Cyclic AMP and cyclic GMP (cAMP and cGMP) are important second messengers in key signal-transduction pathways that mediate various physiological functions in bacteria and eukaryotes. Adenylyl Cyclases (ACs) and Guanylyl Cyclases (GCs) cyclize ATP and GTP to produce cAMP and cGMP, respectively. Though most nucleotide cyclises show exquisite specificity for their substrates, there are instances where ACs were observed to have low GC activity as well, and vice versa. To understand structural basis of substrate (ATP or GTP) recognition, discrimination and binding by an adenylyl cyclase, we have taken up Ma1120, an AC from Mycobacterium avium, for our studies. Work presented in the thesis includes crystal structures of Ma1120 in the presence of substrate (ATP or GTP), by-product pyrophosphate and ATP analogue 2′,5′-dideoxyd-3′-adenosine triphosphate (2′,5′-dd-3′-ATP). A triple mutant of Ma1120 (K101→E, D157→G, A167→Y) was generated to increase specificity of Ma1120 towards GTP by mutation in the substrate specifying residues, but the enzyme showed equal specificity for ATP as well as for GTP. Ma1120 exists as a monomer in solution and crystallized as a monomer in the absence of substrate or inhibitor. The substrate specifying lysine residue plays a dual role of interacting with the substrate and stabilizing the dimer. The dimerization loop region harbouring the second substrate specifying residue, an aspartate, shows significant differences in conformation and position between the monomeric and dimeric structures. Thus, this study has not only revealed that significant structural transitions are required for the interconversion of the inactive and the active forms of the enzyme, but also provided precise nature of these transitions. ATP bound to Ma-Cat has two different conformations, one with C2′-endo and the other with C3′-endo puckering for the ribose. C3′-endo conformation is favourable for catalysis as it brings 3′-OH group of ribose and free oxygen of α-phosphate closer to each other. The crystal structure of GTP bound to Ma-Cat showed a novel mode of GTP binding to AC. This is the first report of GTP bound to AC. ATP bound to Ma-Cat-KDA→EGY forms non-cognate substrate complex and ATP is stabilized by stacking of adenines over each other with Tyr167 flanking on both sides of adenines. Ma-Cat-KDA→EGY+GTP complex is the first report of GTP bound to a guanylyl cyclase. GTP is bound in reverse orientation when compared to ATP bound to AC. Reverse orientation of GTP is attained to stabilize the guanine in highly electronegative guanine binding pocket. Also, O3' of GTP is placed in opposite orientation as compared to ATP bound to Ma-Cat. Therefore, during cyclization reaction guanine and ribose changes their orientation to bring O3' atom of ribose closer to α-phosphate, after cleavage of the bond between α- and β-phosphates. Thus, this study has revealed novel modes of binding of ATP and GTP to catalytic domains of Ma1120 and its triple mutant, mechanism of substrate discrimination and residual activity for the non-cognate substrate.