PDBsum entry 5x89

Hydrolase

PDB id: 5x89

Contents

Protein chain

337 a.a.

Ligands

PO4 ×2

Waters ×292

PDB id:

5x89

Name:

Hydrolase

Title:

The x-ray crystal structure of subunit fusion RNA splicing endonuclease from methanopyrus kandleri

Structure:

Enda-like protein,tRNA-splicing endonuclease. Chain: a. Fragment: unp residues 2-166,unp residues 2-179. Synonym: tRNA-intron endonuclease. Engineered: yes

Source:

Methanopyrus kandleri av19. Organism_taxid: 190192. Gene: mk0397, enda, mk0341. Expressed in: escherichia coli. Expression_system_taxid: 562

Resolution:

1.53Å R-factor: 0.160 R-free: 0.196

Authors:

A.Kaneta,K.Fujishima,W.Morikazu,H.Hori,A.Hirata

Key ref:

A.Kaneta et al. (2018). The RNA-splicing endonuclease from the euryarchaeaon Methanopyrus kandleri is a heterotetramer with constrained substrate specificity. Nucleic Acids Res, 46, 1958-1972. PubMed id: 29346615 DOI: 10.1093/nar/gky003

Date:

01-Mar-17 Release date: 24-Jan-18

Protein chain

Q8TGZ5  (ENDAL_METKA) -  EndA-like protein from Methanopyrus kandleri (strain AV19 / DSM 6324 / JCM 9639 / NBRC 100938)

Seq: 166 a.a.

Struc: 337 a.a.

Protein chain

Q8TGZ7  (ENDA_METKA) -  tRNA-splicing endonuclease from Methanopyrus kandleri (strain AV19 / DSM 6324 / JCM 9639 / NBRC 100938)

Seq: 179 a.a.

Struc: 337 a.a.*

* PDB and UniProt seqs differ at 8 residue positions (black crosses)

Enzyme reactions

• Enzyme class: E.C.4.6.1.16 - tRNA-intron lyase.
• Reaction: pretRNA = a 3'-half-tRNA molecule with a 5'-OH end + a 5'-half-tRNA molecule with a 2',3'-cyclic phosphate end + an intron with a 2',3'-cyclic phosphate and a 5'-hydroxyl terminus

DOI no: 10.1093/nar/gky003

Nucleic Acids Res 46:1958-1972 (2018)

PubMed id: 29346615

The RNA-splicing endonuclease from the euryarchaeaon Methanopyrus kandleri is a heterotetramer with constrained substrate specificity.

A.Kaneta, K.Fujishima, W.Morikazu, H.Hori, A.Hirata.

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.