C-di-GMP specific phosphodiesterases

From Proteopedia

YkuI YukI is a dimer with each protomer composed of an EAL domain (with TIM barrel fold), a long helical linker, and a PAS-like domain. The active site is situated at the C-terminal end of the central β-barrel of the EAL domain. The residues of the active site (here shown with labels) are well conserved, including E33 and L35 of the EAL signature motif. The c-di-GMP substrate is bound flat upon the actve site with the divalent metal (here Ca++) being sandwiched between binding site and C-di-GMP. BlrP1 BlrP1 (3gg0) BlrP1 BLUF domain EAL domain Active site global view Active site with labels Active site + ligand + Mn Active site + ligand + Mn + HOH Additional Resources See also C-di-GMP signaling

spinqualitylabelsall models C-di-GMP specific phosphodiesterase complex with guanosine-5-monophosphate (stick model) and Ca+2 ions (green) (PDB code 2w27) Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image

3D structure of C-di-GMP phosphodiesterase

Phosphodiesterase

References

YkuI structure 2w27:

• Minasov G, Padavattan S, Shuvalova L, Brunzelle JS, Miller DJ, Basle A, Massa C, Collart FR, Schirmer T, Anderson WF. Crystal structures of YkuI and its complex with second messenger cyclic Di-GMP suggest catalytic mechanism of phosphodiester bond cleavage by EAL domains. J Biol Chem. 2009 May 8;284(19):13174-84. Epub 2009 Feb 24. PMID:19244251 doi:10.1074/jbc.M808221200

BlrP1 structure 3gg0:

• Barends TR, Hartmann E, Griese JJ, Beitlich T, Kirienko NV, Ryjenkov DA, Reinstein J, Shoeman RL, Gomelsky M, Schlichting I. Structure and mechanism of a bacterial light-regulated cyclic nucleotide phosphodiesterase. Nature. 2009 Jun 18;459(7249):1015-8. PMID:19536266 doi:10.1038/nature07966