MAP/Microtubule affinity-regulating kinase 4 (MARK4) is a member of adenosine monophosphate-activated protein kinases, directly associated with cancer and neurodegenrative diseases. Here, we have cloned, expressed and purified two variants of MARK4 [the kinase domain (MARK4-F2), and kinase domain alongwith 59 N-terminal residues (MARK4-F1)] and compared their stability at varying pH range. Structural and functional changes were observed by incubating both forms of MARK4 in buffers of different pH. We measured the secondary structure of MARK4 using circular diachroism and tertiary structure by measuring intrinsic fluorescence and absorbance properties alongwith the size of proteins by dynamic light scattering. We observed that at extremes of pH (below pH 3.5 and above pH 9.0), MARK4 is quite stable. However, a remarkable aggregate formation was observed at intermediate pH (between pH 3.5 and 9.0). To further validate this results, we have modelled both forms of MARK4 and performed molecular dymanics simulation for 15 ns. The spectroscopic observations are in excellent agreement with the findings of molecular dymanics simulation. We also performed ATPase activity at varying pH and found a signifcant correlation of structure of MARK4 with its enzyme activity. It is interesting to note that both forms of MARK4 is showing a similar pattern of structure changes with reference to pH.