3P1Y
Crystal structure of the chimeric Archaeoglobus fulgidus RNA splicing endonuclease with the broadest substrate specificity
Summary for 3P1Y
| Entry DOI | 10.2210/pdb3p1y/pdb |
| Descriptor | tRNA-splicing endonuclease (2 entities in total) |
| Functional Keywords | protein homodimer, rna splicing endonuclease, broad substrate specificity, hydrolase |
| Biological source | Archaeoglobus fulgidus More |
| Total number of polymer chains | 4 |
| Total formula weight | 148325.72 |
| Authors | Hirata, A. (deposition date: 2010-10-01, release date: 2011-08-10, Last modification date: 2024-03-20) |
| Primary citation | Hirata, A.,Kitajima, T.,Hori, H. Cleavage of intron from the standard or non-standard position of the precursor tRNA by the splicing endonuclease of Aeropyrum pernix, a hyper-thermophilic Crenarchaeon, involves a novel RNA recognition site in the Crenarchaea specific loop Nucleic Acids Res., 39:9376-9389, 2011 Cited by PubMed Abstract: In Crenarchaea, several tRNA genes are predicted to express precursor-tRNAs (pre-tRNAs) with canonical or non-canonical introns at various positions. We initially focused on the tRNA(Thr) species of hyperthermophilic crenarchaeon, Aeropyrum pernix (APE) and found that in the living APE cells three tRNA(Thr) species were transcribed and subsequently matured to functional tRNAs. During maturation, introns in two of them were cleaved from standard and non-standard positions. Biochemical studies revealed that the APE splicing endonuclease (APE-EndA) removed both types of introns, including the non-canonical introns, without any nucleotide modification. To clarify the underlying reasons for broad substrate specificity of APE-EndA, we determined the crystal structure of wild-type APE-EndA and subsequently compared its structure with that of Archaeaoglobus fulgidus (AFU)-EndA, which has narrow substrate specificity. Remarkably, structural comparison revealed that APE-EndA possesses a Crenarchaea specific loop (CSL). Introduction of CSL into AFU-EndA enhanced its intron-cleaving activity irrespective of the position or motif of the intron. Thus, our biochemical and crystallographic analyses of the chimera-EndA demonstrated that the CSL is responsible for the broad substrate specificity of APE-EndA. Furthermore, mutagenesis studies revealed that Lys44 in CSL functions as the RNA recognition site. PubMed: 21846775DOI: 10.1093/nar/gkr615 PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (2.05 Å) |
Structure validation
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