4erl: Difference between revisions

From Proteopedia
Jump to navigation Jump to search
← Older edit
No edit summary
No edit summary
 
(3 intermediate revisions by the same user not shown)
Line 1: Line 1:
==Crystal structure of the lysine riboswitch bound to a lysine-glycine dipeptide==
==Crystal structure of the lysine riboswitch bound to a lysine-glycine dipeptide==
<StructureSection load='4erl' size='340' side='right' caption='[[4erl]], [[Resolution|resolution]] 3.00&Aring;' scene=''>
<StructureSection load='4erl' size='340' side='right'caption='[[4erl]], [[Resolution|resolution]] 3.00&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[4erl]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Thermotoga_maritima Thermotoga maritima]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4ERL OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4ERL FirstGlance]. <br>
<table><tr><td colspan='2'>[[4erl]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermotoga_maritima Thermotoga maritima]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4ERL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4ERL FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GLY:GLYCINE'>GLY</scene>, <scene name='pdbligand=LYS:LYSINE'>LYS</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&#8491;</td></tr>
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3d0u|3d0u]], [[3d0x|3d0x]], [[4erj|4erj]]</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GLY:GLYCINE'>GLY</scene>, <scene name='pdbligand=LYS:LYSINE'>LYS</scene></td></tr>
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">asd ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2336 Thermotoga maritima])</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=4erl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4erl OCA], [https://pdbe.org/4erl PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4erl RCSB], [https://www.ebi.ac.uk/pdbsum/4erl PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4erl ProSAT]</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=4erl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4erl OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4erl RCSB], [http://www.ebi.ac.uk/pdbsum/4erl PDBsum]</span></td></tr>
</table>
</table>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
A prevalent means of regulating gene expression in bacteria is by riboswitches found within mRNA leader sequences. Like protein repressors, these RNA elements must bind an effector molecule with high specificity against a background of other cellular metabolites of similar chemical structure to elicit the appropriate regulatory response. Current crystal structures of the lysine riboswitch do not provide a complete understanding of selectivity as recognition is substantially mediated through main-chain atoms of the amino acid. Using a directed set of lysine analogs and other amino acids, we have determined the relative contributions of the polar functional groups to binding affinity and the regulatory response. Our results reveal that the lysine riboswitch has &gt;1000-fold specificity for lysine over other amino acids. The aptamer is highly sensitive to the precise placement of the epsilon-amino group and relatively tolerant of alterations to the main-chain functional groups in order to achieve this specificity. At low nucleotide triphosphate (NTP) concentrations, we observe good agreement between the half-maximal regulatory activity (T(50)) and the affinity of the receptor for lysine (K(d)), as well as many of its analogs. However, above 400muM [NTP], the concentration of lysine required to elicit transcription termination rises, moving into the riboswitch into a kinetic control regime. These data demonstrate that, under physiologically relevant conditions, riboswitches can integrate both effector and NTP concentrations to generate a regulatory response appropriate for global metabolic state of the cell.
Insights into the Regulatory Landscape of the Lysine Riboswitch.,Garst AD, Porter EB, Batey RT J Mol Biol. 2012 Jul 3. PMID:22771573<ref>PMID:22771573</ref>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>


==See Also==
==See Also==
*[[Riboswitch|Riboswitch]]
*[[Riboswitch 3D structures|Riboswitch 3D structures]]
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Large Structures]]
[[Category: Thermotoga maritima]]
[[Category: Thermotoga maritima]]
[[Category: Batey, R T]]
[[Category: Batey RT]]
[[Category: Garst, A D]]
[[Category: Garst AD]]
[[Category: Porter, E]]
[[Category: Porter E]]
[[Category: Regulatory mrna]]
[[Category: Riboswitch aptamer domain]]
[[Category: Transcription]]

Latest revision as of 18:08, 14 March 2024

Crystal structure of the lysine riboswitch bound to a lysine-glycine dipeptideCrystal structure of the lysine riboswitch bound to a lysine-glycine dipeptide

Structural highlights

4erl is a 1 chain structure with sequence from Thermotoga maritima. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 3Å
Ligands:,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

See Also

4erl, resolution 3.00Å

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

OCA
Retrieved from "https://proteopedia.openfox.io/wiki/index.php?title=4erl&oldid=4100409"