4lyk: Difference between revisions
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The | ==Crystal structure of the EAL domain of c-di-GMP specific phosphodiesterase YahA in complex with activating cofactor Mg++== | ||
<StructureSection load='4lyk' size='340' side='right'caption='[[4lyk]], [[Resolution|resolution]] 2.40Å' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[4lyk]] is a 4 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=4LYK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4LYK FirstGlance]. <br> | |||
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.4Å</td></tr> | |||
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=HB0:TRANS-4-(HYDROXYMETHYL)CYCLOHEXANOL'>HB0</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></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=4lyk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4lyk OCA], [https://pdbe.org/4lyk PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4lyk RCSB], [https://www.ebi.ac.uk/pdbsum/4lyk PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4lyk ProSAT]</span></td></tr> | |||
</table> | |||
== Function == | |||
[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;"> | |||
== 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<ref>PMID:24451384</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 4lyk" style="background-color:#fffaf0;"></div> | |||
==See Also== | |||
*[[Phosphodiesterase 3D structures|Phosphodiesterase 3D structures]] | |||
== References == | |||
<references/> | |||
__TOC__ | |||
</StructureSection> | |||
[[Category: Escherichia coli K-12]] | |||
[[Category: Large Structures]] | |||
[[Category: Schirmer T]] | |||
[[Category: Sundriyal A]] | |||
Latest revision as of 19:28, 20 September 2023
Crystal structure of the EAL domain of c-di-GMP specific phosphodiesterase YahA in complex with activating cofactor Mg++Crystal structure of the EAL domain of c-di-GMP specific phosphodiesterase YahA in complex with activating cofactor Mg++
Structural highlights
FunctionPDEL_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 PubMedThe 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 AlsoReferences
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