4lvy: Difference between revisions

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==Structure of the THF riboswitch bound to pemetrexed==
==Structure of the THF riboswitch bound to pemetrexed==
<StructureSection load='4lvy' size='340' side='right' caption='[[4lvy]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
<StructureSection load='4lvy' size='340' side='right'caption='[[4lvy]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[4lvy]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4LVY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4LVY FirstGlance]. <br>
<table><tr><td colspan='2'>[[4lvy]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Streptococcus_mutans Streptococcus mutans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4LVY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4LVY FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=LYA:2-{4-[2-(2-AMINO-4-OXO-4,7-DIHYDRO-3H-PYRROLO[2,3-D]PYRIMIDIN-5-YL)-ETHYL]-BENZOYLAMINO}-PENTANEDIOIC+ACID'>LYA</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]] 2&#8491;</td></tr>
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3sd3|3sd3]], [[4lvv|4lvv]], [[4lvw|4lvw]], [[4lvz|4lvz]], [[4lw0|4lw0]]</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=LYA:2-{4-[2-(2-AMINO-4-OXO-4,7-DIHYDRO-3H-PYRROLO[2,3-D]PYRIMIDIN-5-YL)-ETHYL]-BENZOYLAMINO}-PENTANEDIOIC+ACID'>LYA</scene></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=4lvy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4lvy OCA], [http://pdbe.org/4lvy PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4lvy RCSB], [http://www.ebi.ac.uk/pdbsum/4lvy PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4lvy ProSAT]</span></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=4lvy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4lvy OCA], [https://pdbe.org/4lvy PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4lvy RCSB], [https://www.ebi.ac.uk/pdbsum/4lvy PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4lvy ProSAT]</span></td></tr>
</table>
</table>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
The tetrahydrofolate (THF) riboswitch regulates folate transport and metabolism in a number of Firmicutes by cooperatively binding two molecules of THF. To further understand this riboswitch's specificity for THF, binding and regulatory activity of a series of THF analogs and antifolates were examined. Our data reveal that although binding is dominated by the RNA's interactions with the pterin moiety, the para-aminobenzoic acid (pABA) moiety plays a significant role in transcriptional regulation. Further, we find that adenine and several other analogs bind with high affinity by an alternative binding mechanism. Despite a similar affinity to THF, adenine is a poor regulator of transcriptional attenuation. These results demonstrate that binding alone does not determine a compound's effectiveness in regulating the activity of the riboswitch-a complication in current efforts to develop antimicrobials that target these RNAs.
A Disconnect between High-Affinity Binding and Efficient Regulation by Antifolates and Purines in the Tetrahydrofolate Riboswitch.,Trausch JJ, Batey RT Chem Biol. 2014 Feb 20;21(2):205-16. doi: 10.1016/j.chembiol.2013.11.012. Epub, 2014 Jan 2. PMID:24388757<ref>PMID:24388757</ref>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 4lvy" style="background-color:#fffaf0;"></div>


==See Also==
==See Also==
*[[Riboswitch|Riboswitch]]
*[[Riboswitch 3D structures|Riboswitch 3D structures]]
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Batey, R T]]
[[Category: Large Structures]]
[[Category: Trausch, J J]]
[[Category: Streptococcus mutans]]
[[Category: Aptamer]]
[[Category: Batey RT]]
[[Category: Bacillus subtili]]
[[Category: Trausch JJ]]
[[Category: Bacterial]]
[[Category: Bacterial protein]]
[[Category: Base sequence]]
[[Category: Binding site]]
[[Category: Calorimetry]]
[[Category: Folic acid]]
[[Category: Gene expression regulation]]
[[Category: Genetic]]
[[Category: Guanine]]
[[Category: Leucovorin]]
[[Category: Ligand]]
[[Category: Magnesium]]
[[Category: Molecular sequence data]]
[[Category: Mrna]]
[[Category: Ncrna]]
[[Category: Nucleic acid conformation]]
[[Category: Nucleotide]]
[[Category: Pemetrexed binding]]
[[Category: Point mutation]]
[[Category: Protein binding]]
[[Category: Protein structure]]
[[Category: Pseudoknot]]
[[Category: Regulation]]
[[Category: Riboswitch]]
[[Category: Rna]]
[[Category: S-adenosylmethionine]]
[[Category: Secondary]]
[[Category: Streptococcus mutan]]
[[Category: Terminator region]]
[[Category: Tetrahydrofolate]]
[[Category: Thermodynamic]]
[[Category: Three-way junction]]
[[Category: Transcription]]

Latest revision as of 15:22, 1 March 2024

Structure of the THF riboswitch bound to pemetrexedStructure of the THF riboswitch bound to pemetrexed

Structural highlights

4lvy is a 1 chain structure with sequence from Streptococcus mutans. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 2Å
Ligands:
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

See Also

4lvy, resolution 2.00Å

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