3N3T

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

「3II8」から置き換えられました

3N3T の概要

• エントリーDOI: 10.2210/pdb3n3t/pdb
• 関連するPDBエントリー: 2R6o
• 分子名称: 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)
• 機能のキーワード: ggdef & eal domains, structural genomics, psi-2, protein structure initiative, midwest center for structural genomics, mcsg, unknown function
• 由来する生物種: THIOBACILLUS DENITRIFICANS
• タンパク質・核酸の鎖数: 2
• 化学式量合計: 67265.79

構造登録者

Chang, C.,Xu, X.,Cui, H.,Savchenko, A.,Edwards, A.,Joachimiak, A.,Midwest Center for Structural Genomics (MCSG) (登録日: 2010-05-20, 公開日: 2010-06-16, 最終更新日: 2024-10-16)

主引用文献

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

実験手法

X-RAY DIFFRACTION (2.35 Å)