5X89
The X-ray crystal structure of subunit fusion RNA splicing endonuclease from Methanopyrus kandleri
Summary for 5X89
| Entry DOI | 10.2210/pdb5x89/pdb |
| Descriptor | EndA-like protein,tRNA-splicing endonuclease, PHOSPHATE ION (3 entities in total) |
| Functional Keywords | rna splicing, intron, archaea, hydrolase |
| Biological source | Methanopyrus kandleri AV19 More |
| Total number of polymer chains | 1 |
| Total formula weight | 41913.99 |
| Authors | Kaneta, A.,Fujishima, K.,Morikazu, W.,Hori, H.,Hirata, A. (deposition date: 2017-03-01, release date: 2018-01-24, Last modification date: 2024-03-27) |
| Primary citation | 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 Cited by 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: 29346615DOI: 10.1093/nar/gky003 PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (1.53 Å) |
Structure validation
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