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.


3ud3

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (10:21, 1 March 2024) (edit) (undo)
 
(3 intermediate revisions not shown.)
Line 1: Line 1:
 +
==The C92U mutant c-di-GMP-I riboswitch bound to pGpA==
==The C92U mutant c-di-GMP-I riboswitch bound to pGpA==
-
<StructureSection load='3ud3' size='340' side='right' caption='[[3ud3]], [[Resolution|resolution]] 3.10&Aring;' scene=''>
+
<StructureSection load='3ud3' size='340' side='right'caption='[[3ud3]], [[Resolution|resolution]] 3.10&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
-
<table><tr><td colspan='2'>[[3ud3]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3UD3 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3UD3 FirstGlance]. <br>
+
<table><tr><td colspan='2'>[[3ud3]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] and [https://en.wikipedia.org/wiki/Vibrio_cholerae Vibrio cholerae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3UD3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3UD3 FirstGlance]. <br>
-
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
+
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 3.1&#8491;</td></tr>
-
<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=GTP:GUANOSINE-5-TRIPHOSPHATE'>GTP</scene></td></tr>
+
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GTP:GUANOSINE-5-TRIPHOSPHATE'>GTP</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">[[3ucu|3ucu]], [[3ucz|3ucz]], [[3ud4|3ud4]]</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=3ud3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ud3 OCA], [https://pdbe.org/3ud3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3ud3 RCSB], [https://www.ebi.ac.uk/pdbsum/3ud3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3ud3 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 Homo sapiens])</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=3ud3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ud3 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3ud3 RCSB], [http://www.ebi.ac.uk/pdbsum/3ud3 PDBsum]</span></td></tr>
+
</table>
</table>
-
<div style="background-color:#fffaf0;">
+
== Function ==
-
== Publication Abstract from PubMed ==
+
[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>
-
The cyclic dinucleotide c-di-GMP regulates lifestyle transitions in many bacteria, such as the change from a free motile state to a biofilm-forming community. Riboswitches that bind this second messenger are important downstream targets in this bacterial signaling pathway. The breakdown of c-di-GMP in the cell is accomplished enzymatically and results in the linear dinucleotide pGpG. The c-di-GMP-binding riboswitches must be able to discriminate between their cognate cyclic ligand and linear dinucleotides in order to be selective biological switches. It has been reported that the c-di-GMP-I riboswitch binds c-di-GMP five orders of magnitude better than the linear pGpG, but the cause of this large energetic difference in binding is unknown. Here we report binding data and crystal structures of several linear c-di-GMP analogs in complex with the c-di-GMP-I riboswitch. These data reveal the parameters for phosphate recognition and the structural basis of linear dinucleotide binding to the riboswitch. Additionally, the pH dependence of binding shows that exclusion of pGpG is not due to the additional negative charge on the ligand. These data reveal principles that, along with published work, will contribute to the design of c-di-GMP analogs with properties desirable for use as chemical tools and potential therapeutics.
+
-
 
+
-
Structural and biochemical characterization of linear dinucleotide analogs bound to the c-di-GMP-I aptamer.,Smith KD, Lipchock SV, Strobel SA Biochemistry. 2011 Dec 8. PMID:22148472<ref>PMID:22148472</ref>
+
-
 
+
-
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+
-
</div>
+
==See Also==
==See Also==
-
*[[Nucleoprotein|Nucleoprotein]]
+
*[[Nucleoprotein 3D structures|Nucleoprotein 3D structures]]
 +
*[[Riboswitch 3D structures|Riboswitch 3D structures]]
== References ==
== References ==
<references/>
<references/>
Line 25: Line 19:
</StructureSection>
</StructureSection>
[[Category: Homo sapiens]]
[[Category: Homo sapiens]]
-
[[Category: Smith, K D]]
+
[[Category: Large Structures]]
-
[[Category: Strobel, S A]]
+
[[Category: Vibrio cholerae]]
-
[[Category: Riboswitch]]
+
[[Category: Smith KD]]
-
[[Category: Signaling protein-rna complex]]
+
[[Category: Strobel SA]]

Current revision

The C92U mutant c-di-GMP-I riboswitch bound to pGpA

PDB ID 3ud3

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/3ud3"
Personal tools