This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.

Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.

2xnq

From Proteopedia

(Difference between revisions)

Jump to: navigation, search

Revision as of 12:14, 22 July 2020

Structural insights into cis element recognition of non- polyadenylated RNAs by the Nab3-RRM

Structural highlights

2xnq is a 1 chain structure with sequence from Atcc 18824. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:
NonStd Res:
Related:	2xnr
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]

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

Publication Abstract from PubMed

Transcription termination of non-polyadenylated RNAs in Saccharomyces cerevisiae occurs through the action of the Nrd1-Nab3-Sen1 complex. Part of the decision to terminate via this pathway occurs via direct recognition of sequences within the nascent transcript by RNA recognition motifs (RRMs) within Nrd1 and Nab3. Here we present the 1.6 A structure of Nab3-RRM bound to its UCUU recognition sequence. The crystal structure reveals clear density for a UCU trinucleotide and a fourth putative U binding site. Nab3-RRM establishes a clear preference for the central cytidine of the UCUU motif, which forms pseudo-base pairing interactions primarily through hydrogen bonds to main chain atoms and one serine hydroxyl group. Specificity for the flanking uridines is less defined; however, binding experiments confirm that these residues are also important for high affinity binding. Comparison of the Nab3-RRM to other structures of RRMs bound to polypyrimidine RNAs showed that this mode of recognition is similar to what is observed for the polypyrimidine-tract binding RRMs, and that the serine residue involved in pseudo-base pairing is only found in RRMs that bind to polypyrimidine RNAs that contain a cytosine base, suggesting a possible mechanism for discriminating between cytosine and uracil bases in RRMs that bind to polypyrimidine-containing RNA.

Structural insights into cis element recognition of non-polyadenylated RNAs by the Nab3-RRM.,Lunde BM, Horner M, Meinhart A Nucleic Acids Res. 2010 Aug 30. PMID:20805243^[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
↑ Lunde BM, Horner M, Meinhart A. Structural insights into cis element recognition of non-polyadenylated RNAs by the Nab3-RRM. Nucleic Acids Res. 2010 Aug 30. PMID:20805243 doi:10.1093/nar/gkq751

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

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/2xnq"

@@ Line 1: / Line 1: @@
 ==Structural insights into cis element recognition of non- polyadenylated RNAs by the Nab3-RRM==
-<StructureSection load='2xnq' size='340' side='right' caption='[[2xnq]], [[Resolution|resolution]] 1.30&Aring;' scene=''>
+<StructureSection load='2xnq' size='340' side='right'caption='[[2xnq]], [[Resolution|resolution]] 1.30&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2xnq]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_18824 Atcc 18824]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2XNQ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2XNQ FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2xnq]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_18824 Atcc 18824]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2XNQ OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=2XNQ FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene></td></tr>
+</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene></td></tr>
 <tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CAF:S-DIMETHYLARSINOYL-CYSTEINE'>CAF</scene></td></tr>
 <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[2xnr|2xnr]]</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=2xnq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2xnq OCA], [http://pdbe.org/2xnq PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2xnq RCSB], [http://www.ebi.ac.uk/pdbsum/2xnq PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2xnq ProSAT]</span></td></tr>
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=2xnq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2xnq OCA], [http://pdbe.org/2xnq PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2xnq RCSB], [http://www.ebi.ac.uk/pdbsum/2xnq PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2xnq ProSAT]</span></td></tr>
 </table>
 == Function ==
@@ Line 30: / Line 30: @@
 </div>
 <div class="pdbe-citations 2xnq" style="background-color:#fffaf0;"></div>
+==See Also==
+*[[Nuclear polyadenylated RNA-binding protein|Nuclear polyadenylated RNA-binding protein]]
 == References ==
 <references/>
@@ Line 35: / Line 38: @@
 </StructureSection>
 [[Category: Atcc 18824]]
+[[Category: Large Structures]]
 [[Category: Horner, M]]
 [[Category: Lunde, B M]]

2xnq

From Proteopedia

Revision as of 12:14, 22 July 2020

Structural insights into cis element recognition of non- polyadenylated RNAs by the Nab3-RRM

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

Personal tools

Navigation

Search

Toolbox