3f4h: Difference between revisions

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-{{Seed}}
-[[Image:3f4h.png|left|200px]]
-<!--
+==Crystal structure of the FMN riboswitch bound to roseoflavin==
-The line below this paragraph, containing "STRUCTURE_3f4h", creates the "Structure Box" on the page.
+<StructureSection load='3f4h' size='340' side='right'caption='[[3f4h]], [[Resolution|resolution]] 3.00&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'>[[3f4h]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3F4H OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3F4H 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]] 3&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=RS3:1-DEOXY-1-[8-(DIMETHYLAMINO)-7-METHYL-2,4-DIOXO-3,4-DIHYDROBENZO[G]PTERIDIN-10(2H)-YL]-D-RIBITOL'>RS3</scene></td></tr>
-{{STRUCTURE_3f4h|  PDB=3f4h  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3f4h FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3f4h OCA], [https://pdbe.org/3f4h PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3f4h RCSB], [https://www.ebi.ac.uk/pdbsum/3f4h PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3f4h ProSAT]</span></td></tr>
+</table>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+The biosynthesis of several protein cofactors is subject to feedback regulation by riboswitches. Flavin mononucleotide (FMN)-specific riboswitches, also known as RFN elements, direct expression of bacterial genes involved in the biosynthesis and transport of riboflavin (vitamin B(2)) and related compounds. Here we present the crystal structures of the Fusobacterium nucleatum riboswitch bound to FMN, riboflavin and antibiotic roseoflavin. The FMN riboswitch structure, centred on an FMN-bound six-stem junction, does not fold by collinear stacking of adjacent helices, typical for folding of large RNAs. Rather, it adopts a butterfly-like scaffold, stapled together by opposingly directed but nearly identically folded peripheral domains. FMN is positioned asymmetrically within the junctional site and is specifically bound to RNA through interactions with the isoalloxazine ring chromophore and direct and Mg(2+)-mediated contacts with the phosphate moiety. Our structural data, complemented by binding and footprinting experiments, imply a largely pre-folded tertiary RNA architecture and FMN recognition mediated by conformational transitions within the junctional binding pocket. The inherent plasticity of the FMN-binding pocket and the availability of large openings make the riboswitch an attractive target for structure-based design of FMN-like antimicrobial compounds. Our studies also explain the effects of spontaneous and antibiotic-induced deregulatory mutations and provided molecular insights into FMN-based control of gene expression in normal and riboflavin-overproducing bacterial strains.
-===Crystal structure of the FMN riboswitch bound to roseoflavin===
+Coenzyme recognition and gene regulation by a flavin mononucleotide riboswitch.,Serganov A, Huang L, Patel DJ Nature. 2009 Mar 12;458(7235):233-7. Epub 2009 Jan 25. PMID:19169240<ref>PMID:19169240</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 3f4h" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_19169240}}, adds the Publication Abstract to the page
+*[[Riboswitch 3D structures|Riboswitch 3D structures]]
-(as it appears on PubMed at http://www.pubmed.gov), where 19169240 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_19169240}}
+__TOC__
+</StructureSection>
-==About this Structure==
+[[Category: Large Structures]]
-F4H is a [[Protein complex]] structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3F4H OCA].
+[[Category: Huang L]]
+[[Category: Serganov AA]]
-==Reference==
-Coenzyme recognition and gene regulation by a flavin mononucleotide riboswitch., Serganov A, Huang L, Patel DJ, Nature. 2009 Jan 25. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/19169240 19169240]
-[[Category: Protein complex]]
-[[Category: Pdbx_ordinal=, <PDBx:audit_author.]]
-[[Category: Fmn]]
-[[Category: Riboswitch]]
-[[Category: Rna]]
-[[Category: Roseoflavin]]
-[[Category: Transcription]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Mar 18 20:11:34 2009''