Comparison of the sequence and structure of PdeM with Rv0805.

(A) Pairwise sequence alignment between the full length cyclic AMP phosphodiesterase Rv0805 of M. tuberculosis (PDB ID: 3IB7) and PdeM. The annotation of secondary structure is displayed at the top. Identical residues in the alignment are shaded in blue. Regions which are missing in PdeM are shaded in green. All motifs with conserved residues coordinating the metal ions are marked in square bracket (red outline). Residues interacting with the AMP, cAMP and bis(pNPP) are marked in square bracket (black outline). (B) Superimposition of the homology model structure of PdeM (colored as blue) and template Rv0508 structure (colored as pink), and stereoview of the superimposition of active site residues in the homology model of PdeM (colored as blue) and the template structure of Rv0805 (PDB ID: 3IB8; colored as pink). Bound metals/ions are represented as a sphere model. Residues within 5Å interaction zone of metals are shown as sticks. Residues interacting with AMP (3IB8_A), cAMP and bis(pNPP) are enclosed in broken line square bracket. Regions of Rv0805 corresponding to the missing regions in PdeM are shown in green color. Structure visualization and analysis was performed using Chimera tool.