2HOM image
Entry Detail
PDB ID:
2HOM
Keywords:
Title:
Crystal structure of an E. coli thi-box riboswitch bound to thiamine monophosphate
Biological Source:
Source Organism:
PDB Version:
Deposition Date:
2006-07-14
Release Date:
2006-09-19
Method Details:
Experimental Method:
Resolution:
2.89 Å
R-Value Free:
0.26
R-Value Work:
0.20
Space Group:
P 32 1 2
Macromolecular Entities
Polymer Type:polyribonucleotide
Description:thi-box riboswitch
Chain IDs:A
Chain Length:83
Number of Molecules:1
Biological Source:
Primary Citation
Crystal Structures of the Thi-Box Riboswitch Bound to Thiamine Pyrophosphate Analogs Reveal Adaptive RNA-Small Molecule Recognition
Structure 14 1459 1468 (2006)
PMID: 16962976 DOI: 10.1016/j.str.2006.07.008

Abstact

Riboswitches are noncoding mRNA elements that bind small-molecule metabolites with high affinity and specificity, and they regulate the expression of associated genes. The thi-box riboswitch can exhibit a 1000-fold higher affinity for thiamine pyrophosphate over closely related noncognate compounds such as thiamine monophosphate. To understand the chemical basis of thi-box pyrophosphate specificity, we have determined crystal structures of an E. coli thi-box bound to thiamine pyrophosphate, thiamine monophosphate, and the structural analogs benfotiamine and pyrithiamine. When bound to monophosphorylated compounds, the RNA elements that recognize the thiamine and phosphate moieties of the ligand move closer together. This allows the riboswitch to recognize the monophosphate in a manner similar to how it recognizes the beta-phosphate of thiamine pyrophosphate. In the pyrithiamine complex, the pyrophosphate binding site is largely unstructured. These results show how the riboswitch can bind to various metabolites, and why the thi-box preferentially binds thiamine pyrophosphate.

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