1q67: Difference between revisions

Latest revision as of 08:13, 14 February 2024

Crystal structure of Dcp1p

Structural highlights

1q67 is a 2 chain structure with sequence from Saccharomyces cerevisiae. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.3Å
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

DCP1_YEAST 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. DCP1 is activated by the DEAD-box helicase DHH1 and destabilizes the eIF-4F cap-binding complex from the mRNA.^[1] ^[2] ^[3] ^[4] ^[5] ^[6] ^[7] ^[8] ^[9] ^[10] ^[11] ^[12] ^[13] ^[14] ^[15] ^[16]

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

References

↑ Beelman CA, Stevens A, Caponigro G, LaGrandeur TE, Hatfield L, Fortner DM, Parker R. An essential component of the decapping enzyme required for normal rates of mRNA turnover. Nature. 1996 Aug 15;382(6592):642-6. PMID:8757137 doi:https://dx.doi.org/10.1038/382642a0
↑ Hatfield L, Beelman CA, Stevens A, Parker R. Mutations in trans-acting factors affecting mRNA decapping in Saccharomyces cerevisiae. Mol Cell Biol. 1996 Oct;16(10):5830-8. PMID:8816497
↑ LaGrandeur TE, Parker R. Isolation and characterization of Dcp1p, the yeast mRNA decapping enzyme. EMBO J. 1998 Mar 2;17(5):1487-96. PMID:9482745 doi:https://dx.doi.org/10.1093/emboj/17.5.1487
↑ Anderson JS, Parker RP. The 3' to 5' degradation of yeast mRNAs is a general mechanism for mRNA turnover that requires the SKI2 DEVH box protein and 3' to 5' exonucleases of the exosome complex. EMBO J. 1998 Mar 2;17(5):1497-506. PMID:9482746 doi:10.1093/emboj/17.5.1497
↑ 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
↑ Tharun S, Parker R. Analysis of mutations in the yeast mRNA decapping enzyme. Genetics. 1999 Apr;151(4):1273-85. PMID:10101156
↑ Zhang S, Williams CJ, Wormington M, Stevens A, Peltz SW. Monitoring mRNA decapping activity. Methods. 1999 Jan;17(1):46-51. PMID:10075882 doi:https://dx.doi.org/10.1006/meth.1998.0706
↑ Muhlrad D, Parker R. Recognition of yeast mRNAs as "nonsense containing" leads to both inhibition of mRNA translation and mRNA degradation: implications for the control of mRNA decapping. Mol Biol Cell. 1999 Nov;10(11):3971-8. PMID:10564284
↑ Schwartz DC, Parker R. Mutations in translation initiation factors lead to increased rates of deadenylation and decapping of mRNAs in Saccharomyces cerevisiae. Mol Cell Biol. 1999 Aug;19(8):5247-56. PMID:10409716
↑ Vilela C, Velasco C, Ptushkina M, McCarthy JE. The eukaryotic mRNA decapping protein Dcp1 interacts physically and functionally with the eIF4F translation initiation complex. EMBO J. 2000 Aug 15;19(16):4372-82. PMID:10944120 doi:https://dx.doi.org/10.1093/emboj/19.16.4372
↑ 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
↑ Fischer N, Weis K. The DEAD box protein Dhh1 stimulates the decapping enzyme Dcp1. EMBO J. 2002 Jun 3;21(11):2788-97. PMID:12032091 doi:10.1093/emboj/21.11.2788
↑ Ramirez CV, Vilela C, Berthelot K, McCarthy JE. Modulation of eukaryotic mRNA stability via the cap-binding translation complex eIF4F. J Mol Biol. 2002 May 10;318(4):951-62. PMID:12054793 doi:https://dx.doi.org/10.1016/S0022-2836(02)00162-6
↑ 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
↑ Holmes LE, Campbell SG, De Long SK, Sachs AB, Ashe MP. Loss of translational control in yeast compromised for the major mRNA decay pathway. Mol Cell Biol. 2004 Apr;24(7):2998-3010. PMID:15024087

Proteopedia Page Contributors and Editors (what is this?)

