2HOO

Crystal structure of an E. coli thi-box riboswitch bound to benfotiamine

Summary for 2HOO

• Entry DOI: 10.2210/pdb2hoo/pdb
• Related: 2HOJ 2HOK 2HOL 2HOM 2HOP
• Descriptor: thi-box riboswitch, CALCIUM ION, S-BENZOYLTHIAMINE O-MONOPHOSPHATE, ... (4 entities in total)
• Functional Keywords: rna; riboswitch; benfotiamine, rna
• Total number of polymer chains: 1
• Total formula weight: 27547.95

Authors

Edwards, T.E.,Ferre-D'Amare, A.R. (deposition date: 2006-07-14, release date: 2006-09-19, Last modification date: 2024-02-14)

Primary citation

Edwards, T.E.,Ferre-D'Amare, A.R.
Crystal Structures of the Thi-Box Riboswitch Bound to Thiamine Pyrophosphate Analogs Reveal Adaptive RNA-Small Molecule Recognition
Structure, 14:1459-1468, 2006

PubMed Abstract: 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.

PubMed: 16962976
DOI: 10.1016/j.str.2006.07.008

Experimental method

X-RAY DIFFRACTION (3 Å)