2l41: Difference between revisions

Revision as of 08:17, 18 January 2023

Nab3 RRM - UCUU complex

Structural highlights

2l41 is a 2 chain structure with sequence from Saccharomyces cerevisiae. Full experimental information is available from OCA. For a guided tour on the structure components use FirstGlance.
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

NAB3_YEAST May be required for packaging pre-mRNAs into ribonucleoprotein structures amenable to efficient nuclear RNA processing. Binds to poly(A)+ RNA. Appears to act in the maintenance of CLN3 mRNA levels.^[1]

Publication Abstract from PubMed

Non-coding RNA polymerase II transcripts are processed by the poly(A)-independent termination pathway that requires the Nrd1 complex. The Nrd1 complex includes two RNA-binding proteins, the nuclear polyadenylated RNA-binding (Nab) 3 and the nuclear pre-mRNA down-regulation (Nrd) 1 that bind their specific termination elements. Here we report the solution structure of the RNA-recognition motif (RRM) of Nab3 in complex with a UCUU oligonucleotide, representing the Nab3 termination element. The structure shows that the first three nucleotides of UCUU are accommodated on the beta-sheet surface of Nab3 RRM, but reveals a sequence-specific recognition only for the central cytidine and uridine. The specific contacts we identified are important for binding affinity in vitro as well as for yeast viability. Furthermore, we show that both RNA-binding motifs of Nab3 and Nrd1 alone bind their termination elements with a weak affinity. Interestingly, when Nab3 and Nrd1 form a heterodimer, the affinity to RNA is significantly increased due to the cooperative binding. These findings are in accordance with the model of their function in the poly(A) independent termination, in which binding to the combined and/or repetitive termination elements elicits efficient termination.

Recognition of transcription termination signal by the nuclear polyadenylated RNA-binding (NAB) 3 protein.,Hobor F, Pergoli R, Kubicek K, Hrossova D, Bacikova V, Zimmermann M, Pasulka J, Hofr C, Vanacova S, Stefl R J Biol Chem. 2011 Feb 4;286(5):3645-57. Epub 2010 Nov 17. PMID:21084293^[2]

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

References

↑ Sugimoto K, Matsumoto K, Kornberg RD, Reed SI, Wittenberg C. Dosage suppressors of the dominant G1 cyclin mutant CLN3-2: identification of a yeast gene encoding a putative RNA/ssDNA binding protein. Mol Gen Genet. 1995 Oct 25;248(6):712-8. PMID:7476874
↑ Hobor F, Pergoli R, Kubicek K, Hrossova D, Bacikova V, Zimmermann M, Pasulka J, Hofr C, Vanacova S, Stefl R. Recognition of transcription termination signal by the nuclear polyadenylated RNA-binding (NAB) 3 protein. J Biol Chem. 2011 Feb 4;286(5):3645-57. Epub 2010 Nov 17. PMID:21084293 doi:10.1074/jbc.M110.158774

Proteopedia Page Contributors and Editors (what is this?)

OCA

[1] Sugimoto K, Matsumoto K, Kornberg RD, Reed SI, Wittenberg C. Dosage suppressors of the dominant G1 cyclin mutant CLN3-2: identification of a yeast gene encoding a putative RNA/ssDNA binding protein. Mol Gen Genet. 1995 Oct 25;248(6):712-8. PMID:7476874

[2] Hobor F, Pergoli R, Kubicek K, Hrossova D, Bacikova V, Zimmermann M, Pasulka J, Hofr C, Vanacova S, Stefl R. Recognition of transcription termination signal by the nuclear polyadenylated RNA-binding (NAB) 3 protein. J Biol Chem. 2011 Feb 4;286(5):3645-57. Epub 2010 Nov 17. PMID:21084293 doi:10.1074/jbc.M110.158774

[1]

[2]

@@ Line 1: / Line 1: @@
 ==Nab3 RRM - UCUU complex==
-<StructureSection load='2l41' size='340' side='right'caption='[[2l41]], [[NMR_Ensembles_of_Models | 20 NMR models]]' scene=''>
+<StructureSection load='2l41' size='340' side='right'caption='[[2l41]]' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2l41]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Atcc_18824 Atcc 18824]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2L41 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2L41 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2l41]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2L41 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2L41 FirstGlance]. <br>
-</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2kvi|2kvi]]</div></td></tr>
+</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=2l41 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2l41 OCA], [https://pdbe.org/2l41 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2l41 RCSB], [https://www.ebi.ac.uk/pdbsum/2l41 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2l41 ProSAT]</span></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">NAB3 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 ATCC 18824])</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=2l41 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2l41 OCA], [https://pdbe.org/2l41 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2l41 RCSB], [https://www.ebi.ac.uk/pdbsum/2l41 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2l41 ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[https://www.uniprot.org/uniprot/NAB3_YEAST NAB3_YEAST]] May be required for packaging pre-mRNAs into ribonucleoprotein structures amenable to efficient nuclear RNA processing. Binds to poly(A)+ RNA. Appears to act in the maintenance of CLN3 mRNA levels.<ref>PMID:7476874</ref>
+[https://www.uniprot.org/uniprot/NAB3_YEAST NAB3_YEAST] May be required for packaging pre-mRNAs into ribonucleoprotein structures amenable to efficient nuclear RNA processing. Binds to poly(A)+ RNA. Appears to act in the maintenance of CLN3 mRNA levels.<ref>PMID:7476874</ref>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 23: / Line 21: @@
 __TOC__
 </StructureSection>
-[[Category: Atcc 18824]]
 [[Category: Large Structures]]
-[[Category: Hobor, F]]
+[[Category: Saccharomyces cerevisiae]]
-[[Category: Hofr, C]]
+[[Category: Hobor F]]
-[[Category: Kubicek, K]]
+[[Category: Hofr C]]
-[[Category: Pasulka, J]]
+[[Category: Kubicek K]]
-[[Category: Pergoli, R]]
+[[Category: Pasulka J]]
-[[Category: Stefl, R]]
+[[Category: Pergoli R]]
-[[Category: Zimmermann, M]]
+[[Category: Stefl R]]
-[[Category: Nab3 rrm]]
+[[Category: Zimmermann M]]
-[[Category: Rna binding protein-rna complex]]
-[[Category: Ucuu oligonucleotide]]

2l41: Difference between revisions

Revision as of 08:17, 18 January 2023

Nab3 RRM - UCUU complex

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Navigation menu

Page actions

Page actions

Personal tools

Navigation

Search

Tools