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Figure 1 | BMC Bioinformatics

Figure 1

From: Cyclic nucleotide binding proteins in the Arabidopsis thaliana and Oryza sativa genomes

Figure 1

Analysis of plant CNB domains. (A) Arabidopsis CNB domains (CNTE1, KAT1 and CNGC2) were aligned against several well studied CNB domains including regulatory subunits of PKA (RIα and RIIβ), Epac1, Epac2, and cyclic GMP dependent kinase 2 (CGK2) from humans, HCN2 from mouse and E. coli CAP. Highlighted on the alignment are glycine residues involved in loop structures (dark grey arrows), residues forming the hydrophobic pocket for cNMP binding (green arrows) and residues proposed to contact the phosphate of the cNMP (blue arrows). The highly conserved helix capping acidic residue is shown in red. Secondary structure is denoted by arrows above the alignment, with light blue for alpha helices and pink for beta sheets and is based on the secondary structure of HCN2. (B) A homology model of atCNTE1 was generated from the known structures of CNB domains. Key residues are shown as stick representations and are colored and labeled according to the color scheme described in (A). The cGMP ligand is shown in magenta and is based on the structure of cGMP bound to HCN2 [pdb: 1Q3E] superimposed over our model. Figure was generated with Molscript [83] and Raster3D [84].

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