PDBsum entry 4fz2

Hydrolase

PDB id: 4fz2

Contents

Protein chains

386 a.a.

Waters ×152

PDB id:

4fz2

Name:

Hydrolase

Title:

Crystal structure of the fourth type of archaeal tRNA splicing endonuclease from candidatus micrarchaeum acidiphilum arman-2

Structure:

tRNA intron endonuclease. Chain: a, b. Engineered: yes

Source:

Candidatus micrarchaeum acidiphilum. Organism_taxid: 425595. Strain: arman-2. Gene: unlarm2_0797. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

2.25Å R-factor: 0.220 R-free: 0.257

Authors:

A.Hirata,K.Fujishima,R.Yamagami,T.Kawamura,J.F.Banfiled,A.Kanai, H.Hori

Key ref:

A.Hirata et al. (2012). X-ray structure of the fourth type of archaeal tRNA splicing endonuclease: insights into the evolution of a novel three-unit composition and a unique loop involved in broad substrate specificity. Nucleic Acids Res, 40, 10554-10566. PubMed id: 22941657

Date:

06-Jul-12 Release date: 12-Sep-12

Protein chains

C7DIA5  (C7DIA5_MICA2) -  tRNA intron endonuclease from Candidatus Micrarchaeum acidiphilum ARMAN-2

Seq: 387 a.a.

Struc: 386 a.a.

Enzyme reactions

• Enzyme class: E.C.3.1.27.9 - Transferred entry: 4.6.1.16.
• Reaction: Endonucleolytic cleavage of pre-tRNA, producing 5'-hydroxyl and 2',3'-cyclic phosphate termini, and specifically removing the intron.

Nucleic Acids Res 40:10554-10566 (2012)

PubMed id: 22941657

X-ray structure of the fourth type of archaeal tRNA splicing endonuclease: insights into the evolution of a novel three-unit composition and a unique loop involved in broad substrate specificity.

A.Hirata, K.Fujishima, R.Yamagami, T.Kawamura, J.F.Banfield, A.Kanai, H.Hori.

ABSTRACT

Cleavage of introns from precursor transfer RNAs (tRNAs) by tRNA splicing endonuclease (EndA) is essential for tRNA maturation in Archaea and Eukarya. In the past, archaeal EndAs were classified into three types (α'2, α4 and α2β2) according to subunit composition. Recently, we have identified a fourth type of archaeal EndA from an uncultivated archaeon Candidatus Micrarchaeum acidiphilum, referred to as ARMAN-2, which is deeply branched within Euryarchaea. The ARMAN-2 EndA forms an ε2 homodimer and has broad substrate specificity like the α2β2 type EndAs found in Crenarchaea and Nanoarchaea. However, the precise architecture of ARMAN-2 EndA was unknown. Here, we report the crystal structure of the ε2 homodimer of ARMAN-2 EndA. The structure reveals that the ε protomer is separated into three novel units (αN, α and βC) fused by two distinct linkers, although the overall structure of ARMAN-2 EndA is similar to those of the other three types of archaeal EndAs. Structural comparison and mutational analyses reveal that an ARMAN-2 type-specific loop (ASL) is involved in the broad substrate specificity and that K161 in the ASL functions as the RNA recognition site. These findings suggest that the broad substrate specificities of ε2 and α2β2 EndAs were separately acquired through different evolutionary processes.