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5ddq

From Proteopedia

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Revision as of 10:31, 21 June 2023

L-glutamine riboswitch bound with L-glutamine soaked with Mn2+

Structural highlights

5ddq is a 4 chain structure with sequence from Homo sapiens and Synechococcus elongatus. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:	, , ,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

SNRPA_HUMAN Binds stem loop II of U1 snRNA. It is the first snRNP to interact with pre-mRNA. This interaction is required for the subsequent binding of U2 snRNP and the U4/U6/U5 tri-snRNP. In a snRNP-free form (SF-A) may be involved in coupled pre-mRNA splicing and polyadenylation process. Binds preferentially to the 5'-UGCAC-3' motif in vitro.^[1]

Publication Abstract from PubMed

Naturally occurring L-glutamine riboswitches occur in cyanobacteria and marine metagenomes, where they reside upstream of genes involved in nitrogen metabolism. By combining X-ray, NMR, and MD, we characterized an L-glutamine-dependent conformational transition in the Synechococcus elongatus glutamine riboswitch from tuning fork to L-shaped alignment of stem segments. This transition generates an open ligand-binding pocket with L-glutamine selectivity enforced by Mg(2+)-mediated intermolecular interactions. The transition also stabilizes the P1 helix through a long-range "linchpin" Watson-Crick G-C pair-capping interaction, while melting a short helix below P1 potentially capable of modulating downstream readout. NMR data establish that the ligand-free glutamine riboswitch in Mg(2+) solution exists in a slow equilibrium between flexible tuning fork and a minor conformation, similar, but not identical, to the L-shaped bound conformation. We propose that an open ligand-binding pocket combined with a high conformational penalty for forming the ligand-bound state provide mechanisms for reducing binding affinity while retaining high selectivity.

Structural and Dynamic Basis for Low-Affinity, High-Selectivity Binding of L-Glutamine by the Glutamine Riboswitch.,Ren A, Xue Y, Peselis A, Serganov A, Al-Hashimi HM, Patel DJ Cell Rep. 2015 Dec 1;13(9):1800-13. doi: 10.1016/j.celrep.2015.10.062. Epub 2015 , Nov 19. PMID:26655897^[2]

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

References

↑ Lutz CS, Cooke C, O'Connor JP, Kobayashi R, Alwine JC. The snRNP-free U1A (SF-A) complex(es): identification of the largest subunit as PSF, the polypyrimidine-tract binding protein-associated splicing factor. RNA. 1998 Dec;4(12):1493-9. PMID:9848648
↑ Ren A, Xue Y, Peselis A, Serganov A, Al-Hashimi HM, Patel DJ. Structural and Dynamic Basis for Low-Affinity, High-Selectivity Binding of L-Glutamine by the Glutamine Riboswitch. Cell Rep. 2015 Dec 1;13(9):1800-13. doi: 10.1016/j.celrep.2015.10.062. Epub 2015 , Nov 19. PMID:26655897 doi:http://dx.doi.org/10.1016/j.celrep.2015.10.062

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/5ddq"

Categories: Homo sapiens | Large Structures | Synechococcus elongatus | Patel DJ | Ren A

@@ Line 3: / Line 3: @@
 <StructureSection load='5ddq' size='340' side='right'caption='[[5ddq]], [[Resolution|resolution]] 2.40&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[5ddq]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human] and [http://en.wikipedia.org/wiki/Synechococcus_elongatus Synechococcus elongatus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5DDQ OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5DDQ FirstGlance]. <br>
+<table><tr><td colspan='2'>[[5ddq]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] and [https://en.wikipedia.org/wiki/Synechococcus_elongatus Synechococcus elongatus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5DDQ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5DDQ FirstGlance]. <br>
 </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GLN:GLUTAMINE'>GLN</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[5ddo|5ddo]], [[5ddp|5ddp]], [[5ddr|5ddr]]</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=5ddq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ddq OCA], [https://pdbe.org/5ddq PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5ddq RCSB], [https://www.ebi.ac.uk/pdbsum/5ddq PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5ddq ProSAT]</span></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">SNRPA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</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=5ddq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ddq OCA], [http://pdbe.org/5ddq PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ddq RCSB], [http://www.ebi.ac.uk/pdbsum/5ddq PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ddq ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/SNRPA_HUMAN SNRPA_HUMAN]] Binds stem loop II of U1 snRNA. It is the first snRNP to interact with pre-mRNA. This interaction is required for the subsequent binding of U2 snRNP and the U4/U6/U5 tri-snRNP. In a snRNP-free form (SF-A) may be involved in coupled pre-mRNA splicing and polyadenylation process. Binds preferentially to the 5'-UGCAC-3' motif in vitro.<ref>PMID:9848648</ref>
+[https://www.uniprot.org/uniprot/SNRPA_HUMAN SNRPA_HUMAN] Binds stem loop II of U1 snRNA. It is the first snRNP to interact with pre-mRNA. This interaction is required for the subsequent binding of U2 snRNP and the U4/U6/U5 tri-snRNP. In a snRNP-free form (SF-A) may be involved in coupled pre-mRNA splicing and polyadenylation process. Binds preferentially to the 5'-UGCAC-3' motif in vitro.<ref>PMID:9848648</ref>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 27: / Line 25: @@
 __TOC__
 </StructureSection>
-[[Category: Human]]
+[[Category: Homo sapiens]]
 [[Category: Large Structures]]
 [[Category: Synechococcus elongatus]]
-[[Category: Patel, D J]]
+[[Category: Patel DJ]]
-[[Category: Ren, A]]
+[[Category: Ren A]]
-[[Category: Bound-form]]
-[[Category: L-glutamine]]
-[[Category: Riboswitch]]
-[[Category: Rna]]
-[[Category: Rna binding protein-rna complex]]

5ddq

From Proteopedia

Revision as of 10:31, 21 June 2023

L-glutamine riboswitch bound with L-glutamine soaked with Mn2+

Structural highlights

Function

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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