6ro1

From Proteopedia

(Difference between revisions)

Revision as of 17:34, 14 August 2019

X-ray crystal structure of the MTR4 NVL complex

Structural highlights

6ro1 is a 2 chain structure with sequence from Human. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:	, ,
Gene:	MTREX, DOB1, KIAA0052, MTR4, SKIV2L2 (HUMAN), NVL, NVL2 (HUMAN)
Activity:	RNA helicase, with EC number 3.6.4.13
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[MTREX_HUMAN] Component of exosome targeting complexes. Subunit of the trimeric nuclear exosome targeting (NEXT) complex, a complex that directs a subset of non-coding short-lived RNAs for exosomal degradation. Subunit of the trimeric poly(A) tail exosome targeting (PAXT) complex, a complex that directs a subset of long and polyadenylated poly(A) RNAs for exosomal degradation. The RNA exosome is fundamental for the degradation of RNA in eukaryotic nuclei. Substrate targeting is facilitated by its cofactor MTREX, which links to RNA-binding protein adapters (PubMed:27871484). May be involved in pre-mRNA splicing. Associated with the RNA exosome complex and involved in the 3'-processing of the 7S pre-RNA to the mature 5.8S rRNA.^[1] ^[2] [NVL_HUMAN] Participates in the assembly of the telomerase holoenzyme and effecting of telomerase activity via its interaction with TERT (PubMed:22226966). Involved in both early and late stages of the pre-rRNA processing pathways (PubMed:26166824). Spatiotemporally regulates 60S ribosomal subunit biogenesis in the nucleolus (PubMed:15469983, PubMed:16782053, PubMed:29107693, PubMed:26456651). Catalyzes the release of specific assembly factors, such as WDR74, from pre-60S ribosomal particles through the ATPase activity (PubMed:29107693, PubMed:26456651, PubMed:28416111).^[3] ^[4] ^[5] ^[6] ^[7] ^[8] ^[9]

Publication Abstract from PubMed

The nuclear exosome and its essential co-factor, the RNA helicase MTR4, play crucial roles in several RNA degradation pathways. Besides unwinding RNA substrates for exosome-mediated degradation, MTR4 associates with RNA-binding proteins that function as adaptors in different RNA processing and decay pathways. Here, we identify and characterize the interactions of human MTR4 with a ribosome processing adaptor, NVL, and with ZCCHC8, an adaptor involved in the decay of small nuclear RNAs. We show that the unstructured regions of NVL and ZCCHC8 contain short linear motifs that bind the MTR4 arch domain in a mutually exclusive manner. These short sequences diverged from the arch-interacting motif (AIM) of yeast rRNA processing factors. Our results suggest that nuclear exosome adaptors have evolved canonical and non-canonical AIM sequences to target human MTR4 and demonstrate the versatility and specificity with which the MTR4 arch domain can recruit a repertoire of different RNA-binding proteins.

The MTR4 helicase recruits nuclear adaptors of the human RNA exosome using distinct arch-interacting motifs.,Lingaraju M, Johnsen D, Schlundt A, Langer LM, Basquin J, Sattler M, Heick Jensen T, Falk S, Conti E Nat Commun. 2019 Jul 29;10(1):3393. doi: 10.1038/s41467-019-11339-x. PMID:31358741^[10]

