2gdi: Difference between revisions
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[[Image:2gdi.gif|left|200px]] | [[Image:2gdi.gif|left|200px]] | ||
'''Crystal structure of thiamine pyrophosphate-specific riboswitch in complex with thiamine pyrophosphate''' | {{Structure | ||
|PDB= 2gdi |SIZE=350|CAPTION= <scene name='initialview01'>2gdi</scene>, resolution 2.05Å | |||
|SITE= | |||
|LIGAND= <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene> and <scene name='pdbligand=TPP:THIAMINE DIPHOSPHATE'>TPP</scene> | |||
|ACTIVITY= | |||
|GENE= | |||
}} | |||
'''Crystal structure of thiamine pyrophosphate-specific riboswitch in complex with thiamine pyrophosphate''' | |||
==Overview== | ==Overview== | ||
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==About this Structure== | ==About this Structure== | ||
2GDI is a [ | 2GDI is a [[Protein complex]] structure of sequences from [http://en.wikipedia.org/wiki/ ]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2GDI OCA]. | ||
==Reference== | ==Reference== | ||
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:// | 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://www.ncbi.nlm.nih.gov/pubmed/16728979 16728979] | ||
[[Category: Protein complex]] | [[Category: Protein complex]] | ||
[[Category: Serganov, A.]] | [[Category: Serganov, A.]] | ||
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[[Category: thiamine pyrophosphate]] | [[Category: thiamine pyrophosphate]] | ||
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 17:03:25 2008'' | ||
Revision as of 18:03, 20 March 2008
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| Coordinates: | save as pdb, mmCIF, xml | ||||||
Crystal structure of thiamine pyrophosphate-specific riboswitch in complex with thiamine pyrophosphate
OverviewOverview
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.
About this StructureAbout this Structure
2GDI is a Protein complex structure of sequences from [1]. Full crystallographic information is available from OCA.
ReferenceReference
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:16728979
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