5X89

The X-ray crystal structure of subunit fusion RNA splicing endonuclease from Methanopyrus kandleri

5X89 の概要

• エントリーDOI: 10.2210/pdb5x89/pdb
• 分子名称: EndA-like protein,tRNA-splicing endonuclease, PHOSPHATE ION (3 entities in total)
• 機能のキーワード: rna splicing, intron, archaea, hydrolase
• 由来する生物種: Methanopyrus kandleri AV19; 詳細
• タンパク質・核酸の鎖数: 1
• 化学式量合計: 41913.99

構造登録者

Kaneta, A.,Fujishima, K.,Morikazu, W.,Hori, H.,Hirata, A. (登録日: 2017-03-01, 公開日: 2018-01-24, 最終更新日: 2024-03-27)

主引用文献

Kaneta, A.,Fujishima, K.,Morikazu, W.,Hori, H.,Hirata, A.
The RNA-splicing endonuclease from the euryarchaeaon Methanopyrus kandleri is a heterotetramer with constrained substrate specificity
Nucleic Acids Res., 46:1958-1972, 2018

PubMed Abstract: Four different types (α4, α'2, (αβ)2 and ϵ2) of RNA-splicing endonucleases (EndAs) for RNA processing are known to exist in the Archaea. Only the (αβ)2 and ϵ2 types can cleave non-canonical introns in precursor (pre)-tRNA. Both enzyme types possess an insert associated with a specific loop, allowing broad substrate specificity in the catalytic α units. Here, the hyperthermophilic euryarchaeon Methanopyrus kandleri (MKA) was predicted to harbor an (αβ)2-type EndA lacking the specific loop. To characterize MKA EndA enzymatic activity, we constructed a fusion protein derived from MKA α and β subunits (fMKA EndA). In vitro assessment demonstrated complete removal of the canonical bulge-helix-bulge (BHB) intron structure from MKA pre-tRNAAsn. However, removal of the relaxed BHB structure in MKA pre-tRNAGlu was inefficient compared to crenarchaeal (αβ)2 EndA, and the ability to process the relaxed intron within mini-helix RNA was not detected. fMKA EndA X-ray structure revealed a shape similar to that of other EndA types, with no specific loop. Mapping of EndA types and their specific loops and the tRNA gene diversity among various Archaea suggest that MKA EndA is evolutionarily related to other (αβ)2-type EndAs found in the Thaumarchaeota, Crenarchaeota and Aigarchaeota but uniquely represents constrained substrate specificity.

PubMed: 29346615
DOI: 10.1093/nar/gky003

実験手法

X-RAY DIFFRACTION (1.53 Å)