4k6e

From Proteopedia

(Difference between revisions)

Revision as of 10:49, 4 August 2016

Crystal structure of Saccharomyces cerevisiae Dcp2 Nudix domain in complex with Mg

Structural highlights

4k6e is a 1 chain structure with sequence from Baker's yeast. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:
Gene:	DCP2, N1917, PSU1, YNL118C (Baker's yeast)
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[DCP2_YEAST] Catalytic component of the decapping complex necessary for the degradation of mRNAs, both in normal mRNA turnover and in nonsense-mediated mRNA decay. Removes the 7-methyl guanine cap structure from mRNA molecules, yielding a 5'-phosphorylated mRNA fragment and 7m-GDP. Decapping is the major pathway of mRNA degradation in yeast. It occurs through deadenylation, decapping and subsequent 5' to 3' exonucleolytic decay of the transcript body.^[1] ^[2] ^[3] ^[4]

Publication Abstract from PubMed

Removal of the 5' cap structure by Dcp2 is a major step in several 5'-3' mRNA decay pathways. The activity of Dcp2 is enhanced by Dcp1 and bound coactivators, yet the details of how these interactions are linked to chemistry are poorly understood. Here, we report three crystal structures of the catalytic Nudix hydrolase domain of Dcp2 that demonstrate binding of a catalytically essential metal ion, and enzyme kinetics are used to identify several key active site residues involved in acid/base chemistry of decapping. Using nuclear magnetic resonance and molecular dynamics, we find that a conserved metal binding loop on the catalytic domain undergoes conformational changes during the catalytic cycle. These findings describe key events during the chemical step of decapping, suggest local active site conformational changes are important for activity, and provide a framework to explain stimulation of catalysis by the regulatory domain of Dcp2 and associated coactivators.

Active Site Conformational Dynamics Are Coupled to Catalysis in the mRNA Decapping Enzyme Dcp2.,Aglietti RA, Floor SN, McClendon CL, Jacobson MP, Gross JD Structure. 2013 Jul 31. pii: S0969-2126(13)00245-1. doi:, 10.1016/j.str.2013.06.021. PMID:23911090^[5]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Dunckley T, Parker R. The DCP2 protein is required for mRNA decapping in Saccharomyces cerevisiae and contains a functional MutT motif. EMBO J. 1999 Oct 1;18(19):5411-22. PMID:10508173 doi:10.1093/emboj/18.19.5411
↑ Dunckley T, Tucker M, Parker R. Two related proteins, Edc1p and Edc2p, stimulate mRNA decapping in Saccharomyces cerevisiae. Genetics. 2001 Jan;157(1):27-37. PMID:11139489
↑ Tharun S, Parker R. Targeting an mRNA for decapping: displacement of translation factors and association of the Lsm1p-7p complex on deadenylated yeast mRNAs. Mol Cell. 2001 Nov;8(5):1075-83. PMID:11741542
↑ Steiger M, Carr-Schmid A, Schwartz DC, Kiledjian M, Parker R. Analysis of recombinant yeast decapping enzyme. RNA. 2003 Feb;9(2):231-8. PMID:12554866
↑ Aglietti RA, Floor SN, McClendon CL, Jacobson MP, Gross JD. Active Site Conformational Dynamics Are Coupled to Catalysis in the mRNA Decapping Enzyme Dcp2. Structure. 2013 Jul 31. pii: S0969-2126(13)00245-1. doi:, 10.1016/j.str.2013.06.021. PMID:23911090 doi:10.1016/j.str.2013.06.021

1 Structural highlights
2 Function
3 Publication Abstract from PubMed
4 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/4k6e"

@@ Line 1: / Line 1: @@
 ==Crystal structure of Saccharomyces cerevisiae Dcp2 Nudix domain in complex with Mg==
 <StructureSection load='4k6e' size='340' side='right' caption='[[4k6e]], [[Resolution|resolution]] 2.10&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[4k6e]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae_s288c Saccharomyces cerevisiae s288c]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4K6E OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4K6E FirstGlance]. <br>
+<table><tr><td colspan='2'>[[4k6e]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Baker's_yeast Baker's yeast]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4K6E OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4K6E FirstGlance]. <br>
 </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">DCP2, N1917, PSU1, YNL118C ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=559292 Saccharomyces cerevisiae S288c])</td></tr>
+<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">DCP2, N1917, PSU1, YNL118C ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=559292 Baker's yeast])</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=4k6e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4k6e OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4k6e RCSB], [http://www.ebi.ac.uk/pdbsum/4k6e PDBsum]</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=4k6e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4k6e OCA], [http://pdbe.org/4k6e PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4k6e RCSB], [http://www.ebi.ac.uk/pdbsum/4k6e PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4k6e ProSAT]</span></td></tr>
 </table>
 == Function ==
@@ Line 17: / Line 18: @@
 From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 </div>
+<div class="pdbe-citations 4k6e" style="background-color:#fffaf0;"></div>
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Saccharomyces cerevisiae s288c]]
+[[Category: Baker's yeast]]
 [[Category: Aglietti, R A]]
 [[Category: Floor, S N]]

4k6e

From Proteopedia

Revision as of 10:49, 4 August 2016

Crystal structure of Saccharomyces cerevisiae Dcp2 Nudix domain in complex with Mg

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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