OCA

[1] Beelman CA, Stevens A, Caponigro G, LaGrandeur TE, Hatfield L, Fortner DM, Parker R. An essential component of the decapping enzyme required for normal rates of mRNA turnover. Nature. 1996 Aug 15;382(6592):642-6. PMID:8757137 doi:https://dx.doi.org/10.1038/382642a0

[2] Hatfield L, Beelman CA, Stevens A, Parker R. Mutations in trans-acting factors affecting mRNA decapping in Saccharomyces cerevisiae. Mol Cell Biol. 1996 Oct;16(10):5830-8. PMID:8816497

[3] LaGrandeur TE, Parker R. Isolation and characterization of Dcp1p, the yeast mRNA decapping enzyme. EMBO J. 1998 Mar 2;17(5):1487-96. PMID:9482745 doi:https://dx.doi.org/10.1093/emboj/17.5.1487

[4] Anderson JS, Parker RP. The 3' to 5' degradation of yeast mRNAs is a general mechanism for mRNA turnover that requires the SKI2 DEVH box protein and 3' to 5' exonucleases of the exosome complex. EMBO J. 1998 Mar 2;17(5):1497-506. PMID:9482746 doi:10.1093/emboj/17.5.1497

[5] 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

[6] Tharun S, Parker R. Analysis of mutations in the yeast mRNA decapping enzyme. Genetics. 1999 Apr;151(4):1273-85. PMID:10101156

[7] Zhang S, Williams CJ, Wormington M, Stevens A, Peltz SW. Monitoring mRNA decapping activity. Methods. 1999 Jan;17(1):46-51. PMID:10075882 doi:https://dx.doi.org/10.1006/meth.1998.0706

[8] Muhlrad D, Parker R. Recognition of yeast mRNAs as "nonsense containing" leads to both inhibition of mRNA translation and mRNA degradation: implications for the control of mRNA decapping. Mol Biol Cell. 1999 Nov;10(11):3971-8. PMID:10564284

[9] Schwartz DC, Parker R. Mutations in translation initiation factors lead to increased rates of deadenylation and decapping of mRNAs in Saccharomyces cerevisiae. Mol Cell Biol. 1999 Aug;19(8):5247-56. PMID:10409716

[10] Vilela C, Velasco C, Ptushkina M, McCarthy JE. The eukaryotic mRNA decapping protein Dcp1 interacts physically and functionally with the eIF4F translation initiation complex. EMBO J. 2000 Aug 15;19(16):4372-82. PMID:10944120 doi:https://dx.doi.org/10.1093/emboj/19.16.4372

[11] 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

[12] 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

[13] Fischer N, Weis K. The DEAD box protein Dhh1 stimulates the decapping enzyme Dcp1. EMBO J. 2002 Jun 3;21(11):2788-97. PMID:12032091 doi:10.1093/emboj/21.11.2788

[14] Ramirez CV, Vilela C, Berthelot K, McCarthy JE. Modulation of eukaryotic mRNA stability via the cap-binding translation complex eIF4F. J Mol Biol. 2002 May 10;318(4):951-62. PMID:12054793 doi:https://dx.doi.org/10.1016/S0022-2836(02)00162-6

[15] 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

[16] Holmes LE, Campbell SG, De Long SK, Sachs AB, Ashe MP. Loss of translational control in yeast compromised for the major mRNA decay pathway. Mol Cell Biol. 2004 Apr;24(7):2998-3010. PMID:15024087

