5qpc: Difference between revisions

Revision as of 11:13, 10 May 2019

Crystal Structure of DCP2 (NUDT20) after initial refinement with no ligand modelled (structure $n)

Structural highlights

5qpc is a 1 chain structure. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:	ACT, DMS, EDO, PEG
Activity:	[mRNA_hydrolase 5'-(N(7)-methylguanosine 5'-triphospho)-[mRNA] hydrolase], with EC number 3.6.1.62
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[DCP2_HUMAN] Decapping metalloenzyme that catalyzes the cleavage of the cap structure on mRNAs (PubMed:12417715, PubMed:12218187, PubMed:12923261, PubMed:21070968). Removes the 7-methyl guanine cap structure from mRNA molecules, yielding a 5'-phosphorylated mRNA fragment and 7m-GDP (PubMed:12486012, PubMed:12923261, PubMed:21070968). Necessary for the degradation of mRNAs, both in normal mRNA turnover and in nonsense-mediated mRNA decay (PubMed:14527413). Plays a role in replication-dependent histone mRNA degradation (PubMed:18172165). Has higher activity towards mRNAs that lack a poly(A) tail (PubMed:21070968). Has no activity towards a cap structure lacking an RNA moiety (PubMed:21070968). Blocks autophagy in nutrient-rich conditions by repressing the expression of ATG-related genes through degration of their transcripts (PubMed:26098573).^[1] ^[2] ^[3] ^[4] ^[5] ^[6] ^[7] ^[8]

References

↑ Wang Z, Jiao X, Carr-Schmid A, Kiledjian M. The hDcp2 protein is a mammalian mRNA decapping enzyme. Proc Natl Acad Sci U S A. 2002 Oct 1;99(20):12663-8. Epub 2002 Sep 6. PMID:12218187 doi:https://dx.doi.org/10.1073/pnas.192445599
↑ Lykke-Andersen J. Identification of a human decapping complex associated with hUpf proteins in nonsense-mediated decay. Mol Cell Biol. 2002 Dec;22(23):8114-21. PMID:12417715
↑ van Dijk E, Cougot N, Meyer S, Babajko S, Wahle E, Seraphin B. Human Dcp2: a catalytically active mRNA decapping enzyme located in specific cytoplasmic structures. EMBO J. 2002 Dec 16;21(24):6915-24. PMID:12486012
↑ Piccirillo C, Khanna R, Kiledjian M. Functional characterization of the mammalian mRNA decapping enzyme hDcp2. RNA. 2003 Sep;9(9):1138-47. PMID:12923261
↑ Lejeune F, Li X, Maquat LE. Nonsense-mediated mRNA decay in mammalian cells involves decapping, deadenylating, and exonucleolytic activities. Mol Cell. 2003 Sep;12(3):675-87. PMID:14527413
↑ Mullen TE, Marzluff WF. Degradation of histone mRNA requires oligouridylation followed by decapping and simultaneous degradation of the mRNA both 5' to 3' and 3' to 5'. Genes Dev. 2008 Jan 1;22(1):50-65. doi: 10.1101/gad.1622708. PMID:18172165 doi:10.1101/gad.1622708
↑ Song MG, Li Y, Kiledjian M. Multiple mRNA decapping enzymes in mammalian cells. Mol Cell. 2010 Nov 12;40(3):423-32. doi: 10.1016/j.molcel.2010.10.010. PMID:21070968 doi:https://dx.doi.org/10.1016/j.molcel.2010.10.010
↑ Hu G, McQuiston T, Bernard A, Park YD, Qiu J, Vural A, Zhang N, Waterman SR, Blewett NH, Myers TG, Maraia RJ, Kehrl JH, Uzel G, Klionsky DJ, Williamson PR. A conserved mechanism of TOR-dependent RCK-mediated mRNA degradation regulates autophagy. Nat Cell Biol. 2015 Jul;17(7):930-942. doi: 10.1038/ncb3189. Epub 2015 Jun 22. PMID:26098573 doi:https://dx.doi.org/10.1038/ncb3189

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OCA

[1] Wang Z, Jiao X, Carr-Schmid A, Kiledjian M. The hDcp2 protein is a mammalian mRNA decapping enzyme. Proc Natl Acad Sci U S A. 2002 Oct 1;99(20):12663-8. Epub 2002 Sep 6. PMID:12218187 doi:https://dx.doi.org/10.1073/pnas.192445599

[2] Lykke-Andersen J. Identification of a human decapping complex associated with hUpf proteins in nonsense-mediated decay. Mol Cell Biol. 2002 Dec;22(23):8114-21. PMID:12417715

[3] van Dijk E, Cougot N, Meyer S, Babajko S, Wahle E, Seraphin B. Human Dcp2: a catalytically active mRNA decapping enzyme located in specific cytoplasmic structures. EMBO J. 2002 Dec 16;21(24):6915-24. PMID:12486012

[4] Piccirillo C, Khanna R, Kiledjian M. Functional characterization of the mammalian mRNA decapping enzyme hDcp2. RNA. 2003 Sep;9(9):1138-47. PMID:12923261

[5] Lejeune F, Li X, Maquat LE. Nonsense-mediated mRNA decay in mammalian cells involves decapping, deadenylating, and exonucleolytic activities. Mol Cell. 2003 Sep;12(3):675-87. PMID:14527413

