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2r6o
From Proteopedia
| 2r6o, resolution 1.80Å () | |||||||||
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| Ligands: | , | ||||||||
| Non-Standard Residues: | |||||||||
| Gene: | Tbd_1265 (Thiobacillus denitrificans ATCC 25259) | ||||||||
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| Resources: | FirstGlance, OCA, RCSB, PDBsum, TOPSAN | ||||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||||
Crystal structure of putative diguanylate cyclase/phosphodiesterase from Thiobacillus denitrificans
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 A) 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.
Structural insight into the mechanism of c-di-GMP hydrolysis by EAL domain phosphodiesterases., Tchigvintsev A, Xu X, Singer A, Chang C, Brown G, Proudfoot M, Cui H, Flick R, Anderson WF, Joachimiak A, Galperin MY, Savchenko A, Yakunin AF, J Mol Biol. 2010 Sep 24;402(3):524-38. Epub 2010 Aug 4. PMID:20691189
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
About this Structure
2r6o is a 2 chain structure with sequence from Thiobacillus denitrificans atcc 25259. Full crystallographic information is available from OCA.
Reference
- Tchigvintsev A, Xu X, Singer A, Chang C, Brown G, Proudfoot M, Cui H, Flick R, Anderson WF, Joachimiak A, Galperin MY, Savchenko A, Yakunin AF. Structural insight into the mechanism of c-di-GMP hydrolysis by EAL domain phosphodiesterases. J Mol Biol. 2010 Sep 24;402(3):524-38. Epub 2010 Aug 4. PMID:20691189 doi:10.1016/j.jmb.2010.07.050
Categories: Thiobacillus denitrificans atcc 25259 | Chang, C. | Edwards, A M. | Joachimiak, A. | MCSG, Midwest Center for Structural Genomics. | Savchenko, A. | Xu, X. | Zheng, H. | Diguanylate cyclase | Ggdef and eal domain | Mcsg | Midwest center for structural genomic | Protein structure initiative | Psi-2 | Structural genomic | Thiobacillus denitrifican | Transferase | Unknown function
