3dig - Revision history

OCA at 09:41, 21 February 2024

2024-02-21T09:41:35Z

← Older revision		Revision as of 09:41, 21 February 2024
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	<StructureSection load='3dig' size='340' side='right'caption='[[3dig]], [[Resolution\|resolution]] 2.80Å' scene=''>		<StructureSection load='3dig' size='340' side='right'caption='[[3dig]], [[Resolution\|resolution]] 2.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[3dig]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3DIG OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3DIG FirstGlance]. <br>		<table><tr><td colspan='2'>[[3dig]] 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=3DIG OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3DIG FirstGlance]. <br>
	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=IPA:ISOPROPYL+ALCOHOL'>IPA</scene>~~, ~~<scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=SLZ:L-THIALYSINE'>SLZ</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]] 2.8Å</td></tr>
	<tr id='~~NonStdRes~~'><td class="sblockLbl"><b>[[~~Non-Standard_Residue~~\|~~NonStd Res~~:]]</b></td><td class="sblockDat"><scene name='pdbligand=CCC:CYTIDINE-5-PHOSPHATE-2,3-CYCLIC+PHOSPHATE'>CCC</scene><~~/td~~></tr>		<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CCC:CYTIDINE-5-PHOSPHATE-2,3-CYCLIC+PHOSPHATE'>CCC</scene>, <scene name='pdbligand=IPA:ISOPROPYL+ALCOHOL'>IPA</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=SLZ:L-THIALYSINE'>SLZ</scene></td></tr>
	<~~tr id~~='~~related~~'><~~td class="sblockLbl"~~><~~b>[[Related_structure\|Related~~:~~]]</b~~></td><~~td class~~=~~"sblockDat"><div style~~=~~'overflow~~: ~~auto; max~~-~~height: 3em;~~'>~~[[3dil\|3dil]], [[3dim\|3dim]], [[3dio\|3dio]], [[3diq\|3diq]], [[3dir\|3dir]], [[3dis\|3dis]], [[3dix\|3dix]], [[3diy\|3diy]], [[3diz\|3diz]], [[3dj0\|3dj0]], [[3dj2\|3dj2]]~~</~~div~~></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=3dig FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3dig OCA], [https://pdbe.org/3dig PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3dig RCSB], [https://www.ebi.ac.uk/pdbsum/3dig PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3dig 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=3dig FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3dig OCA], [https://pdbe.org/3dig PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3dig RCSB], [https://www.ebi.ac.uk/pdbsum/3dig PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3dig ProSAT]</span></td></tr>
	</table>		</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.

	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®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~
	~~</div>~~
	~~<div class="pdbe-citations 3dig" style="background-color:#fffaf0;"></div>~~

	~~==See Also==~~
	*[[Riboswitch 3D structures\|Riboswitch 3D structures]]
	~~== References ==~~
	~~<references/>~~
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: ~~Serganov, A A~~]]		[[Category: Thermotoga maritima]]
	[[Category: ~~Lysine]]~~		[[Category: Serganov AA]]
	~~[[Category: Riboswitch]]~~
	~~[[Category: Rna~~]]

OCA at 08:28, 25 May 2022

2022-05-25T08:28:53Z

← Older revision		Revision as of 08:28, 25 May 2022
Line 3:		Line 3:
	<StructureSection load='3dig' size='340' side='right'caption='[[3dig]], [[Resolution\|resolution]] 2.80Å' scene=''>		<StructureSection load='3dig' size='340' side='right'caption='[[3dig]], [[Resolution\|resolution]] 2.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[3dig]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3DIG OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=3DIG FirstGlance]. <br>		<table><tr><td colspan='2'>[[3dig]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3DIG OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3DIG FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=IPA:ISOPROPYL+ALCOHOL'>IPA</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=SLZ:L-THIALYSINE'>SLZ</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=IPA:ISOPROPYL+ALCOHOL'>IPA</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=SLZ:L-THIALYSINE'>SLZ</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CCC:CYTIDINE-5-PHOSPHATE-2,3-CYCLIC+PHOSPHATE'>CCC</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CCC:CYTIDINE-5-PHOSPHATE-2,3-CYCLIC+PHOSPHATE'>CCC</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3dil\|3dil]], [[3dim\|3dim]], [[3dio\|3dio]], [[3diq\|3diq]], [[3dir\|3dir]], [[3dis\|3dis]], [[3dix\|3dix]], [[3diy\|3diy]], [[3diz\|3diz]], [[3dj0\|3dj0]], [[3dj2\|3dj2]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3dil\|3dil]], [[3dim\|3dim]], [[3dio\|3dio]], [[3diq\|3diq]], [[3dir\|3dir]], [[3dis\|3dis]], [[3dix\|3dix]], [[3diy\|3diy]], [[3diz\|3diz]], [[3dj0\|3dj0]], [[3dj2\|3dj2]]</div></td></tr>
	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://proteopedia.org/fgij/fg.htm?mol=3dig FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3dig OCA], [~~http~~://pdbe.org/3dig PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3dig RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3dig PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3dig 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=3dig FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3dig OCA], [https://pdbe.org/3dig PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3dig RCSB], [https://www.ebi.ac.uk/pdbsum/3dig PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3dig ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 06:58, 19 August 2020