[6] Mullen TE, Marzluff WF. Degradation of histone mRNA requires oligouridylation followed by decapping and simultaneous degradation of the mRNA both 5' to 3' and 3' to 5'. Genes Dev. 2008 Jan 1;22(1):50-65. doi: 10.1101/gad.1622708. PMID:18172165 doi:10.1101/gad.1622708

[7] Song MG, Li Y, Kiledjian M. Multiple mRNA decapping enzymes in mammalian cells. Mol Cell. 2010 Nov 12;40(3):423-32. doi: 10.1016/j.molcel.2010.10.010. PMID:21070968 doi:https://dx.doi.org/10.1016/j.molcel.2010.10.010

[8] Hu G, McQuiston T, Bernard A, Park YD, Qiu J, Vural A, Zhang N, Waterman SR, Blewett NH, Myers TG, Maraia RJ, Kehrl JH, Uzel G, Klionsky DJ, Williamson PR. A conserved mechanism of TOR-dependent RCK-mediated mRNA degradation regulates autophagy. Nat Cell Biol. 2015 Jul;17(7):930-942. doi: 10.1038/ncb3189. Epub 2015 Jun 22. PMID:26098573 doi:https://dx.doi.org/10.1038/ncb3189

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@@ Line 1: / Line 1: @@
-'''Unreleased structure'''
-The entry 5qpc is ON HOLD
+==Crystal Structure of DCP2 (NUDT20) after initial refinement with no ligand modelled (structure $n)==
+<StructureSection load='5qpc' size='340' side='right'caption='[[5qpc]], [[Resolution|resolution]] 1.66&Aring;' scene=''>
-Authors: Nelson, E.R., Velupillai, S., Talon, R., Collins, P.M., Krojer, T., Wang, D., Brandao-Neto, J., Douangamath, A., Burgess-Brown, N., Arrowsmith, C.H., Bountra, C., Huber, K., von Delft, F.
+== Structural highlights ==
+<table><tr><td colspan='2'>[[5qpc]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5QPC OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5QPC FirstGlance]. <br>
-Description: Crystal Structure of DCP2 (NUDT20) after initial refinement with no ligand modelled (structure $n)
+</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=DMS:DIMETHYL+SULFOXIDE'>DMS</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene></td></tr>
-[[Category: Unreleased Structures]]
+<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/5'-(N(7)-methylguanosine_5'-triphospho)-[mRNA]_hydrolase 5'-(N(7)-methylguanosine 5'-triphospho)-[mRNA] hydrolase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.6.1.62 3.6.1.62] </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=5qpc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5qpc OCA], [http://pdbe.org/5qpc PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5qpc RCSB], [http://www.ebi.ac.uk/pdbsum/5qpc PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5qpc ProSAT]</span></td></tr>
+</table>
+== Function ==
+[[http://www.uniprot.org/uniprot/DCP2_HUMAN DCP2_HUMAN]] Decapping metalloenzyme that catalyzes the cleavage of the cap structure on mRNAs (PubMed:12417715, PubMed:12218187, PubMed:12923261, PubMed:21070968). Removes the 7-methyl guanine cap structure from mRNA molecules, yielding a 5'-phosphorylated mRNA fragment and 7m-GDP (PubMed:12486012, PubMed:12923261, PubMed:21070968). Necessary for the degradation of mRNAs, both in normal mRNA turnover and in nonsense-mediated mRNA decay (PubMed:14527413). Plays a role in replication-dependent histone mRNA degradation (PubMed:18172165). Has higher activity towards mRNAs that lack a poly(A) tail (PubMed:21070968). Has no activity towards a cap structure lacking an RNA moiety (PubMed:21070968). Blocks autophagy in nutrient-rich conditions by repressing the expression of ATG-related genes through degration of their transcripts (PubMed:26098573).<ref>PMID:12218187</ref> <ref>PMID:12417715</ref> <ref>PMID:12486012</ref> <ref>PMID:12923261</ref> <ref>PMID:14527413</ref> <ref>PMID:18172165</ref> <ref>PMID:21070968</ref> <ref>PMID:26098573</ref>
+== References ==
+<references/>
+__TOC__
+</StructureSection>
+[[Category: Large Structures]]
+[[Category: Arrowsmith, C H]]
+[[Category: Bountra, C]]
+[[Category: Brandao-Neto, J]]
+[[Category: Burgess-Brown, N]]
+[[Category: Collins, P M]]
+[[Category: Delft, F von]]
+[[Category: Douangamath, A]]
 [[Category: Huber, K]]
-[[Category: Nelson, E.R]]
+[[Category: Krojer, T]]
-[[Category: Arrowsmith, C.H]]
+[[Category: Nelson, E R]]
-[[Category: Burgess-Brown, N]]
-[[Category: Brandao-Neto, J]]
 [[Category: Talon, R]]
-[[Category: Collins, P.M]]
-[[Category: Douangamath, A]]
 [[Category: Velupillai, S]]
-[[Category: Krojer, T]]
 [[Category: Wang, D]]
-[[Category: Von Delft, F]]
+[[Category: Hydrolase]]
-[[Category: Bountra, C]]
+[[Category: Pandda]]
+[[Category: Sgc - diamond i04-1 fragment screening]]
+[[Category: Xchemexplorer]]

5qpc: Difference between revisions

Revision as of 11:13, 10 May 2019

Crystal Structure of DCP2 (NUDT20) after initial refinement with no ligand modelled (structure $n)

Structural highlights

Function

References

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