3N3T

Crystal structure of putative diguanylate cyclase/phosphodiesterase complex with cyclic di-gmp

Replaces:  3II8

Summary for 3N3T

• Entry DOI: 10.2210/pdb3n3t/pdb
• Related: 2R6o
• Descriptor: PUTATIVE DIGUANYLATE CYCLASE/PHOSPHODIESTERASE, 9,9'-[(2R,3R,3aS,5S,7aR,9R,10R,10aS,12S,14aR)-3,5,10,12-tetrahydroxy-5,12-dioxidooctahydro-2H,7H-difuro[3,2-d:3',2'-j][1,3,7,9,2,8]tetraoxadiphosphacyclododecine-2,9-diyl]bis(2-amino-1,9-dihydro-6H-purin-6-one), MAGNESIUM ION, ... (5 entities in total)
• Functional Keywords: ggdef & eal domains, structural genomics, psi-2, protein structure initiative, midwest center for structural genomics, mcsg, unknown function
• Biological source: THIOBACILLUS DENITRIFICANS
• Total number of polymer chains: 2
• Total formula weight: 67265.79

Authors

Chang, C.,Xu, X.,Cui, H.,Savchenko, A.,Edwards, A.,Joachimiak, A.,Midwest Center for Structural Genomics (MCSG) (deposition date: 2010-05-20, release date: 2010-06-16, Last modification date: 2024-10-16)

Primary citation

Tchigvintsev, A.,Xu, X.,Singer, A.,Chang, C.,Brown, G.,Proudfoot, M.,Cui, H.,Flick, R.,Anderson, W.F.,Joachimiak, A.,Galperin, M.Y.,Savchenko, A.,Yakunin, A.F.
Structural insight into the mechanism of c-di-GMP hydrolysis by EAL domain phosphodiesterases.
J.Mol.Biol., 402:524-538, 2010

PubMed Abstract: Cyclic diguanylate (or bis-(3'-5') cyclic dimeric guanosine monophosphate; c-di-GMP) is a ubiquitous second messenger that regulates diverse cellular functions, including motility, biofilm formation, cell cycle progression, and virulence in bacteria. In the cell, degradation of c-di-GMP is catalyzed by highly specific EAL domain phosphodiesterases whose catalytic mechanism is still unclear. Here, we purified 13 EAL domain proteins from various organisms and demonstrated that their catalytic activity is associated with the presence of 10 conserved EAL domain residues. The crystal structure of the TBD1265 EAL domain was determined in free state (1.8 Å) and in complex with c-di-GMP (2.35 A), and unveiled the role of conserved residues in substrate binding and catalysis. The structure revealed the presence of two metal ions directly coordinated by six conserved residues, two oxygens of c-di-GMP phosphate, and potential catalytic water molecule. Our results support a two-metal-ion catalytic mechanism of c-di-GMP hydrolysis by EAL domain phosphodiesterases.

PubMed: 20691189
DOI: 10.1016/j.jmb.2010.07.050

Experimental method

X-RAY DIFFRACTION (2.35 Å)