6Q8U

Structure of the standard kink turn HmKt-7 variant A2bm6A bound with AfL7Ae protein

Summary for 6Q8U

• Entry DOI: 10.2210/pdb6q8u/pdb
• Descriptor: RNA (5'-R(*CP*GP*GP*CP*GP*AP*AP*GP*(6MZ)P*AP*CP*CP*GP*GP*GP*GP*AP*GP*CP*CP*G)-3'), 50S ribosomal protein L7Ae, SODIUM ION, ... (4 entities in total)
• Functional Keywords: gene regulation; rna structure; kink-turn; x-ray crystallography; rna modification, rna
• Biological source: Archaeoglobus fulgidus (strain ATCC 49558 / VC-16 / DSM 4304 / JCM 9628 / NBRC 100126); More
• Total number of polymer chains: 4
• Total formula weight: 41071.51

Authors

Huang, L.,Lilley, D.M.J. (deposition date: 2018-12-16, release date: 2019-07-03, Last modification date: 2024-01-24)

Primary citation

Ashraf, S.,Huang, L.,Lilley, D.M.J.
Effect of methylation of adenine N6on kink turn structure depends on location.
Rna Biol., 16:1377-1385, 2019

PubMed Abstract: N-methyladenine is the most common covalent modification in cellular RNA species, with demonstrated functional consequences. At the molecular level this methylation could alter local RNA structure, and/or modulate the binding of specific proteins. We have previously shown that -Hoogsteen-sugar (sheared) A:G base pairs can be completely disrupted by methylation, and that this occurs in a sub-set ofD/D k-turn structures. In this work we have investigated to what extent sequence context affects the severity with which inclusion of N-methyladenine into different A:G base pairs of a standard k-turn affects RNA folding and L7Ae protein binding. We find that local sequence has a major influence, ranging from complete absence of folding and protein binding to a relatively mild effect. We have determined the crystal structure of one of these species both free and protein-bound, showing the environment of the methyl group and the way the modification is accommodated into the k-turn structure.

PubMed: 31234702
DOI: 10.1080/15476286.2019.1630797

Experimental method

X-RAY DIFFRACTION (1.99 Å)