2gdi: Difference between revisions

From Proteopedia
Jump to navigation Jump to search
← Older edit
No edit summary
No edit summary
 
(13 intermediate revisions by the same user not shown)
Line 1: Line 1:
[[Image:2gdi.gif|left|200px]]<br /><applet load="2gdi" size="350" color="white" frame="true" align="right" spinBox="true"
caption="2gdi, resolution 2.05&Aring;" />
'''Crystal structure of thiamine pyrophosphate-specific riboswitch in complex with thiamine pyrophosphate'''<br />


==Overview==
==Crystal structure of thiamine pyrophosphate-specific riboswitch in complex with thiamine pyrophosphate==
Riboswitches are metabolite-sensing RNAs, typically located in the non-coding portions of messenger RNAs, that control the synthesis of metabolite-related proteins. Here we describe a 2.05 angstroms crystal structure of a riboswitch domain from the Escherichia coli thiM mRNA that responds to the coenzyme thiamine pyrophosphate (TPP). TPP is an active form of vitamin B1, an essential participant in many protein-catalysed reactions. Organisms from all three domains of life, including bacteria, plants and fungi, use TPP-sensing riboswitches to control genes responsible for importing or synthesizing thiamine and its phosphorylated derivatives, making this riboswitch class the most widely distributed member of the metabolite-sensing RNA regulatory system. The structure reveals a complex folded RNA in which one subdomain forms an intercalation pocket for the 4-amino-5-hydroxymethyl-2-methylpyrimidine moiety of TPP, whereas another subdomain forms a wider pocket that uses bivalent metal ions and water molecules to make bridging contacts to the pyrophosphate moiety of the ligand. The two pockets are positioned to function as a molecular measuring device that recognizes TPP in an extended conformation. The central thiazole moiety is not recognized by the RNA, which explains why the antimicrobial compound pyrithiamine pyrophosphate targets this riboswitch and downregulates the expression of thiamine metabolic genes. Both the natural ligand and its drug-like analogue stabilize secondary and tertiary structure elements that are harnessed by the riboswitch to modulate the synthesis of the proteins coded by the mRNA. In addition, this structure provides insight into how folded RNAs can form precision binding pockets that rival those formed by protein genetic factors.
<StructureSection load='2gdi' size='340' side='right'caption='[[2gdi]], [[Resolution|resolution]] 2.05&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[2gdi]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2GDI OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2GDI FirstGlance]. <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]] 2.05&#8491;</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=GTP:GUANOSINE-5-TRIPHOSPHATE'>GTP</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=TPP:THIAMINE+DIPHOSPHATE'>TPP</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=2gdi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2gdi OCA], [https://pdbe.org/2gdi PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2gdi RCSB], [https://www.ebi.ac.uk/pdbsum/2gdi PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2gdi ProSAT]</span></td></tr>
</table>


==About this Structure==
==See Also==
2GDI is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/ ] with <scene name='pdbligand=NA:'>NA</scene>, <scene name='pdbligand=K:'>K</scene>, <scene name='pdbligand=MG:'>MG</scene> and <scene name='pdbligand=TPP:'>TPP</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2GDI OCA].
*[[Riboswitch 3D structures|Riboswitch 3D structures]]
 
__TOC__
==Reference==
</StructureSection>
Structural basis for gene regulation by a thiamine pyrophosphate-sensing riboswitch., Serganov A, Polonskaia A, Phan AT, Breaker RR, Patel DJ, Nature. 2006 Jun 29;441(7097):1167-71. Epub 2006 May 21. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=16728979 16728979]
[[Category: Escherichia coli]]
[[Category: Protein complex]]
[[Category: Large Structures]]
[[Category: Serganov, A.]]
[[Category: Serganov A]]
[[Category: K]]
[[Category: MG]]
[[Category: NA]]
[[Category: TPP]]
[[Category: riboswitch]]
[[Category: thiamine pyrophosphate]]
 
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 17:30:38 2008''

Latest revision as of 12:27, 14 February 2024

Crystal structure of thiamine pyrophosphate-specific riboswitch in complex with thiamine pyrophosphateCrystal structure of thiamine pyrophosphate-specific riboswitch in complex with thiamine pyrophosphate

Structural highlights

2gdi is a 2 chain structure with sequence from Escherichia coli. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 2.05Å
Ligands:, , , , ,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

See Also

2gdi, resolution 2.05Å

Drag the structure with the mouse to rotate

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

OCA
Retrieved from "https://proteopedia.openfox.io/wiki/index.php?title=2gdi&oldid=4058662"