PDBsum entry 1h3e

Ligase

PDB id: 1h3e

Contents

Protein chain

427 a.a. *

DNA/RNA

Ligands

ATP

TYE

Waters ×13

* Residue conservation analysis

PDB id:

1h3e

Name:

Ligase

Title:

Tyrosyl-tRNA synthetase from thermus thermophilus complexed with wild- type trnatyr(gua) and with atp and tyrosinol

Structure:

Tyrosyl-tRNA synthetase. Chain: a. Synonym: tyrosine--tRNA ligase. Engineered: yes. Wild-type trnatyr(gua). Chain: b. Engineered: yes

Source:

Thermus thermophilus. Organism_taxid: 262724. Strain: hb27. Expressed in: escherichia coli. Expression_system_taxid: 469008. Synthetic: yes. Organism_taxid: 274

Biol. unit:

Tetramer (from PDB file)

Resolution:

2.90Å R-factor: 0.219 R-free: 0.269

Authors:

S.Cusack,A.Yaremchuk,I.Kriklivyi,M.Tukalo

Key ref:

A.Yaremchuk et al. (2002). Class I tyrosyl-tRNA synthetase has a class II mode of cognate tRNA recognition. EMBO J, 21, 3829-3840. PubMed id: 12110594 DOI: 10.1093/emboj/cdf373

Date:

28-Aug-02 Release date: 27-Oct-02

Protein chain

P83453  (SYY_THET2) -  Tyrosine--tRNA ligase from Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27)

Seq: 432 a.a.

Struc: 427 a.a.

DNA/RNA chain

G-G-G-C-A-G-G-U-U-C-C-C-G-A-G-C-G-G-C-C-A-A-A-G-G-G-G-A-C-G-G-U-C-U-G-PSU-A-A- 84 bases

Enzyme reactions

• Enzyme class: E.C.6.1.1.1 - tyrosine--tRNA ligase.
• Reaction: tRNA(Tyr) + L-tyrosine + ATP = L-tyrosyl-tRNA(Tyr) + AMP + diphosphate + H⁺

tRNA(Tyr) (Bound ligand (Het Group name = ATP) corresponds exactly) + L-tyrosine (Bound ligand (Het Group name = TYE) matches with 92.31% similarity) + ATP = L-tyrosyl-tRNA(Tyr) + AMP + diphosphate + H(+)

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

reference

DOI no: 10.1093/emboj/cdf373

EMBO J 21:3829-3840 (2002)

PubMed id: 12110594

Class I tyrosyl-tRNA synthetase has a class II mode of cognate tRNA recognition.

A.Yaremchuk, I.Kriklivyi, M.Tukalo, S.Cusack.

ABSTRACT

Bacterial tyrosyl-tRNA synthetases (TyrRS) possess a flexibly linked C-terminal domain of approximately 80 residues, which has hitherto been disordered in crystal structures of the enzyme. We have determined the structure of Thermus thermophilus TyrRS at 2.0 A resolution in a crystal form in which the C-terminal domain is ordered, and confirm that the fold is similar to part of the C-terminal domain of ribosomal protein S4. We have also determined the structure at 2.9 A resolution of the complex of T.thermophilus TyrRS with cognate tRNA(tyr)(G Psi A). In this structure, the C-terminal domain binds between the characteristic long variable arm of the tRNA and the anti-codon stem, thus recognizing the unique shape of the tRNA. The anticodon bases have a novel conformation with A-36 stacked on G-34, and both G-34 and Psi-35 are base-specifically recognized. The tRNA binds across the two subunits of the dimeric enzyme and, remarkably, the mode of recognition of the class I TyrRS for its cognate tRNA resembles that of a class II synthetase in being from the major groove side of the acceptor stem.

Selected figure(s)

Figure 3.
Figure 3 Interactions between tyrosyl-tRNA synthetase and tRNA^tyr. (A) The C-terminal domain (orange) binds in the elbow between the long variable arm and the anti-codon stem of the tRNA (red backbone, green bases). The anti-codon stem loop interacts with both the C-terminal domain and the -helical domain (pink). The tRNA makes no contact with the catalytic domain of the same subunit (cyan). (B) The unusual conformation of the anti-codon triplet in which Ade-36 is stacked on Gua-34, while Psu-35 bulges out. (C) Base-specific interactions of Asp-259 from the -helical domain with Gua-34 and Asp-423 from the C-terminal domain with Psu-35.

Figure 4.
Figure 4 Structure of tRNAtyr compared with that of tRNA^ser. (A) Comparison of the secondary structures of T.thermophilus tRNA^tyr(G A) (left) and tRNA^tyr(GGA) (right), highlighting differences, conserved in other prokaryotic organisms, that determine the orientation of the long variable arm. tRNA^tyr nucleotides with only backbone contacts to TyrRSTT are shown in purple, those with only base contacts are shown in green and those with backbone and base contacts are shown in orange. (B) Comparison of the 3D structures of the base of the long variable arm in T.thermophilus tRNA^tyr and T.thermophilus tRNA^ser (Biou et al., 1994), based on the structural alignment in (C). In tRNA^ser, Gua-20B is unpaired and stacks against the first base pair of the long variable arm, which comprises A45:U48-1 (top). In tRNA^tyr, U48-1 is unpaired and stacks against the first base pair of the long variable arm, which comprises A20B:U48−2 (bottom). (C) View looking down the anticodon stem-loop of the structural alignment of tRNA^tyr (blue) and tRNA^ser (red) based on superposition of 46 phosphates from the acceptor stem, D- and T-loops (r.m.s.d. = 1.16 Å). The tRNA cores have a very similar structure, but the variable arms project at an angle differing by 50°.

The above figures are reprinted from an Open Access publication published by Macmillan Publishers Ltd: EMBO J (2002, 21, 3829-3840) copyright 2002.

Figures were selected by an automated process.