3CJZ

Effects of N2,N2-dimethylguanosine on RNA structure and stability: crystal structure of an RNA duplex with tandem m22G:A pairs

Summary for 3CJZ

• Entry DOI: 10.2210/pdb3cjz/pdb
• Descriptor: RNA (5'-R(*GP*GP*AP*CP*GP*(M2G)P*AP*CP*GP*UP*CP*CP*U)-3') (2 entities in total)
• Functional Keywords: rna, n2, n2-dimethyl guanosine, x-ray crystal structure, m22g:a pair, rrna, trna
• Total number of polymer chains: 2
• Total formula weight: 8401.19

Authors

Pallan, P.S.,Kreutz, C.,Bosio, S.,Micura, R.,Egli, M. (deposition date: 2008-03-14, release date: 2008-10-14, Last modification date: 2024-04-03)

Primary citation

Pallan, P.S.,Kreutz, C.,Bosio, S.,Micura, R.,Egli, M.
Effects of N2,N2-dimethylguanosine on RNA structure and stability: crystal structure of an RNA duplex with tandem m2 2G:A pairs.
Rna, 14:2125-2135, 2008

PubMed Abstract: Methylation of the exocyclic amino group of guanine is a relatively common modification in rRNA and tRNA. Single methylation (N(2)-methylguanosine, m(2)G) is the second most frequently encountered nucleoside analog in Escherichia coli rRNAs. The most prominent case of dual methylation (N(2),N(2)-dimethylguanosine, m(2) (2)G) is found in the majority of eukaryotic tRNAs at base pair m(2) (2)G26:A44. The latter modification eliminates the ability of the N(2) function to donate in hydrogen bonds and alters its pairing behavior, notably vis-à-vis C. Perhaps a less obvious consequence of the N(2),N(2)-dimethyl modification is its role in controlling the pairing modes between G and A. We have determined the crystal structure of a 13-mer RNA duplex with central tandem m(2) (2)G:A pairs. In the structure both pairs adopt an imino-hydrogen bonded, pseudo-Watson-Crick conformation. Thus, the sheared conformation frequently seen in tandem G:A pairs is avoided due to a potential steric clash between an N(2)-methyl group and the major groove edge of A. Additionally, for a series of G:A containing self-complementary RNAs we investigated how methylation affects competitive hairpin versus duplex formation based on UV melting profile analysis.

PubMed: 18772248
DOI: 10.1261/rna.1078508

Experimental method

X-RAY DIFFRACTION (1.8 Å)