To investigate the underlying mechanism for metal-induced difference in catalytic activity in the H. pylori enzyme, we used biochemical, biophysical and microsecond molecular dynamics simulations studies. The study shows that the difference in binding affinity of Co 2+ and Mn 2+ ions with the protein is linked to a different positioning of a loop (– 122 HTAYDSDSKHI H G 134 –) that contains a conserved catalytic His133. Consequently, the proximity of His133 and conserved Glu281 is varied. We found that the Glu281–His133 interaction is crucial for catalytic function and was previously unexplored in other homologs. We suggest that the proximity difference between these two residues in the Co 2+ - and Mn 2+ -proteins alters the proportion of protonated His133 via variation in its p K a . This affects the efficiency of proton transfer — an essential step of l -arginine hydrolysis reaction catalyzed by arginase and thus activity. Unlike in human arginase, the flexibility of the above segment observed in H. pylori homolog suggests that this region in the H. pylori enzyme may be explored to design its specific inhibitors.