6tf3: Difference between revisions
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==Crystal structure of the ADP-binding domain of the NAD+ riboswitch with Cordycepin 5-triphosphate (3-dATP)== | ==Crystal structure of the ADP-binding domain of the NAD+ riboswitch with Cordycepin 5-triphosphate (3-dATP)== | ||
<StructureSection load='6tf3' size='340' side='right'caption='[[6tf3]]' scene=''> | <StructureSection load='6tf3' size='340' side='right'caption='[[6tf3]], [[Resolution|resolution]] 2.66Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6TF3 OCA]. For a <b>guided tour on the structure components</b> use [ | <table><tr><td colspan='2'>[[6tf3]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Candidatus_Koribacter_versatilis_Ellin345 Candidatus Koribacter versatilis Ellin345]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6TF3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6TF3 FirstGlance]. <br> | ||
</td></tr><tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[ | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.66Å</td></tr> | ||
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=3AT:3-DEOXYADENOSINE-5-TRIPHOSPHATE'>3AT</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></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=6tf3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6tf3 OCA], [https://pdbe.org/6tf3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6tf3 RCSB], [https://www.ebi.ac.uk/pdbsum/6tf3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6tf3 ProSAT]</span></td></tr> | |||
</table> | </table> | ||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
The nadA motif is the first known NAD(+)-dependent riboswitch, comprising two similar tandem bulged stem-loop structures. We have determined the structure of the 5' domain 1 of the riboswitch. It has three coaxial helical segments, separated by an ACANCCCC bulge and by an internal loop, with a tertiary contact between them that includes two C:G base pairs. We have determined the structure with a number of ligands related to NADH, but in each case only the ADP moiety is observed. The adenosine adopts an anti conformation, forms multiple hydrogen bonds across the width of the sugar edge of the penultimate C:G base pair of the helix preceding the bulge, and the observed contacts have been confirmed by mutagenesis and calorimetry. Two divalent metal ions play a key structural role at the narrow neck of the bulge. One makes direct bonding contacts to the diphosphate moiety, locking it into position. Thus the nucleobase, ribose, and phosphate groups of the ADP moiety are all specifically recognized by the RNA. The NAD(+) riboswitch is modular. Domain 1 is an ADP binding domain that may be ancient and could potentially be used in combination with other ligand binding motifs such as CoA. | |||
Structure and ligand binding of the ADP-binding domain of the NAD(+) riboswitch.,Huang L, Wang J, Lilley DMJ RNA. 2020 Jul;26(7):878-887. doi: 10.1261/rna.074898.120. Epub 2020 Apr 15. PMID:32295864<ref>PMID:32295864</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 6tf3" style="background-color:#fffaf0;"></div> | |||
==See Also== | |||
*[[Riboswitch 3D structures|Riboswitch 3D structures]] | |||
== References == | |||
<references/> | |||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
[[Category: Candidatus Koribacter versatilis Ellin345]] | |||
[[Category: Large Structures]] | [[Category: Large Structures]] | ||
[[Category: Huang L]] | [[Category: Huang L]] | ||
[[Category: Lilley DMJ]] | [[Category: Lilley DMJ]] | ||
Latest revision as of 16:01, 24 January 2024
Crystal structure of the ADP-binding domain of the NAD+ riboswitch with Cordycepin 5-triphosphate (3-dATP)Crystal structure of the ADP-binding domain of the NAD+ riboswitch with Cordycepin 5-triphosphate (3-dATP)
Structural highlights
Publication Abstract from PubMedThe nadA motif is the first known NAD(+)-dependent riboswitch, comprising two similar tandem bulged stem-loop structures. We have determined the structure of the 5' domain 1 of the riboswitch. It has three coaxial helical segments, separated by an ACANCCCC bulge and by an internal loop, with a tertiary contact between them that includes two C:G base pairs. We have determined the structure with a number of ligands related to NADH, but in each case only the ADP moiety is observed. The adenosine adopts an anti conformation, forms multiple hydrogen bonds across the width of the sugar edge of the penultimate C:G base pair of the helix preceding the bulge, and the observed contacts have been confirmed by mutagenesis and calorimetry. Two divalent metal ions play a key structural role at the narrow neck of the bulge. One makes direct bonding contacts to the diphosphate moiety, locking it into position. Thus the nucleobase, ribose, and phosphate groups of the ADP moiety are all specifically recognized by the RNA. The NAD(+) riboswitch is modular. Domain 1 is an ADP binding domain that may be ancient and could potentially be used in combination with other ligand binding motifs such as CoA. Structure and ligand binding of the ADP-binding domain of the NAD(+) riboswitch.,Huang L, Wang J, Lilley DMJ RNA. 2020 Jul;26(7):878-887. doi: 10.1261/rna.074898.120. Epub 2020 Apr 15. PMID:32295864[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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