4yb1

From Proteopedia

(Difference between revisions)

Revision as of 14:20, 27 April 2017

20A Mutant c-di-GMP Vc2 Riboswitch bound with 3',3'-cGAMP

Structural highlights

4yb1 is a 2 chain structure. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:	,
Related:	4yaz, 4yb0
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

Cyclic dinucleotides are second messengers that target the adaptor STING and stimulate the innate immune response in mammals. Besides protein receptors, there are bacterial riboswitches that selectively recognize cyclic dinucleotides. We recently discovered a natural riboswitch that targets 3',3'-cGAMP, which is distinguished from the endogenous mammalian signal 2',3'-cGAMP by its backbone connectivity. Here, we report on structures of the aptamer domain of the 3',3'-cGAMP riboswitch from Geobacter in the 3',3'-cGAMP and c-di-GMP bound states. The riboswitch adopts a tuning fork-like architecture with a junctional ligand-binding pocket and different orientations of the arms are correlated with the identity of the bound cyclic dinucleotide. Subsequent biochemical experiments revealed that specificity of ligand recognition can be affected by point mutations outside of the binding pocket, which has implications for both the assignment and reengineering of riboswitches in this structural class.

Structural Basis for Molecular Discrimination by a 3',3'-cGAMP Sensing Riboswitch.,Ren A, Wang XC, Kellenberger CA, Rajashankar KR, Jones RA, Hammond MC, Patel DJ Cell Rep. 2015 Apr 7;11(1):1-12. doi: 10.1016/j.celrep.2015.03.004. Epub 2015 Mar, 26. PMID:25818298^[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, Wang XC, Kellenberger CA, Rajashankar KR, Jones RA, Hammond MC, Patel DJ. Structural Basis for Molecular Discrimination by a 3',3'-cGAMP Sensing Riboswitch. Cell Rep. 2015 Apr 7;11(1):1-12. doi: 10.1016/j.celrep.2015.03.004. Epub 2015 Mar, 26. PMID:25818298 doi:http://dx.doi.org/10.1016/j.celrep.2015.03.004

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

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/4yb1"

@@ Line 1: / Line 1: @@
 ==20A Mutant c-di-GMP Vc2 Riboswitch bound with 3',3'-cGAMP==
 <StructureSection load='4yb1' size='340' side='right' caption='[[4yb1]], [[Resolution|resolution]] 2.08&Aring;' scene=''>
@@ Line 5: / Line 6: @@
 </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=4BW:2-AMINO-9-[(2R,3R,3AS,5R,7AR,9R,10R,10AS,12R,14AR)-9-(6-AMINO-9H-PURIN-9-YL)-3,5,10,12-TETRAHYDROXY-5,12-DIOXIDOOCTAHYDRO-2H,7H-DIFURO[3,2-D 3,2-J][1,3,7,9,2,8]TETRAOXADIPHOSPHACYCLODODECIN-2-YL]-1,9-DIHYDRO-6H-PURIN-6-ONE'>4BW</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
 <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4yaz|4yaz]], [[4yb0|4yb0]]</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=4yb1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4yb1 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4yb1 RCSB], [http://www.ebi.ac.uk/pdbsum/4yb1 PDBsum]</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=4yb1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4yb1 OCA], [http://pdbe.org/4yb1 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4yb1 RCSB], [http://www.ebi.ac.uk/pdbsum/4yb1 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4yb1 ProSAT]</span></td></tr>
 </table>
 == Function ==
@@ Line 17: / Line 18: @@
 From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 </div>
+<div class="pdbe-citations 4yb1" style="background-color:#fffaf0;"></div>
 == References ==
 <references/>

4yb1

From Proteopedia

Revision as of 14:20, 27 April 2017

20A Mutant c-di-GMP Vc2 Riboswitch bound with 3',3'-cGAMP

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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