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Crystal structure of leucyl-tRNA synthetase from the archaeon Pyrococcus horikoshii reveals a novel editing domain orientation.
J Mol Biol. 2005 Feb 11; 346(1):57-71.JM

Abstract

The editing domains of the closely homologous leucyl, isoleucyl, and valyl-tRNA synthetases (LeuRS, IleRS, and ValRS, respectively) contribute to accurate aminoacylation, by hydrolyzing misformed non-cognate aminoacyl-tRNAs. The editing domain is inserted at the same point of the sequence in IleRS, ValRS, and the archaeal/eukaryal LeuRS, but at a distinct point in the bacterial LeuRS. Here, we showed that LeuRS from the archaeon Pyrococcus horikoshii has editing activity against the nearly cognate isoleucine. The conserved Asp332 in the editing domain is crucial for this activity. A deletion mutant lacking the C-terminal region has only negligible aminoacylation activity, but retains the full activity of adenylate synthesis and editing. We determined the crystal structure of this editing-active, truncated form of P.horikoshii LeuRS at 2.1 A resolution. The structure revealed that it has a novel editing domain orientation. The editing domain of P.horikoshii LeuRS is rotated by approximately 180 degrees (rotational state II), with the two-beta-stranded linker untwisted by a half-turn, as compared to those in IleRS and ValRS (rotational state I). This editing domain rotational state in the archaeal LeuRS is similar to that in the bacterial LeuRS. However, because of the insertion point difference, the orientation of the editing domain relative to the enzyme core in the archaeal LeuRS differs completely from that in the bacterial LeuRS. An insertion region specific to the archaeal/eukaryal LeuRS editing domains interacts with the enzyme core and stabilizes the unique orientation. Thus, we established that there are three types of editing domain orientations relative to the enzyme core, depending on the combination of the editing domain insertion point (i or ii) and the rotational state (I or II): [i, I] for IleRS and ValRS, [ii, II] for the bacterial LeuRS, and now [i, II] for the archaeal/eukaryal LeuRS.

Authors+Show Affiliations

Fukunaga R
Department of Biophysics and Biochemistry, Graduate School of Science, University of Tokyo, Japan.
Yokoyama S
No affiliation info available

MeSH

AminationAmino Acid SequenceBinding SitesCrystallography, X-RayEvolution, MolecularLeucine-tRNA LigaseModels, MolecularMolecular Sequence DataOligopeptidesProtein Structure, TertiaryPyrococcus horikoshiiSequence Alignment

Pub Type(s)

Journal Article
Research Support, Non-U.S. Gov't

Language

eng

PubMed ID

15663927

Citation

Fukunaga, Ryuya, and Shigeyuki Yokoyama. "Crystal Structure of leucyl-tRNA Synthetase From the Archaeon Pyrococcus Horikoshii Reveals a Novel Editing Domain Orientation." Journal of Molecular Biology, vol. 346, no. 1, 2005, pp. 57-71.
Fukunaga R, Yokoyama S. Crystal structure of leucyl-tRNA synthetase from the archaeon Pyrococcus horikoshii reveals a novel editing domain orientation. J Mol Biol. 2005;346(1):57-71.
Fukunaga, R., & Yokoyama, S. (2005). Crystal structure of leucyl-tRNA synthetase from the archaeon Pyrococcus horikoshii reveals a novel editing domain orientation. Journal of Molecular Biology, 346(1), 57-71.
Fukunaga R, Yokoyama S. Crystal Structure of leucyl-tRNA Synthetase From the Archaeon Pyrococcus Horikoshii Reveals a Novel Editing Domain Orientation. J Mol Biol. 2005 Feb 11;346(1):57-71. PubMed PMID: 15663927.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Crystal structure of leucyl-tRNA synthetase from the archaeon Pyrococcus horikoshii reveals a novel editing domain orientation. AU - Fukunaga,Ryuya, AU - Yokoyama,Shigeyuki, Y1 - 2004/12/19/ PY - 2004/09/21/received PY - 2004/11/21/revised PY - 2004/11/22/accepted PY - 2005/1/25/pubmed PY - 2005/3/12/medline PY - 2005/1/25/entrez SP - 57 EP - 71 JF - Journal of molecular biology JO - J Mol Biol VL - 346 IS - 1 N2 - The editing domains of the closely homologous leucyl, isoleucyl, and valyl-tRNA synthetases (LeuRS, IleRS, and ValRS, respectively) contribute to accurate aminoacylation, by hydrolyzing misformed non-cognate aminoacyl-tRNAs. The editing domain is inserted at the same point of the sequence in IleRS, ValRS, and the archaeal/eukaryal LeuRS, but at a distinct point in the bacterial LeuRS. Here, we showed that LeuRS from the archaeon Pyrococcus horikoshii has editing activity against the nearly cognate isoleucine. The conserved Asp332 in the editing domain is crucial for this activity. A deletion mutant lacking the C-terminal region has only negligible aminoacylation activity, but retains the full activity of adenylate synthesis and editing. We determined the crystal structure of this editing-active, truncated form of P.horikoshii LeuRS at 2.1 A resolution. The structure revealed that it has a novel editing domain orientation. The editing domain of P.horikoshii LeuRS is rotated by approximately 180 degrees (rotational state II), with the two-beta-stranded linker untwisted by a half-turn, as compared to those in IleRS and ValRS (rotational state I). This editing domain rotational state in the archaeal LeuRS is similar to that in the bacterial LeuRS. However, because of the insertion point difference, the orientation of the editing domain relative to the enzyme core in the archaeal LeuRS differs completely from that in the bacterial LeuRS. An insertion region specific to the archaeal/eukaryal LeuRS editing domains interacts with the enzyme core and stabilizes the unique orientation. Thus, we established that there are three types of editing domain orientations relative to the enzyme core, depending on the combination of the editing domain insertion point (i or ii) and the rotational state (I or II): [i, I] for IleRS and ValRS, [ii, II] for the bacterial LeuRS, and now [i, II] for the archaeal/eukaryal LeuRS. SN - 0022-2836 UR - https://www.unboundmedicine.com/medline/citation/15663927/Crystal_structure_of_leucyl_tRNA_synthetase_from_the_archaeon_Pyrococcus_horikoshii_reveals_a_novel_editing_domain_orientation_ DB - PRIME DP - Unbound Medicine ER -