Open AccessmRNA cap recognition: Dominant role of enhanced stacking interactions between methylated bases and protein aromatic side chains
Author(s) -
Guanghui Hu,
Paul D. Gershon,
A.E. Hodel,
Florante A. Quiocho
Publication year - 1999
Publication title -
proceedings of the national academy of sciences of the united states of america
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 5.011
H-Index - 771
eISSN - 1091-6490
pISSN - 0027-8424
DOI - 10.1073/pnas.96.13.7149
Subject(s) - stacking , nucleobase , side chain , chemistry , nucleoside , stereochemistry , methylation , methyltransferase , dna , nucleotide , base pair , crystallography , biochemistry , gene , organic chemistry , polymer
We have determined, by high resolution x-ray analysis, 10 structures comprising the mRNA cap-specific methyltransferase VP39 or specific mutants thereof in the presence of methylated nucleobase analogs (N1-methyladenine, N3-methyladenine, N1-methylcytosine, N3-methylcytosine) and their unmethylated counterparts, or nucleoside N7-methylguanosine. Together with solution affinity studies and previous crystallographic data for N7-methylguanosine and its phosphorylated derivatives, these data demonstrate that only methylated, positively charged bases are bound, indicating that their enhanced stacking with two aromatic side chains of VP39 (Tyr 22 and Phe 180) plays a dominant role in cap recognition. Four key features characterize this stacking interaction: (i ) near perfect parallel alignment between the sandwiched methylated bases and aromatic side chains, (ii ) substantial areas of overlap in the two-stacked rings, (iii ) a 3.4-Å interplanar spacing within the overlapping region, and (iv ) positive charge in the heterocyclic nucleobase.