3iki | pdb_00003iki

5-SMe-dU containing DNA octamer

spinqualitylabelsall models 3iki, resolution 1.38Å Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image   Print3D Structural highlights 3iki is a 1 chain structure. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance. Ligands: MG NonStd Res: UMS, US2 Resources: FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT Publication Abstract from PubMed Natural RNAs, especially tRNAs, are extensively modified to tailor structure and function diversities. Uracil is the most modified nucleobase among all natural nucleobases. Interestingly, >76% of uracil modifications are located on its 5-position. We have investigated the natural 5-methoxy (5-O-CH(3)) modification of uracil in the context of A-form oligonucleotide duplex. Our X-ray crystal structure indicates first a H-bond formation between the uracil 5-O-CH(3) and its 5'-phosphate. This novel H-bond is not observed when the oxygen of 5-O-CH(3) is replaced with a larger atom (selenium or sulfur). The 5-O-CH(3) modification does not cause significant structure and stability alterations. Moreover, our computational study is consistent with the experimental observation. The investigation on the uracil 5-position demonstrates the importance of this RNA modification at the atomic level. Our finding suggests a general interaction between the nucleobase and backbone and reveals a plausible function of the tRNA 5-O-CH(3) modification, which might potentially rigidify the local conformation and facilitates translation. Hydrogen bond formation between the naturally modified nucleobase and phosphate backbone.,Sheng J, Zhang W, Hassan AE, Gan J, Soares AS, Geng S, Ren Y, Huang Z Nucleic Acids Res. 2012 May 28. PMID:22641848 From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

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