3diq: Difference between revisions

← Older edit

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

OCA

@@ Line 1: / Line 1: @@
-{{Seed}}
-[[Image:3diq.png|left|200px]]
-<!--
+==Crystallization of the Thermotoga maritima lysine riboswitch bound to homoarginine==
-The line below this paragraph, containing "STRUCTURE_3diq", creates the "Structure Box" on the page.
+<StructureSection load='3diq' size='340' side='right'caption='[[3diq]], [[Resolution|resolution]] 2.70&Aring;' scene=''>
-You may change the PDB parameter (which sets the PDB file loaded into the applet)
+== Structural highlights ==
-or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
+<table><tr><td colspan='2'>[[3diq]] 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=3DIQ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3DIQ FirstGlance]. <br>
-or leave the SCENE parameter empty for the default display.
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.7&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=1PE:PENTAETHYLENE+GLYCOL'>1PE</scene>, <scene name='pdbligand=CCC:CYTIDINE-5-PHOSPHATE-2,3-CYCLIC+PHOSPHATE'>CCC</scene>, <scene name='pdbligand=HRG:L-HOMOARGININE'>HRG</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>
-{{STRUCTURE_3diq|  PDB=3diq  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3diq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3diq OCA], [https://pdbe.org/3diq PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3diq RCSB], [https://www.ebi.ac.uk/pdbsum/3diq PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3diq ProSAT]</span></td></tr>
+</table>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+In bacteria, the intracellular concentration of several amino acids is controlled by riboswitches. One of the important regulatory circuits involves lysine-specific riboswitches, which direct the biosynthesis and transport of lysine and precursors common for lysine and other amino acids. To understand the molecular basis of amino acid recognition by riboswitches, here we present the crystal structure of the 174-nucleotide sensing domain of the Thermotoga maritima lysine riboswitch in the lysine-bound (1.9 angstrom (A)) and free (3.1 A) states. The riboswitch features an unusual and intricate architecture, involving three-helical and two-helical bundles connected by a compact five-helical junction and stabilized by various long-range tertiary interactions. Lysine interacts with the junctional core of the riboswitch and is specifically recognized through shape-complementarity within the elongated binding pocket and through several direct and K(+)-mediated hydrogen bonds to its charged ends. Our structural and biochemical studies indicate preformation of the riboswitch scaffold and identify conformational changes associated with the formation of a stable lysine-bound state, which prevents alternative folding of the riboswitch and facilitates formation of downstream regulatory elements. We have also determined several structures of the riboswitch bound to different lysine analogues, including antibiotics, in an effort to understand the ligand-binding capabilities of the lysine riboswitch and understand the nature of antibiotic resistance. Our results provide insights into a mechanism of lysine-riboswitch-dependent gene control at the molecular level, thereby contributing to continuing efforts at exploration of the pharmaceutical and biotechnological potential of riboswitches.
-===Crystallization of the Thermotoga maritima lysine riboswitch bound to homoarginine===
+Structural insights into amino acid binding and gene control by a lysine riboswitch.,Serganov A, Huang L, Patel DJ Nature. 2008 Oct 30;455(7217):1263-7. Epub 2008 Sep 10. PMID:18784651<ref>PMID:18784651</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-<!--
+</div>
-The line below this paragraph, {{ABSTRACT_PUBMED_18784651}}, adds the Publication Abstract to the page
+<div class="pdbe-citations 3diq" style="background-color:#fffaf0;"></div>
-(as it appears on PubMed at http://www.pubmed.gov), where 18784651 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_18784651}}
+__TOC__
+</StructureSection>
-==About this Structure==
+[[Category: Large Structures]]
-DIQ is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3DIQ OCA].
+[[Category: Thermotoga maritima]]
+[[Category: Serganov AA]]
-==Reference==
-Structural insights into amino acid binding and gene control by a lysine riboswitch., Serganov A, Huang L, Patel DJ, Nature. 2008 Oct 30;455(7217):1263-7. Epub 2008 Sep 10. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/18784651 18784651]
-[[Category: Serganov, A A.]]
-[[Category: Lysine]]
-[[Category: Riboswitch]]
-[[Category: Rna]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Nov 12 10:05:36 2008''