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@@ Line 1: / Line 1: @@
 ==Crystal structure of Dcp1p==
-<StructureSection load='1q67' size='340' side='right' caption='[[1q67]], [[Resolution|resolution]] 2.30&Aring;' scene=''>
+<StructureSection load='1q67' size='340' side='right'caption='[[1q67]], [[Resolution|resolution]] 2.30&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[1q67]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_18824 Atcc 18824]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1Q67 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1Q67 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[1q67]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1Q67 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1Q67 FirstGlance]. <br>
-</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">DCP1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 ATCC 18824])</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]] 2.3&#8491;</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=1q67 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1q67 OCA], [http://pdbe.org/1q67 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1q67 RCSB], [http://www.ebi.ac.uk/pdbsum/1q67 PDBsum]</span></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=1q67 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1q67 OCA], [https://pdbe.org/1q67 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1q67 RCSB], [https://www.ebi.ac.uk/pdbsum/1q67 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1q67 ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/DCP1_YEAST DCP1_YEAST]] 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. DCP1 is activated by the DEAD-box helicase DHH1 and destabilizes the eIF-4F cap-binding complex from the mRNA.<ref>PMID:8757137</ref> <ref>PMID:8816497</ref> <ref>PMID:9482745</ref> <ref>PMID:9482746</ref> <ref>PMID:10508173</ref> <ref>PMID:10101156</ref> <ref>PMID:10075882</ref> <ref>PMID:10564284</ref> <ref>PMID:10409716</ref> <ref>PMID:10944120</ref> <ref>PMID:11139489</ref> <ref>PMID:11741542</ref> <ref>PMID:12032091</ref> <ref>PMID:12054793</ref> <ref>PMID:12554866</ref> <ref>PMID:15024087</ref>
+[https://www.uniprot.org/uniprot/DCP1_YEAST DCP1_YEAST] 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. DCP1 is activated by the DEAD-box helicase DHH1 and destabilizes the eIF-4F cap-binding complex from the mRNA.<ref>PMID:8757137</ref> <ref>PMID:8816497</ref> <ref>PMID:9482745</ref> <ref>PMID:9482746</ref> <ref>PMID:10508173</ref> <ref>PMID:10101156</ref> <ref>PMID:10075882</ref> <ref>PMID:10564284</ref> <ref>PMID:10409716</ref> <ref>PMID:10944120</ref> <ref>PMID:11139489</ref> <ref>PMID:11741542</ref> <ref>PMID:12032091</ref> <ref>PMID:12054793</ref> <ref>PMID:12554866</ref> <ref>PMID:15024087</ref>
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
 Check<jmol>
    <jmolCheckbox>
-     <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/q6/1q67_consurf.spt"</scriptWhenChecked>
+     <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/q6/1q67_consurf.spt"</scriptWhenChecked>
      <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
      <text>to colour the structure by Evolutionary Conservation</text>
    </jmolCheckbox>
-</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/chain_selection.php?pdb_ID=2ata ConSurf].
+</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1q67 ConSurf].
 <div style="clear:both"></div>
-<div style="background-color:#fffaf0;">
-== Publication Abstract from PubMed ==
-A major pathway of eukaryotic mRNA turnover begins with deadenylation, followed by decapping and 5'--&gt;3' exonucleolytic degradation. A critical step in this pathway is decapping, which is carried out by an enzyme composed of Dcp1p and Dcp2p. The crystal structure of Dcp1p shows that it markedly resembles the EVH1 family of protein domains. Comparison of the proline-rich sequence (PRS)-binding sites in this family of proteins with Dcp1p indicates that it belongs to a novel class of EVH1 domains. Mapping of the sequence conservation on the molecular surface of Dcp1p reveals two prominent sites. One of these is required for the function of the Dcp1p-Dcp2p complex, and the other, corresponding to the PRS-binding site of EVH1 domains, is probably a binding site for decapping regulatory proteins. Moreover, a conserved hydrophobic patch is shown to be critical for decapping.
-Crystal structure of Dcp1p and its functional implications in mRNA decapping.,She M, Decker CJ, Sundramurthy K, Liu Y, Chen N, Parker R, Song H Nat Struct Mol Biol. 2004 Mar;11(3):249-56. Epub 2004 Feb 1. PMID:14758354<ref>PMID:14758354</ref>
-From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-</div>
-<div class="pdbe-citations 1q67" style="background-color:#fffaf0;"></div>
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Atcc 18824]]
+[[Category: Large Structures]]
-[[Category: Chen, N]]
+[[Category: Saccharomyces cerevisiae]]
-[[Category: Decker, C J]]
+[[Category: Chen N]]
-[[Category: Liu, Y]]
+[[Category: Decker CJ]]
-[[Category: Parker, R]]
+[[Category: Liu Y]]
-[[Category: She, M]]
+[[Category: Parker R]]
-[[Category: Song, H]]
+[[Category: She M]]
-[[Category: Beta sandwich]]
+[[Category: Song H]]
-[[Category: Transcription]]

1q67: Difference between revisions

Latest revision as of 08:13, 14 February 2024

Crystal structure of Dcp1p

Structural highlights

Function

Evolutionary Conservation

References

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