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

References

↑ Schilders G, van Dijk E, Pruijn GJ. C1D and hMtr4p associate with the human exosome subunit PM/Scl-100 and are involved in pre-rRNA processing. Nucleic Acids Res. 2007;35(8):2564-72. Epub 2007 Apr 4. PMID:17412707 doi:http://dx.doi.org/10.1093/nar/gkm082
↑ Meola N, Domanski M, Karadoulama E, Chen Y, Gentil C, Pultz D, Vitting-Seerup K, Lykke-Andersen S, Andersen JS, Sandelin A, Jensen TH. Identification of a Nuclear Exosome Decay Pathway for Processed Transcripts. Mol Cell. 2016 Nov 3;64(3):520-533. doi: 10.1016/j.molcel.2016.09.025. Epub 2016 , Oct 27. PMID:27871484 doi:http://dx.doi.org/10.1016/j.molcel.2016.09.025
↑ Nagahama M, Hara Y, Seki A, Yamazoe T, Kawate Y, Shinohara T, Hatsuzawa K, Tani K, Tagaya M. NVL2 is a nucleolar AAA-ATPase that interacts with ribosomal protein L5 through its nucleolar localization sequence. Mol Biol Cell. 2004 Dec;15(12):5712-23. doi: 10.1091/mbc.e04-08-0692. Epub 2004, Oct 6. PMID:15469983 doi:http://dx.doi.org/10.1091/mbc.e04-08-0692
↑ Nagahama M, Yamazoe T, Hara Y, Tani K, Tsuji A, Tagaya M. The AAA-ATPase NVL2 is a component of pre-ribosomal particles that interacts with the DExD/H-box RNA helicase DOB1. Biochem Biophys Res Commun. 2006 Aug 4;346(3):1075-82. doi:, 10.1016/j.bbrc.2006.06.017. Epub 2006 Jun 12. PMID:16782053 doi:http://dx.doi.org/10.1016/j.bbrc.2006.06.017
↑ Her J, Chung IK. The AAA-ATPase NVL2 is a telomerase component essential for holoenzyme assembly. Biochem Biophys Res Commun. 2012 Jan 20;417(3):1086-92. doi:, 10.1016/j.bbrc.2011.12.101. Epub 2011 Dec 27. PMID:22226966 doi:http://dx.doi.org/10.1016/j.bbrc.2011.12.101
↑ Yoshikatsu Y, Ishida Y, Sudo H, Yuasa K, Tsuji A, Nagahama M. NVL2, a nucleolar AAA-ATPase, is associated with the nuclear exosome and is involved in pre-rRNA processing. Biochem Biophys Res Commun. 2015 Aug 28;464(3):780-6. doi:, 10.1016/j.bbrc.2015.07.032. Epub 2015 Jul 10. PMID:26166824 doi:http://dx.doi.org/10.1016/j.bbrc.2015.07.032
↑ Hiraishi N, Ishida Y, Nagahama M. AAA-ATPase NVL2 acts on MTR4-exosome complex to dissociate the nucleolar protein WDR74. Biochem Biophys Res Commun. 2015 Nov 20;467(3):534-40. doi:, 10.1016/j.bbrc.2015.09.160. Epub 2015 Oct 8. PMID:26456651 doi:http://dx.doi.org/10.1016/j.bbrc.2015.09.160
↑ Lo YH, Romes EM, Pillon MC, Sobhany M, Stanley RE. Structural Analysis Reveals Features of Ribosome Assembly Factor Nsa1/WDR74 Important for Localization and Interaction with Rix7/NVL2. Structure. 2017 May 2;25(5):762-772.e4. doi: 10.1016/j.str.2017.03.008. Epub 2017, Apr 13. PMID:28416111 doi:http://dx.doi.org/10.1016/j.str.2017.03.008
↑ Hiraishi N, Ishida YI, Sudo H, Nagahama M. WDR74 participates in an early cleavage of the pre-rRNA processing pathway in cooperation with the nucleolar AAA-ATPase NVL2. Biochem Biophys Res Commun. 2018 Jan 1;495(1):116-123. doi:, 10.1016/j.bbrc.2017.10.148. Epub 2017 Oct 28. PMID:29107693 doi:http://dx.doi.org/10.1016/j.bbrc.2017.10.148
↑ Lingaraju M, Johnsen D, Schlundt A, Langer LM, Basquin J, Sattler M, Heick Jensen T, Falk S, Conti E. The MTR4 helicase recruits nuclear adaptors of the human RNA exosome using distinct arch-interacting motifs. Nat Commun. 2019 Jul 29;10(1):3393. doi: 10.1038/s41467-019-11339-x. PMID:31358741 doi:http://dx.doi.org/10.1038/s41467-019-11339-x

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

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/6ro1"

