4lj3

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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++==
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<StructureSection load='4lj3' size='340' side='right' caption='[[4lj3]], [[Resolution|resolution]] 1.70&Aring;' scene=''>
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<StructureSection load='4lj3' size='340' side='right'caption='[[4lj3]], [[Resolution|resolution]] 1.70&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
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<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>
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<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>
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</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>
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</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>
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<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4kie|4kie]], [[4lyk|4lyk]]</td></tr>
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<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>
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<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>
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<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://pdbe.org/4lj3 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4lj3 RCSB], [http://www.ebi.ac.uk/pdbsum/4lj3 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4lj3 ProSAT]</span></td></tr>
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</table>
</table>
== Function ==
== Function ==
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[[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.
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[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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==See Also==
==See Also==
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*[[Phosphodiesterase|Phosphodiesterase]]
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*[[Phosphodiesterase 3D structures|Phosphodiesterase 3D structures]]
== References ==
== References ==
<references/>
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
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[[Category: Ecoli]]
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[[Category: Escherichia coli K-12]]
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[[Category: Schirmer, T]]
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[[Category: Large Structures]]
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[[Category: Sundriyal, A]]
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[[Category: Schirmer T]]
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[[Category: Hydrolase]]
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[[Category: Sundriyal A]]
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[[Category: Pgpg]]
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[[Category: Phosphodiesterase]]
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[[Category: Tim-barrel]]
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Revision as of 11:04, 14 December 2022

Crystal structure of the EAL domain of c-di-GMP specific phosphodiesterase YahA in complex with substrate c-di-GMP and Ca++

PDB ID 4lj3

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