2020-08-19T06:58:41Z

← Older revision		Revision as of 06:58, 19 August 2020
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	==CRYSTAL STRUCTURE OF THE THERMOTOGA MARITIMA LYSINE RIBOSWITCH BOUND TO S-(2-aminoethyl)-L-cysteine==		==CRYSTAL STRUCTURE OF THE THERMOTOGA MARITIMA LYSINE RIBOSWITCH BOUND TO S-(2-aminoethyl)-L-cysteine==
	<StructureSection load='3dig' size='340' side='right' caption='[[3dig]], [[Resolution\|resolution]] 2.80Å' scene=''>		<StructureSection load='3dig' size='340' side='right'caption='[[3dig]], [[Resolution\|resolution]] 2.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[3dig]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3DIG OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3DIG FirstGlance]. <br>		<table><tr><td colspan='2'>[[3dig]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3DIG OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=3DIG FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=IPA:ISOPROPYL+ALCOHOL'>IPA</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=SLZ:L-THIALYSINE'>SLZ</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=IPA:ISOPROPYL+ALCOHOL'>IPA</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=SLZ:L-THIALYSINE'>SLZ</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CCC:CYTIDINE-5-PHOSPHATE-2,3-CYCLIC+PHOSPHATE'>CCC</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CCC:CYTIDINE-5-PHOSPHATE-2,3-CYCLIC+PHOSPHATE'>CCC</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3dil\|3dil]], [[3dim\|3dim]], [[3dio\|3dio]], [[3diq\|3diq]], [[3dir\|3dir]], [[3dis\|3dis]], [[3dix\|3dix]], [[3diy\|3diy]], [[3diz\|3diz]], [[3dj0\|3dj0]], [[3dj2\|3dj2]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3dil\|3dil]], [[3dim\|3dim]], [[3dio\|3dio]], [[3diq\|3diq]], [[3dir\|3dir]], [[3dis\|3dis]], [[3dix\|3dix]], [[3diy\|3diy]], [[3diz\|3diz]], [[3dj0\|3dj0]], [[3dj2\|3dj2]]</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=3dig FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3dig OCA], [http://pdbe.org/3dig PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3dig RCSB], [http://www.ebi.ac.uk/pdbsum/3dig PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3dig ProSAT]</span></td></tr>		<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=3dig FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3dig OCA], [http://pdbe.org/3dig PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3dig RCSB], [http://www.ebi.ac.uk/pdbsum/3dig PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3dig ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
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	==See Also==		==See Also==
	*[[Riboswitch\|Riboswitch]]		*[[Riboswitch 3D structures\|Riboswitch 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
			[[Category: Large Structures]]
	[[Category: Serganov, A A]]		[[Category: Serganov, A A]]
	[[Category: Lysine]]		[[Category: Lysine]]
	[[Category: Riboswitch]]		[[Category: Riboswitch]]
	[[Category: Rna]]		[[Category: Rna]]

OCA at 09:48, 14 November 2018

2018-11-14T09:48:25Z

← Older revision		Revision as of 09:48, 14 November 2018
Line 18:		Line 18:
	</div>		</div>
	<div class="pdbe-citations 3dig" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 3dig" style="background-color:#fffaf0;"></div>

			==See Also==
			*[[Riboswitch\|Riboswitch]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 19:15, 11 August 2016