@@ Line 3: / Line 3: @@
 <StructureSection load='6ro1' size='340' side='right'caption='[[6ro1]], [[Resolution|resolution]] 3.07&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[6ro1]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6RO1 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6RO1 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[6ro1]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6RO1 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6RO1 FirstGlance]. <br>
 </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
+<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">MTREX, DOB1, KIAA0052, MTR4, SKIV2L2 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN]), NVL, NVL2 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</td></tr>
 <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/RNA_helicase RNA helicase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.6.4.13 3.6.4.13] </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=6ro1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ro1 OCA], [http://pdbe.org/6ro1 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6ro1 RCSB], [http://www.ebi.ac.uk/pdbsum/6ro1 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6ro1 ProSAT]</span></td></tr>
@@ Line 10: / Line 11: @@
 == Function ==
 [[http://www.uniprot.org/uniprot/MTREX_HUMAN MTREX_HUMAN]] Component of exosome targeting complexes. Subunit of the trimeric nuclear exosome targeting (NEXT) complex, a complex that directs a subset of non-coding short-lived RNAs for exosomal degradation. Subunit of the trimeric poly(A) tail exosome targeting (PAXT) complex, a complex that directs a subset of long and polyadenylated poly(A) RNAs for exosomal degradation. The RNA exosome is fundamental for the degradation of RNA in eukaryotic nuclei. Substrate targeting is facilitated by its cofactor MTREX, which links to RNA-binding protein adapters (PubMed:27871484). May be involved in pre-mRNA splicing. Associated with the RNA exosome complex and involved in the 3'-processing of the 7S pre-RNA to the mature 5.8S rRNA.<ref>PMID:17412707</ref> <ref>PMID:27871484</ref>  [[http://www.uniprot.org/uniprot/NVL_HUMAN NVL_HUMAN]] Participates in the assembly of the telomerase holoenzyme and effecting of telomerase activity via its interaction with TERT (PubMed:22226966). Involved in both early and late stages of the pre-rRNA processing pathways (PubMed:26166824). Spatiotemporally regulates 60S ribosomal subunit biogenesis in the nucleolus (PubMed:15469983, PubMed:16782053, PubMed:29107693, PubMed:26456651). Catalyzes the release of specific assembly factors, such as WDR74, from pre-60S ribosomal particles through the ATPase activity (PubMed:29107693, PubMed:26456651, PubMed:28416111).<ref>PMID:15469983</ref> <ref>PMID:16782053</ref> <ref>PMID:22226966</ref> <ref>PMID:26166824</ref> <ref>PMID:26456651</ref> <ref>PMID:28416111</ref> <ref>PMID:29107693</ref>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+The nuclear exosome and its essential co-factor, the RNA helicase MTR4, play crucial roles in several RNA degradation pathways. Besides unwinding RNA substrates for exosome-mediated degradation, MTR4 associates with RNA-binding proteins that function as adaptors in different RNA processing and decay pathways. Here, we identify and characterize the interactions of human MTR4 with a ribosome processing adaptor, NVL, and with ZCCHC8, an adaptor involved in the decay of small nuclear RNAs. We show that the unstructured regions of NVL and ZCCHC8 contain short linear motifs that bind the MTR4 arch domain in a mutually exclusive manner. These short sequences diverged from the arch-interacting motif (AIM) of yeast rRNA processing factors. Our results suggest that nuclear exosome adaptors have evolved canonical and non-canonical AIM sequences to target human MTR4 and demonstrate the versatility and specificity with which the MTR4 arch domain can recruit a repertoire of different RNA-binding proteins.
+The MTR4 helicase recruits nuclear adaptors of the human RNA exosome using distinct arch-interacting motifs.,Lingaraju M, Johnsen D, Schlundt A, Langer LM, Basquin J, Sattler M, Heick Jensen T, Falk S, Conti E Nat Commun. 2019 Jul 29;10(1):3393. doi: 10.1038/s41467-019-11339-x. PMID:31358741<ref>PMID:31358741</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 6ro1" style="background-color:#fffaf0;"></div>
+==See Also==
+*[[Helicase 3D structures|Helicase 3D structures]]
 == References ==
 <references/>
 __TOC__
 </StructureSection>
+[[Category: Human]]
 [[Category: Large Structures]]
 [[Category: RNA helicase]]

6ro1

From Proteopedia

Revision as of 17:34, 14 August 2019

X-ray crystal structure of the MTR4 NVL complex

Structural highlights

Function

Publication Abstract from PubMed

See Also

References

Contents

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