4fe5

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (11:15, 1 March 2024) (edit) (undo)
 
(4 intermediate revisions not shown.)
Line 1: Line 1:
 +
==Crystal structure of the xpt-pbuX guanine riboswitch aptamer domain in complex with hypoxanthine==
==Crystal structure of the xpt-pbuX guanine riboswitch aptamer domain in complex with hypoxanthine==
-
<StructureSection load='4fe5' size='340' side='right' caption='[[4fe5]], [[Resolution|resolution]] 1.32&Aring;' scene=''>
+
<StructureSection load='4fe5' size='340' side='right'caption='[[4fe5]], [[Resolution|resolution]] 1.32&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
-
<table><tr><td colspan='2'>[[4fe5]] is a 1 chain structure. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1u8d 1u8d]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4FE5 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4FE5 FirstGlance]. <br>
+
<table><tr><td colspan='2'>[[4fe5]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_subtilis Bacillus subtilis]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1u8d 1u8d]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4FE5 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4FE5 FirstGlance]. <br>
-
</td></tr><tr><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=HPA:HYPOXANTHINE'>HPA</scene>, <scene name='pdbligand=NCO:COBALT+HEXAMMINE(III)'>NCO</scene><br>
+
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.32&#8491;</td></tr>
-
<tr><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4fej|4fej]], [[4fel|4fel]], [[4fen|4fen]], [[4feo|4feo]], [[4fep|4fep]]</td></tr>
+
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=HPA:HYPOXANTHINE'>HPA</scene>, <scene name='pdbligand=NCO:COBALT+HEXAMMINE(III)'>NCO</scene></td></tr>
-
<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4fe5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4fe5 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4fe5 RCSB], [http://www.ebi.ac.uk/pdbsum/4fe5 PDBsum]</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=4fe5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4fe5 OCA], [https://pdbe.org/4fe5 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4fe5 RCSB], [https://www.ebi.ac.uk/pdbsum/4fe5 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4fe5 ProSAT]</span></td></tr>
-
<table>
+
</table>
-
<div style="background-color:#fffaf0;">
+
-
== Publication Abstract from PubMed ==
+
-
Riboswitches are genetic regulatory elements found in the 5' untranslated region of messenger RNA that act in the absence of protein cofactors. They are broadly distributed across bacteria and account for the regulation of more than 2% of all genes in Bacillus subtilis, underscoring their importance in the control of cellular metabolism. The 5' untranslated region of many mRNAs of genes involved in purine metabolism and transport contain a guanine-responsive riboswitch that directly binds guanine, hypoxanthine or xanthine to terminate transcription. Here we report the crystal structure at 1.95 A resolution of the purine-binding domain of the guanine riboswitch from the xpt-pbuX operon of B. subtilis bound to hypoxanthine, a prevalent metabolite in the bacterial purine salvage pathway. This structure reveals a complex RNA fold involving several phylogenetically conserved nucleotides that create a binding pocket that almost completely envelops the ligand. Hypoxanthine functions to stabilize this structure and to promote the formation of a downstream transcriptional terminator element, thereby providing a mechanism for directly repressing gene expression in response to an increase in intracellular concentrations of metabolite.
+
-
 
+
-
Structure of a natural guanine-responsive riboswitch complexed with the metabolite hypoxanthine.,Batey RT, Gilbert SD, Montange RK Nature. 2004 Nov 18;432(7015):411-5. PMID:15549109<ref>PMID:15549109</ref>
+
-
 
+
-
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+
-
</div>
+
==See Also==
==See Also==
-
*[[Guanine-Binding Riboswitch|Guanine-Binding Riboswitch]]
+
*[[Riboswitch 3D structures|Riboswitch 3D structures]]
-
*[[Riboswitch|Riboswitch]]
+
-
== References ==
+
-
<references/>
+
__TOC__
__TOC__
</StructureSection>
</StructureSection>
-
[[Category: Batey, R T.]]
+
[[Category: Bacillus subtilis]]
-
[[Category: Knight, R.]]
+
[[Category: Large Structures]]
-
[[Category: Marcano, J.]]
+
[[Category: Batey RT]]
-
[[Category: Stoddard, C D.]]
+
[[Category: Knight R]]
-
[[Category: Trausch, J J.]]
+
[[Category: Marcano J]]
-
[[Category: Widmann, J.]]
+
[[Category: Stoddard CD]]
-
[[Category: Gene regulatory element]]
+
[[Category: Trausch JJ]]
-
[[Category: Hypoxanthine]]
+
[[Category: Widmann J]]
-
[[Category: Rna]]
+
-
[[Category: Three-way junction with distal tertiary interaction]]
+

Current revision

Crystal structure of the xpt-pbuX guanine riboswitch aptamer domain in complex with hypoxanthine

PDB ID 4fe5

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/4fe5"
Personal tools