2016-08-11T19:15:53Z

← Older revision		Revision as of 19:15, 11 August 2016
Line 1:		Line 1:

	==CRYSTAL STRUCTURE OF THE THERMOTOGA MARITIMA LYSINE RIBOSWITCH BOUND TO S-(2-aminoethyl)-L-cysteine==		==CRYSTAL STRUCTURE OF THE THERMOTOGA MARITIMA LYSINE RIBOSWITCH BOUND TO S-(2-aminoethyl)-L-cysteine==
	<StructureSection load='3dig' size='340' side='right' caption='[[3dig]], [[Resolution\|resolution]] 2.80Å' scene=''>		<StructureSection load='3dig' size='340' side='right' caption='[[3dig]], [[Resolution\|resolution]] 2.80Å' scene=''>
Line 6:		Line 7:
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CCC:CYTIDINE-5-PHOSPHATE-2,3-CYCLIC+PHOSPHATE'>CCC</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CCC:CYTIDINE-5-PHOSPHATE-2,3-CYCLIC+PHOSPHATE'>CCC</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3dil\|3dil]], [[3dim\|3dim]], [[3dio\|3dio]], [[3diq\|3diq]], [[3dir\|3dir]], [[3dis\|3dis]], [[3dix\|3dix]], [[3diy\|3diy]], [[3diz\|3diz]], [[3dj0\|3dj0]], [[3dj2\|3dj2]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3dil\|3dil]], [[3dim\|3dim]], [[3dio\|3dio]], [[3diq\|3diq]], [[3dir\|3dir]], [[3dis\|3dis]], [[3dix\|3dix]], [[3diy\|3diy]], [[3diz\|3diz]], [[3dj0\|3dj0]], [[3dj2\|3dj2]]</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=3dig FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3dig OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3dig RCSB], [http://www.ebi.ac.uk/pdbsum/3dig 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=3dig FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3dig OCA], [http://pdbe.org/3dig PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3dig RCSB], [http://www.ebi.ac.uk/pdbsum/3dig PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3dig ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 16:		Line 17:
	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
			<div class="pdbe-citations 3dig" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 08:05, 12 November 2014

2014-11-12T08:05:19Z

← Older revision		Revision as of 08:05, 12 November 2014
Line 1:		Line 1:
	[[~~Image~~:~~3dig~~.~~png~~\|~~left~~\|~~200px~~]]		==CRYSTAL STRUCTURE OF THE THERMOTOGA MARITIMA LYSINE RIBOSWITCH BOUND TO S-(2-aminoethyl)-L-cysteine==
			<StructureSection load='3dig' size='340' side='right' caption='[[3dig]], [[Resolution\|resolution]] 2.80Å' scene=''>
			== Structural highlights ==
			<table><tr><td colspan='2'>[[3dig]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3DIG OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3DIG FirstGlance]. <br>
			</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=IPA:ISOPROPYL+ALCOHOL'>IPA</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=SLZ:L-THIALYSINE'>SLZ</scene></td></tr>
			<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CCC:CYTIDINE-5-PHOSPHATE-2,3-CYCLIC+PHOSPHATE'>CCC</scene></td></tr>
			<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3dil\|3dil]], [[3dim\|3dim]], [[3dio\|3dio]], [[3diq\|3diq]], [[3dir\|3dir]], [[3dis\|3dis]], [[3dix\|3dix]], [[3diy\|3diy]], [[3diz\|3diz]], [[3dj0\|3dj0]], [[3dj2\|3dj2]]</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=3dig FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3dig OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3dig RCSB], [http://www.ebi.ac.uk/pdbsum/3dig PDBsum]</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.

	~~{{STRUCTURE_3dig\| PDB=3dig \| SCENE= }}~~		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>

	~~===CRYSTAL STRUCTURE OF THE THERMOTOGA MARITIMA LYSINE RIBOSWITCH BOUND TO~~ S~~-(2-aminoethyl)-L-cysteine===~~		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
			</div>
	~~{{ABSTRACT_PUBMED_18784651}}~~		== References ==
			<references/>
	==~~About this Structure~~==		__TOC__
	~~[[3dig]] is a 1 chain structure. Full crystallographic information is available from [http:~~//~~oca.weizmann.ac.il/oca-bin/ocashort?id=3DIG OCA].~~		</StructureSection>
	[[Category: Serganov, A A.]]		[[Category: Serganov, A A]]
	[[Category: Lysine]]		[[Category: Lysine]]
	[[Category: Riboswitch]]		[[Category: Riboswitch]]
	[[Category: Rna]]		[[Category: Rna]]

