2m3d: Difference between revisions

Latest revision as of 05:58, 15 May 2024

NMR structure of the GUCT domain from human DEAD box polypeptide 21

Structural highlights

2m3d is a 1 chain structure with sequence from Homo sapiens. Full experimental information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	Solution NMR
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

DDX21_HUMAN RNA helicase that acts as a sensor of the transcriptional status of both RNA polymerase (Pol) I and II: promotes ribosomal RNA (rRNA) processing and transcription from polymerase II (Pol II) (PubMed:25470060). Binds various RNAs, such as rRNAs, snoRNAs, 7SK and, at lower extent, mRNAs (PubMed:25470060). In the nucleolus, localizes to rDNA locus, where it directly binds rRNAs and snoRNAs, and promotes rRNA transcription, processing and modification. Required for rRNA 2'-O-methylation, possibly by promoting the recruitment of late-acting snoRNAs SNORD56 and SNORD58 with pre-ribosomal complexes (PubMed:25470060, PubMed:25477391). In the nucleoplasm, binds 7SK RNA and is recruited to the promoters of Pol II-transcribed genes: acts by facilitating the release of P-TEFb from inhibitory 7SK snRNP in a manner that is dependent on its helicase activity, thereby promoting transcription of its target genes (PubMed:25470060). Functions as cofactor for JUN-activated transcription: required for phosphorylation of JUN at 'Ser-77' (PubMed:11823437, PubMed:25260534). Can unwind double-stranded RNA (helicase) and can fold or introduce a secondary structure to a single-stranded RNA (foldase) (PubMed:9461305). Involved in rRNA processing (PubMed:14559904, PubMed:18180292).^[1] ^[2] ^[3] ^[4] ^[5] ^[6] ^[7]

References

↑ Westermarck J, Weiss C, Saffrich R, Kast J, Musti AM, Wessely M, Ansorge W, Seraphin B, Wilm M, Valdez BC, Bohmann D. The DEXD/H-box RNA helicase RHII/Gu is a co-factor for c-Jun-activated transcription. EMBO J. 2002 Feb 1;21(3):451-60. PMID:11823437
↑ Henning D, So RB, Jin R, Lau LF, Valdez BC. Silencing of RNA helicase II/Gualpha inhibits mammalian ribosomal RNA production. J Biol Chem. 2003 Dec 26;278(52):52307-14. Epub 2003 Oct 13. PMID:14559904 doi:https://dx.doi.org/10.1074/jbc.M310846200
↑ Holmstrom TH, Mialon A, Kallio M, Nymalm Y, Mannermaa L, Holm T, Johansson H, Black E, Gillespie D, Salminen TA, Langel U, Valdez BC, Westermarck J. c-Jun supports ribosomal RNA processing and nucleolar localization of RNA helicase DDX21. J Biol Chem. 2008 Mar 14;283(11):7046-53. doi: 10.1074/jbc.M709613200. Epub 2008 , Jan 7. PMID:18180292 doi:https://dx.doi.org/10.1074/jbc.M709613200
↑ Zhang Y, Baysac KC, Yee LF, Saporita AJ, Weber JD. Elevated DDX21 regulates c-Jun activity and rRNA processing in human breast cancers. Breast Cancer Res. 2014 Sep 28;16(5):449. doi: 10.1186/s13058-014-0449-z. PMID:25260534 doi:https://dx.doi.org/10.1186/s13058-014-0449-z
↑ Calo E, Flynn RA, Martin L, Spitale RC, Chang HY, Wysocka J. RNA helicase DDX21 coordinates transcription and ribosomal RNA processing. Nature. 2015 Feb 12;518(7538):249-53. doi: 10.1038/nature13923. Epub 2014 Nov 24. PMID:25470060 doi:https://dx.doi.org/10.1038/nature13923
↑ Sloan KE, Leisegang MS, Doebele C, Ramirez AS, Simm S, Safferthal C, Kretschmer J, Schorge T, Markoutsa S, Haag S, Karas M, Ebersberger I, Schleiff E, Watkins NJ, Bohnsack MT. The association of late-acting snoRNPs with human pre-ribosomal complexes requires the RNA helicase DDX21. Nucleic Acids Res. 2015 Jan;43(1):553-64. doi: 10.1093/nar/gku1291. Epub 2014 Dec, 4. PMID:25477391 doi:https://dx.doi.org/10.1093/nar/gku1291
↑ Valdez BC, Henning D, Perumal K, Busch H. RNA-unwinding and RNA-folding activities of RNA helicase II/Gu--two activities in separate domains of the same protein. Eur J Biochem. 1997 Dec 15;250(3):800-7. PMID:9461305

Proteopedia Page Contributors and Editors (what is this?)

OCA

[1] Westermarck J, Weiss C, Saffrich R, Kast J, Musti AM, Wessely M, Ansorge W, Seraphin B, Wilm M, Valdez BC, Bohmann D. The DEXD/H-box RNA helicase RHII/Gu is a co-factor for c-Jun-activated transcription. EMBO J. 2002 Feb 1;21(3):451-60. PMID:11823437

[2] Henning D, So RB, Jin R, Lau LF, Valdez BC. Silencing of RNA helicase II/Gualpha inhibits mammalian ribosomal RNA production. J Biol Chem. 2003 Dec 26;278(52):52307-14. Epub 2003 Oct 13. PMID:14559904 doi:https://dx.doi.org/10.1074/jbc.M310846200

