5M3C

Structure of the hybrid domain (GGDEF-EAL) of PA0575 from Pseudomonas aeruginosa PAO1 at 2.8 Ang. with GTP and Ca2+ bound to the active site of the GGDEF domain

Summary for 5M3C

• Entry DOI: 10.2210/pdb5m3c/pdb
• Descriptor: Diguanylate cyclase, CALCIUM ION, GUANOSINE-5'-TRIPHOSPHATE, ... (4 entities in total)
• Functional Keywords: phosphodiesterase, c-di-gmp, cyclic-di-gmp, diguanylate, cyclase, eal, ggdef, hydrolase
• Biological source: Pseudomonas aeruginosa
• Total number of polymer chains: 2
• Total formula weight: 99412.38

Authors

Giardina, G.,Brunotti, P.,Cutruzzola, F.,Rinaldo, S. (deposition date: 2016-10-14, release date: 2017-12-20, Last modification date: 2024-01-17)

Primary citation

Mantoni, F.,Paiardini, A.,Brunotti, P.,D'Angelo, C.,Cervoni, L.,Paone, A.,Cappellacci, L.,Petrelli, R.,Ricciutelli, M.,Leoni, L.,Rampioni, G.,Arcovito, A.,Rinaldo, S.,Cutruzzola, F.,Giardina, G.
Insights into the GTP-dependent allosteric control of c-di-GMP hydrolysis from the crystal structure of PA0575 protein from Pseudomonas aeruginosa.
FEBS J., 285:3815-3834, 2018

PubMed Abstract: Bis-(3'-5')-cyclic diguanylic acid (c-di-GMP) belongs to the class of cyclic dinucleotides, key carriers of cellular information in prokaryotic and eukaryotic signal transduction pathways. In bacteria, the intracellular levels of c-di-GMP and their complex physiological outputs are dynamically regulated by environmental and internal stimuli, which control the antagonistic activities of diguanylate cyclases (DGCs) and c-di-GMP specific phosphodiesterases (PDEs). Allostery is one of the major modulators of the c-di-GMP-dependent response. Both the c-di-GMP molecule and the proteins interacting with this second messenger are characterized by an extraordinary structural plasticity, which has to be taken into account when defining and possibly predicting c-di-GMP-related processes. Here, we report a structure-function relationship study on the catalytic portion of the PA0575 protein from Pseudomonas aeruginosa, bearing both putative DGC and PDE domains. The kinetic and structural studies indicate that the GGDEF-EAL portion is a GTP-dependent PDE. Moreover, the crystal structure confirms the high degree of conformational flexibility of this module. We combined structural analysis and protein engineering studies to propose the possible molecular mechanism guiding the nucleotide-dependent allosteric control of catalysis; we propose that the role exerted by GTP via the GGDEF domain is to allow the two EAL domains to form a dimer, the species competent to enter PDE catalysis.

PubMed: 30106221
DOI: 10.1111/febs.14634

Experimental method

X-RAY DIFFRACTION (2.8 Å)