OCA: Protected "3dig" [edit=sysop:move=sysop]

2013-01-07T21:38:02Z

Protected "3dig" [edit=sysop:move=sysop]

← Older revision	Revision as of 21:38, 7 January 2013
(No difference)

OCA at 21:38, 7 January 2013

2013-01-07T21:38:00Z

← Older revision		Revision as of 21:38, 7 January 2013
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	~~{{Seed}}~~
	[[Image:3dig.png\|left\|200px]]		[[Image:3dig.png\|left\|200px]]

	~~<!--~~
	~~The line below this paragraph, containing "STRUCTURE_3dig", creates the "Structure Box" on the page.~~
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	~~or the SCENE parameter (which sets the initial scene displayed when the page is loaded),~~
	~~or leave the SCENE parameter empty for the default display.~~
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	{{STRUCTURE_3dig\| PDB=3dig \| SCENE= }}		{{STRUCTURE_3dig\| PDB=3dig \| SCENE= }}

	===CRYSTAL STRUCTURE OF THE THERMOTOGA MARITIMA LYSINE RIBOSWITCH BOUND TO S-(2-aminoethyl)-L-cysteine===		===CRYSTAL STRUCTURE OF THE THERMOTOGA MARITIMA LYSINE RIBOSWITCH BOUND TO S-(2-aminoethyl)-L-cysteine===


	~~<!--~~
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	{{ABSTRACT_PUBMED_18784651}}		{{ABSTRACT_PUBMED_18784651}}

	==About this Structure==		==About this Structure==
	~~3DIG is a~~ [[~~Single protein~~]] structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3DIG OCA].		[[3dig]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3DIG OCA].

	~~==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: Single protein]]~~
	[[Category: Serganov, A A.]]		[[Category: Serganov, A A.]]
	[[Category: Lysine]]		[[Category: Lysine]]
	[[Category: Riboswitch]]		[[Category: Riboswitch]]
	[[Category: Rna]]		[[Category: Rna]]

	~~''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Nov 12 20:36:48 2008''~~

OCA at 19:06, 12 November 2008

2008-11-12T19:06:58Z

← Older revision		Revision as of 19:06, 12 November 2008
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	==About this Structure==		==About this Structure==
	3DIG is a ~~1 chain~~ structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3DIG OCA].		3DIG is a [[Single protein]] structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3DIG OCA].

	==Reference==		==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]		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: Single protein]]
	[[Category: Serganov, A A.]]		[[Category: Serganov, A A.]]
	[[Category: Lysine]]		[[Category: Lysine]]
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	[[Category: Rna]]		[[Category: Rna]]

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OCA at 08:01, 12 November 2008

2008-11-12T08:01:26Z

← Older revision		Revision as of 08:01, 12 November 2008
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	[[Image:3dig.~~jpg~~\|left\|200px]]		[[Image:3dig.png\|left\|200px]]

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	===CRYSTAL STRUCTURE OF THE THERMOTOGA MARITIMA LYSINE RIBOSWITCH BOUND TO S-(2-aminoethyl)-L-cysteine===		===CRYSTAL STRUCTURE OF THE THERMOTOGA MARITIMA LYSINE RIBOSWITCH BOUND TO S-(2-aminoethyl)-L-cysteine===


			<!--
			The line below this paragraph, {{ABSTRACT_PUBMED_18784651}}, adds the Publication Abstract to the page
			(as it appears on PubMed at http://www.pubmed.gov), where 18784651 is the PubMed ID number.
			-->
			{{ABSTRACT_PUBMED_18784651}}

	==About this Structure==		==About this Structure==
	3DIG is a ~~[[Single protein]]~~ structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3DIG OCA].		3DIG is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3DIG OCA].
	[~~[Category~~: ~~Single protein]~~]
			==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: Serganov, A A.]]
	[[Category: Lysine]]		[[Category: Lysine]]
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	[[Category: Rna]]		[[Category: Rna]]

	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed ~~Sep 17 14~~:31:18 2008''		''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Nov 12 10:01:25 2008''