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| | ==Crystal structure of the EAL domain of c-di-GMP specific phosphodiesterase YahA in complex with substrate c-di-GMP and Ca++== | | ==Crystal structure of the EAL domain of c-di-GMP specific phosphodiesterase YahA in complex with substrate c-di-GMP and Ca++== |
| - | <StructureSection load='4lj3' size='340' side='right' caption='[[4lj3]], [[Resolution|resolution]] 1.70Å' scene=''> | + | <StructureSection load='4lj3' size='340' side='right'caption='[[4lj3]], [[Resolution|resolution]] 1.70Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[4lj3]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Ecoli Ecoli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4LJ3 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4LJ3 FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[4lj3]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_K-12 Escherichia coli K-12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4LJ3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4LJ3 FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=C2E: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)'>C2E</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=HB0:TRANS-4-(HYDROXYMETHYL)CYCLOHEXANOL'>HB0</scene>, <scene name='pdbligand=IMD:IMIDAZOLE'>IMD</scene></td></tr> | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.7Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4kie|4kie]], [[4lyk|4lyk]]</td></tr>
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=C2E: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)'>C2E</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=HB0:TRANS-4-(HYDROXYMETHYL)CYCLOHEXANOL'>HB0</scene>, <scene name='pdbligand=IMD:IMIDAZOLE'>IMD</scene></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">yahA, b0315, JW0307 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI])</td></tr>
| + | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=4lj3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4lj3 OCA], [https://pdbe.org/4lj3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4lj3 RCSB], [https://www.ebi.ac.uk/pdbsum/4lj3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4lj3 ProSAT]</span></td></tr> |
| - | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4lj3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4lj3 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4lj3 RCSB], [http://www.ebi.ac.uk/pdbsum/4lj3 PDBsum]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/YAHA_ECOLI YAHA_ECOLI]] Hydrolyzes c-di-GMP (cyclic bis(3'-5') dimeric GMP) to 5'-pGpG, known as PDE-A activity. PDE-B activity, that is hydrolysis of 5'-pGpG to GMP, proceeds only very slowly. | + | [https://www.uniprot.org/uniprot/PDEL_ECOLI PDEL_ECOLI] Acts both as an enzyme and as a c-di-GMP sensor to couple transcriptional activity to the c-di-GMP status of the cell (PubMed:26553851). Phosphodiesterase (PDE) that catalyzes the hydrolysis of cyclic-di-GMP (c-di-GMP) to 5'-pGpG (PubMed:15995192, PubMed:24451384, PubMed:26553851). Also acts as a transcription factor to control its own expression (PubMed:26553851).<ref>PMID:15995192</ref> <ref>PMID:24451384</ref> <ref>PMID:26553851</ref> |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> |
| | </div> | | </div> |
| | + | <div class="pdbe-citations 4lj3" style="background-color:#fffaf0;"></div> |
| | | | |
| | ==See Also== | | ==See Also== |
| - | *[[Phosphodiesterase|Phosphodiesterase]] | + | *[[Phosphodiesterase 3D structures|Phosphodiesterase 3D structures]] |
| | == References == | | == References == |
| | <references/> | | <references/> |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Ecoli]] | + | [[Category: Escherichia coli K-12]] |
| - | [[Category: Schirmer, T]] | + | [[Category: Large Structures]] |
| - | [[Category: Sundriyal, A]] | + | [[Category: Schirmer T]] |
| - | [[Category: Hydrolase]] | + | [[Category: Sundriyal A]] |
| - | [[Category: Pgpg]]
| + | |
| - | [[Category: Phosphodiesterase]]
| + | |
| - | [[Category: Tim-barrel]]
| + | |
| Structural highlights
Function
PDEL_ECOLI Acts both as an enzyme and as a c-di-GMP sensor to couple transcriptional activity to the c-di-GMP status of the cell (PubMed:26553851). Phosphodiesterase (PDE) that catalyzes the hydrolysis of cyclic-di-GMP (c-di-GMP) to 5'-pGpG (PubMed:15995192, PubMed:24451384, PubMed:26553851). Also acts as a transcription factor to control its own expression (PubMed:26553851).[1] [2] [3]
Publication Abstract from PubMed
The universal second messenger cyclic di-GMP (cdG) is involved in the regulation of a diverse range of cellular processes in bacteria. The intracellular concentration of the dinucleotide is determined by the opposing actions of diguanylate cyclases (DGCs) and cdG specific phosphodiesterases (PDEs). While most PDEs have accessory domains that are involved in the regulation of their activity, the regulatory mechanism of this class of enzymes has remained unclear. Here, we use biophysical and functional analyses to show that the isolated EAL domain of a PDE from E. coli (YahA) is in a fast thermodynamic monomer - dimer equilibrium, and that the domain is active only in its dimeric state. Furthermore, our data indicate thermodynamic coupling between substrate binding and EAL dimerization with the dimerization affinity being increased about 100-fold upon substrate binding. Crystal structures of the YahA-EAL domain determined under various conditions (apo, Mg2+, c-di-GMP/Mg2+ complex) confirm structural coupling between the dimer interface and the catalytic center. The in-built regulatory properties of the EAL domain probably facilitates its modular, functional combination with the diverse repertoire of accessory domains.
Inherent regulation of EAL domain-catalyzed hydrolysis of second messenger c-di-GMP.,Sundriyal A, Massa C, Samoray D, Zehender F, Sharpe T, Jenal U, Schirmer T J Biol Chem. 2014 Jan 22. PMID:24451384[4]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Schmidt AJ, Ryjenkov DA, Gomelsky M. The ubiquitous protein domain EAL is a cyclic diguanylate-specific phosphodiesterase: enzymatically active and inactive EAL domains. J Bacteriol. 2005 Jul;187(14):4774-81. PMID:15995192 doi:http://dx.doi.org/187/14/4774
- ↑ Sundriyal A, Massa C, Samoray D, Zehender F, Sharpe T, Jenal U, Schirmer T. Inherent regulation of EAL domain-catalyzed hydrolysis of second messenger c-di-GMP. J Biol Chem. 2014 Jan 22. PMID:24451384 doi:http://dx.doi.org/10.1074/jbc.M113.516195
- ↑ Reinders A, Hee CS, Ozaki S, Mazur A, Boehm A, Schirmer T, Jenal U. Expression and Genetic Activation of Cyclic Di-GMP-Specific Phosphodiesterases in Escherichia coli. J Bacteriol. 2015 Nov 9;198(3):448-62. doi: 10.1128/JB.00604-15. PMID:26553851 doi:http://dx.doi.org/10.1128/JB.00604-15
- ↑ Sundriyal A, Massa C, Samoray D, Zehender F, Sharpe T, Jenal U, Schirmer T. Inherent regulation of EAL domain-catalyzed hydrolysis of second messenger c-di-GMP. J Biol Chem. 2014 Jan 22. PMID:24451384 doi:http://dx.doi.org/10.1074/jbc.M113.516195
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