5O25

Structure of wildtype T.maritima PDE (TM1595) in ligand-free state

Summary for 5O25

• Entry DOI: 10.2210/pdb5o25/pdb
• Related: 5O1U 5O4Z 5O58 5O70 5O7F
• Descriptor: TmPDE, MANGANESE (II) ION, TETRAETHYLENE GLYCOL, ... (6 entities in total)
• Functional Keywords: phosphodiesterase, hydrolase
• Biological source: Thermotoga maritima
• Total number of polymer chains: 2
• Total formula weight: 77261.13

Authors

Witte, G.,Drexler, D.,Mueller, M. (deposition date: 2017-05-19, release date: 2017-10-25, Last modification date: 2024-01-17)

Primary citation

Drexler, D.J.,Muller, M.,Rojas-Cordova, C.A.,Bandera, A.M.,Witte, G.
Structural and Biophysical Analysis of the Soluble DHH/DHHA1-Type Phosphodiesterase TM1595 from Thermotoga maritima.
Structure, 25:1887-1897.e4, 2017

PubMed Abstract: The concentration of messenger molecules in bacterial cells needs to be tightly regulated. This can be achieved by either controlling the synthesis rate, degradation, or export by specific transporters, respectively. The regulation of the essential second messenger c-di-AMP is achieved by modulation of the diadenylate cyclase activity as well as by specific phosphodiesterases that hydrolyze c-di-AMP in the cell. We provide here structural and biochemical data on the DHH-type phosphodiesterase TmPDE (TM1595) from Thermotoga maritima. Our analysis shows that TmPDE is preferentially degrading linear dinucleotides, such as 5'-pApA, 5'-pGpG, and 5'-pApG, compared with cyclic dinucleotide substrates. The high-resolution structural data provided here describe all steps of the PDE reaction: the ligand-free enzyme, two substrate-bound states, and three post-reaction states. We can furthermore show that Pde2 from Streptococcus pneumoniae shares both structural features and substrate specificity based on small-angle X-ray scattering data and biochemical assays.

PubMed: 29107484
DOI: 10.1016/j.str.2017.10.001

Experimental method

X-RAY DIFFRACTION (1.75 Å)