6am0
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==Crystal structure of K. lactis Edc1-Dcp1-Dcp2-Edc3 decapping complex with synthetic cap substrate analog== | ==Crystal structure of K. lactis Edc1-Dcp1-Dcp2-Edc3 decapping complex with synthetic cap substrate analog== | ||
| - | <StructureSection load='6am0' size='340' side='right' caption='[[6am0]], [[Resolution|resolution]] 2.84Å' scene=''> | + | <StructureSection load='6am0' size='340' side='right'caption='[[6am0]], [[Resolution|resolution]] 2.84Å' scene=''> |
== Structural highlights == | == Structural highlights == | ||
| - | <table><tr><td colspan='2'>[[6am0]] is a 8 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6AM0 OCA]. For a <b>guided tour on the structure components</b> use [ | + | <table><tr><td colspan='2'>[[6am0]] is a 8 chain structure with sequence from [https://en.wikipedia.org/wiki/Kluyveromyces_lactis_NRRL_Y-1140 Kluyveromyces lactis NRRL Y-1140]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6AM0 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6AM0 FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=6VQ:[[(2~{R},3~{S},4~{R},5~{R})-5-(2-AZANYL-7-METHYL-6-OXIDANYLIDENE-3~{H}-PURIN-7-IUM-9-YL)-3,4-BIS(OXIDANYL)OXOLAN-2-YL]METHOXY-SULFANYL-PHOSPHORYL]+[[[(2~{R},3~{S},4~{R},5~{R})-5-(2-AZANYL-7-METHYL-6-OXIDANYLIDENE-3~{H}-PURIN-7-IUM-9-YL)-3,4-BIS(OXIDANYL)OXOLAN-2-YL]METHOXY-SULFANYL-PHOSPHORYL]OXY-OXIDANYL-PHOSPHORYL]+HYDROGEN+PHOSPHATE'>6VQ</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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]] 2.84Å</td></tr> |
| - | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[ | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=6VQ:[[(2~{R},3~{S},4~{R},5~{R})-5-(2-AZANYL-7-METHYL-6-OXIDANYLIDENE-3~{H}-PURIN-7-IUM-9-YL)-3,4-BIS(OXIDANYL)OXOLAN-2-YL]METHOXY-SULFANYL-PHOSPHORYL]+[[[(2~{R},3~{S},4~{R},5~{R})-5-(2-AZANYL-7-METHYL-6-OXIDANYLIDENE-3~{H}-PURIN-7-IUM-9-YL)-3,4-BIS(OXIDANYL)OXOLAN-2-YL]METHOXY-SULFANYL-PHOSPHORYL]OXY-OXIDANYL-PHOSPHORYL]+HYDROGEN+PHOSPHATE'>6VQ</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=6am0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6am0 OCA], [https://pdbe.org/6am0 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6am0 RCSB], [https://www.ebi.ac.uk/pdbsum/6am0 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6am0 ProSAT]</span></td></tr> | ||
</table> | </table> | ||
| + | == Function == | ||
| + | [https://www.uniprot.org/uniprot/Q6CIU1_KLULA Q6CIU1_KLULA] | ||
| + | <div style="background-color:#fffaf0;"> | ||
| + | == Publication Abstract from PubMed == | ||
| + | The conserved decapping enzyme Dcp2 recognizes and removes the 5' eukaryotic cap from mRNA transcripts in a critical step of many cellular RNA decay pathways. Dcp2 is a dynamic enzyme that functions in concert with the essential activator Dcp1 and a diverse set of coactivators to selectively and efficiently decap target mRNAs in the cell. Here we present a 2.84 A crystal structure of K. lactis Dcp1-Dcp2 in complex with coactivators Edc1 and Edc3, and with substrate analog bound to the Dcp2 active site. Our structure shows how Dcp2 recognizes cap substrate in the catalytically active conformation of the enzyme, and how coactivator Edc1 forms a three-way interface that bridges the domains of Dcp2 to consolidate the active conformation. Kinetic data reveal Dcp2 has selectivity for the first transcribed nucleotide during the catalytic step. The heterotetrameric Edc1-Dcp1-Dcp2-Edc3 structure shows how coactivators Edc1 and Edc3 can act simultaneously to activate decapping catalysis. | ||
| + | |||
| + | Structure of the activated Edc1-Dcp1-Dcp2-Edc3 mRNA decapping complex with substrate analog poised for catalysis.,Mugridge JS, Tibble RW, Ziemniak M, Jemielity J, Gross JD Nat Commun. 2018 Mar 20;9(1):1152. doi: 10.1038/s41467-018-03536-x. PMID:29559651<ref>PMID:29559651</ref> | ||
| + | |||
| + | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | ||
| + | </div> | ||
| + | <div class="pdbe-citations 6am0" style="background-color:#fffaf0;"></div> | ||
| + | == References == | ||
| + | <references/> | ||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
| - | [[Category: | + | [[Category: Kluyveromyces lactis NRRL Y-1140]] |
| - | [[Category: | + | [[Category: Large Structures]] |
| - | [[Category: | + | [[Category: Gross JD]] |
| - | [[Category: | + | [[Category: Mugridge JS]] |
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Current revision
Crystal structure of K. lactis Edc1-Dcp1-Dcp2-Edc3 decapping complex with synthetic cap substrate analog
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