[3] Holmstrom TH, Mialon A, Kallio M, Nymalm Y, Mannermaa L, Holm T, Johansson H, Black E, Gillespie D, Salminen TA, Langel U, Valdez BC, Westermarck J. c-Jun supports ribosomal RNA processing and nucleolar localization of RNA helicase DDX21. J Biol Chem. 2008 Mar 14;283(11):7046-53. doi: 10.1074/jbc.M709613200. Epub 2008 , Jan 7. PMID:18180292 doi:https://dx.doi.org/10.1074/jbc.M709613200

[4] Zhang Y, Baysac KC, Yee LF, Saporita AJ, Weber JD. Elevated DDX21 regulates c-Jun activity and rRNA processing in human breast cancers. Breast Cancer Res. 2014 Sep 28;16(5):449. doi: 10.1186/s13058-014-0449-z. PMID:25260534 doi:https://dx.doi.org/10.1186/s13058-014-0449-z

[5] Calo E, Flynn RA, Martin L, Spitale RC, Chang HY, Wysocka J. RNA helicase DDX21 coordinates transcription and ribosomal RNA processing. Nature. 2015 Feb 12;518(7538):249-53. doi: 10.1038/nature13923. Epub 2014 Nov 24. PMID:25470060 doi:https://dx.doi.org/10.1038/nature13923

[6] Sloan KE, Leisegang MS, Doebele C, Ramirez AS, Simm S, Safferthal C, Kretschmer J, Schorge T, Markoutsa S, Haag S, Karas M, Ebersberger I, Schleiff E, Watkins NJ, Bohnsack MT. The association of late-acting snoRNPs with human pre-ribosomal complexes requires the RNA helicase DDX21. Nucleic Acids Res. 2015 Jan;43(1):553-64. doi: 10.1093/nar/gku1291. Epub 2014 Dec, 4. PMID:25477391 doi:https://dx.doi.org/10.1093/nar/gku1291

[7] Valdez BC, Henning D, Perumal K, Busch H. RNA-unwinding and RNA-folding activities of RNA helicase II/Gu--two activities in separate domains of the same protein. Eur J Biochem. 1997 Dec 15;250(3):800-7. PMID:9461305

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@@ Line 1: / Line 1: @@
-[[Image:2m3d.jpg|left|200px]]
-{{STRUCTURE_2m3d|  PDB=2m3d  |  SCENE=  }}
+==NMR structure of the GUCT domain from human DEAD box polypeptide 21==
+<StructureSection load='2m3d' size='340' side='right'caption='[[2m3d]]' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[2m3d]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2M3D OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2M3D FirstGlance]. <br>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Solution NMR</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=2m3d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2m3d OCA], [https://pdbe.org/2m3d PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2m3d RCSB], [https://www.ebi.ac.uk/pdbsum/2m3d PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2m3d ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/DDX21_HUMAN DDX21_HUMAN] RNA helicase that acts as a sensor of the transcriptional status of both RNA polymerase (Pol) I and II: promotes ribosomal RNA (rRNA) processing and transcription from polymerase II (Pol II) (PubMed:25470060). Binds various RNAs, such as rRNAs, snoRNAs, 7SK and, at lower extent, mRNAs (PubMed:25470060). In the nucleolus, localizes to rDNA locus, where it directly binds rRNAs and snoRNAs, and promotes rRNA transcription, processing and modification. Required for rRNA 2'-O-methylation, possibly by promoting the recruitment of late-acting snoRNAs SNORD56 and SNORD58 with pre-ribosomal complexes (PubMed:25470060, PubMed:25477391). In the nucleoplasm, binds 7SK RNA and is recruited to the promoters of Pol II-transcribed genes: acts by facilitating the release of P-TEFb from inhibitory 7SK snRNP in a manner that is dependent on its helicase activity, thereby promoting transcription of its target genes (PubMed:25470060). Functions as cofactor for JUN-activated transcription: required for phosphorylation of JUN at 'Ser-77' (PubMed:11823437, PubMed:25260534). Can unwind double-stranded RNA (helicase) and can fold or introduce a secondary structure to a single-stranded RNA (foldase) (PubMed:9461305). Involved in rRNA processing (PubMed:14559904, PubMed:18180292).<ref>PMID:11823437</ref> <ref>PMID:14559904</ref> <ref>PMID:18180292</ref> <ref>PMID:25260534</ref> <ref>PMID:25470060</ref> <ref>PMID:25477391</ref> <ref>PMID:9461305</ref>
-===NMR structure of the GUCT domain from human DEAD box polypeptide 21===
+==See Also==
+*[[Helicase 3D structures|Helicase 3D structures]]
+== References ==
-==About this Structure==
+<references/>
-[[2m3d]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2M3D OCA].
+__TOC__
+</StructureSection>
 [[Category: Homo sapiens]]
-[[Category: RNA helicase]]
+[[Category: Large Structures]]
-[[Category: Dutta, S K.]]
+[[Category: Dutta SK]]
-[[Category: Geralt, M.]]
+[[Category: Geralt M]]
-[[Category: JCSG, Joint Center for Structural Genomics.]]
+[[Category: Serrano P]]
-[[Category: Serrano, P.]]
+[[Category: Wuthrich K]]
-[[Category: TCELL, Partnership for T-Cell Biology.]]
-[[Category: Wuthrich, K.]]
-[[Category: Guct domain]]
-[[Category: Hydrolase]]
-[[Category: Rrm fold]]

2m3d: Difference between revisions

Latest revision as of 05:58, 15 May 2024

NMR structure of the GUCT domain from human DEAD box polypeptide 21

Structural highlights

Function

See Also

References

Contents

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