5qoz: Difference between revisions

Latest revision as of 10:09, 14 February 2024

PanDDA analysis group deposition -- Crystal Structure of DCP2 (NUDT20) in complex with PB1787571279

Structural highlights

5qoz is a 1 chain structure with sequence from Homo sapiens. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 1.7Å
Ligands:	ACT, DMS, EDO, LFG
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

Proteopedia Page Contributors and Editors (what is this?)

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 5qoz is ON HOLD
+==PanDDA analysis group deposition -- Crystal Structure of DCP2 (NUDT20) in complex with PB1787571279==
+<StructureSection load='5qoz' size='340' side='right'caption='[[5qoz]], [[Resolution|resolution]] 1.70&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., Delft, F.V.
+== Structural highlights ==
+<table><tr><td colspan='2'>[[5qoz]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5QOZ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5QOZ FirstGlance]. <br>
-Description: PanDDA analysis group deposition --Crystal Structure of DCP2 (NUDT20) in complex with PB1787571279
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.7&#8491;</td></tr>
-[[Category: Unreleased Structures]]
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><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=LFG:N-cycloheptyl-5-cyclopropyl-1,3,4-oxadiazol-2-amine'>LFG</scene></td></tr>
-[[Category: Huber, K]]
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=5qoz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5qoz OCA], [https://pdbe.org/5qoz PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5qoz RCSB], [https://www.ebi.ac.uk/pdbsum/5qoz PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5qoz ProSAT]</span></td></tr>
-[[Category: Nelson, E.R]]
+</table>
-[[Category: Arrowsmith, C.H]]
+== Function ==
-[[Category: Burgess-Brown, N]]
+[https://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>
-[[Category: Brandao-Neto, J]]
+== References ==
-[[Category: Talon, R]]
+<references/>
-[[Category: Delft, F.V]]
+__TOC__
-[[Category: Collins, P.M]]
+</StructureSection>
-[[Category: Douangamath, A]]
+[[Category: Homo sapiens]]
-[[Category: Krojer, T]]
+[[Category: Large Structures]]
-[[Category: Velupillai, S]]
+[[Category: Arrowsmith CH]]
-[[Category: Wang, D]]
+[[Category: Bountra C]]
-[[Category: Bountra, C]]
+[[Category: Brandao-Neto J]]
+[[Category: Burgess-Brown N]]
+[[Category: Collins PM]]
+[[Category: Douangamath A]]
+[[Category: Huber K]]
+[[Category: Krojer T]]
+[[Category: Nelson ER]]
+[[Category: Talon R]]
+[[Category: Velupillai S]]
+[[Category: Wang D]]
+[[Category: Von Delft F]]

5qoz: Difference between revisions

Latest revision as of 10:09, 14 February 2024

PanDDA analysis group deposition -- Crystal Structure of DCP2 (NUDT20) in complex with PB1787571279

Structural highlights

Function

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