2b57
From Proteopedia
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|PDB= 2b57 |SIZE=350|CAPTION= <scene name='initialview01'>2b57</scene>, resolution 2.15Å | |PDB= 2b57 |SIZE=350|CAPTION= <scene name='initialview01'>2b57</scene>, resolution 2.15Å | ||
|SITE= | |SITE= | ||
| - | |LIGAND= <scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=NCO:COBALT+HEXAMMINE+ION'>NCO</scene> | + | |LIGAND= <scene name='pdbligand=6AP:9H-PURINE-2,6-DIAMINE'>6AP</scene>, <scene name='pdbligand=A:ADENOSINE-5'-MONOPHOSPHATE'>A</scene>, <scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=C:CYTIDINE-5'-MONOPHOSPHATE'>C</scene>, <scene name='pdbligand=G:GUANOSINE-5'-MONOPHOSPHATE'>G</scene>, <scene name='pdbligand=NCO:COBALT+HEXAMMINE+ION'>NCO</scene>, <scene name='pdbligand=U:URIDINE-5'-MONOPHOSPHATE'>U</scene> |
|ACTIVITY= | |ACTIVITY= | ||
|GENE= | |GENE= | ||
| + | |DOMAIN= | ||
| + | |RELATEDENTRY= | ||
| + | |RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2b57 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2b57 OCA], [http://www.ebi.ac.uk/pdbsum/2b57 PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=2b57 RCSB]</span> | ||
}} | }} | ||
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[[Category: Stoddard, C D.]] | [[Category: Stoddard, C D.]] | ||
[[Category: Wise, S J.]] | [[Category: Wise, S J.]] | ||
| - | [[Category: 6AP]] | ||
| - | [[Category: ACT]] | ||
| - | [[Category: NCO]] | ||
[[Category: base quadruple]] | [[Category: base quadruple]] | ||
[[Category: base triple]] | [[Category: base triple]] | ||
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[[Category: rna-ligand complex]] | [[Category: rna-ligand complex]] | ||
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 02:01:37 2008'' |
Revision as of 23:01, 30 March 2008
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| , resolution 2.15Å | |||||||
|---|---|---|---|---|---|---|---|
| Ligands: | , , , , , , | ||||||
| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
Guanine Riboswitch C74U mutant bound to 2,6-diaminopurine
Overview
Riboswitches are cis-acting genetic regulatory elements found commonly in bacterial mRNAs that consist of a metabolite-responsive aptamer domain coupled to a regulatory switch. Purine riboswitches respond to intracellular concentrations of either adenine or guanine/hypoxanthine to control gene expression. The aptamer domain of the purine riboswitch contains a pyrimidine residue (Y74) that forms a Watson-Crick base-pairing interaction with the bound purine nucleobase ligand that discriminates between adenine and guanine. We sought to understand the structural basis of this specificity and the mechanism of ligand recognition by the purine riboswitch. Here, we present the 2,6-diaminopurine-bound structure of a C74U mutant of the xpt-pbuX guanine riboswitch, along with a detailed thermodynamic and kinetic analysis of nucleobase recognition by both the native and mutant riboswitches. These studies demonstrate clearly that the pyrimidine at position 74 is the sole determinant of purine riboswitch specificity. In addition, the mutant riboswitch binds adenine and adenine derivatives well compared with the guanine-responsive riboswitch. Under our experimental conditions, 2,6-diaminopurine binds the RNA with DeltaH=-40.3 kcal mol(-1), DeltaS=-97.6 cal mol(-1)K(-1), and DeltaG=-10.73 kcal mol(-1). A kinetic determination of the slow rate (0.15 x 10(5)M(-1)s(-1) and 2.1 x 10(5)mM(-1)s(-1) for 2-aminopurine binding the adenine-responsive mutant riboswitch and 7-deazaguanine-binding guanine riboswitch, respectively) of association under varying experimental conditions allowed us to propose a mechanism for ligand recognition by the purine riboswitch. A conformationally dynamic unliganded state for the binding pocket is stabilized first by the Watson-Crick base pairing between the ligand and Y74, and by the subsequent ordering of the J2/3 loop, enclosing the ligand within the three-way junction.
About this Structure
2B57 is a Single protein structure of sequence from [1]. Full crystallographic information is available from OCA.
Reference
Thermodynamic and kinetic characterization of ligand binding to the purine riboswitch aptamer domain., Gilbert SD, Stoddard CD, Wise SJ, Batey RT, J Mol Biol. 2006 Jun 9;359(3):754-68. Epub 2006 Apr 21. PMID:16650860
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