1EAM

mRNA cap recognition: dominant role of enhanced stacking interactions between methylated bases and protein aromatic side chains.

(1999) Proc Natl Acad Sci U S A 96: 7149-7154

• PubMed: 10377383 Search on PubMedSearch on PubMed Central
• DOI: https://doi.org/10.1073/pnas.96.13.7149
• Primary Citation of Related Structures:  
  1B42, 1BKY, 1EAM, 1EQA, 3MAG, 3MCT, 4DCG


• PubMed Abstract: 
  

  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-A interplanar spacing within the overlapping region, and (iv) positive charge in the heterocyclic nucleobase.

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Organizational Affiliation: 

Graduate Program in Structural and Computational Biology and Molecular Biophysics, Baylor College of Medicine, Houston, TX 77030, USA.