PDBsum entry: 1f7u

Ligase/RNA

PDB id: 1f7u

Contents

Protein chain

606 a.a. *

DNA/RNA

Ligands

SO4

ARG

Waters ×588

* Residue conservation analysis

PDB id:

1f7u

Name:

Ligase/RNA

Title:

Crystal structure of the arginyl-tRNA synthetase complexed w tRNA(arg) and l-arg

Structure:

tRNA(arg). Chain: b. Engineered: yes. Arginyl-tRNA synthetase. Chain: a. Synonym: cytoplasmic arginine-tRNA ligase, argrs. Engineered: yes

Source:

Synthetic: yes. Other_details: this sequence occurs naturally in yeast sacc cerevisae. Saccharomyces cerevisiae. Baker's yeast. Organism_taxid: 4932. Expressed in: escherichia coli. Expression_system_taxid: 562.

Biol. unit:

Dimer (from PQS)

Resolution:

2.20Å R-factor: 0.190 R-free: 0.233

Authors:

B.Delagoutte,D.Moras,J.Cavarelli

Key ref:

B.Delagoutte et al. (2000). tRNA aminoacylation by arginyl-tRNA synthetase: induced conformations during substrates binding. EMBO J, 19, 5599-5610. PubMed id: 11060012 DOI: 10.1093/emboj/19.21.5599

Date:

28-Jun-00 Release date: 27-Jun-01

Protein chain

Q05506  (SYRC_YEAST) -  Arginyl-tRNA synthetase, cytoplasmic

Seq: 607 a.a.

Struc: 606 a.a.

Enzyme reactions

• Enzyme class: E.C.6.1.1.19 - Arginine--tRNA ligase.
• Reaction: ATP + L-arginine + tRNA(Arg) = AMP + diphosphate + L-arginyl-tRNA(Arg)

ATP + L-arginine (Bound ligand (Het Group name = ARG) corresponds exactly) + tRNA(Arg) = AMP + diphosphate + L-arginyl-tRNA(Arg)

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

 Gene Ontology (GO) functional annotation 

• Cellular component: cytoplasm (2 terms)
• Biological process: translation (3 terms)
• Biochemical function: nucleotide binding (5 terms)

reference

DOI no: 10.1093/emboj/19.21.5599

EMBO J 19:5599-5610 (2000)

PubMed id: 11060012

tRNA aminoacylation by arginyl-tRNA synthetase: induced conformations during substrates binding.

B.Delagoutte, D.Moras, J.Cavarelli.

ABSTRACT

The 2.2 A crystal structure of a ternary complex formed by yeast arginyl-tRNA synthetase and its cognate tRNA(Arg) in the presence of the L-arginine substrate highlights new atomic features used for specific substrate recognition. This first example of an active complex formed by a class Ia aminoacyl-tRNA synthetase and its natural cognate tRNA illustrates additional strategies used for specific tRNA selection. The enzyme specifically recognizes the D-loop and the anticodon of the tRNA, and the mutually induced fit produces a conformation of the anticodon loop never seen before. Moreover, the anticodon binding triggers conformational changes in the catalytic center of the protein. The comparison with the 2.9 A structure of a binary complex formed by yeast arginyl-tRNA synthetase and tRNA(Arg) reveals that L-arginine binding controls the correct positioning of the CCA end of the tRNA(Arg). Important structural changes induced by substrate binding are observed in the enzyme. Several key residues of the active site play multiple roles in the catalytic pathway and thus highlight the structural dynamics of the aminoacylation reaction.

Selected figure(s)

Figure 1.
Figure 1 Overview of yArgRS–tRNA^Arg interactions. (A) The cloverleaf structure of tRNA^Arg[ICG]. The one-letter code is used for the nucleotides in all figures. The following code has been used for the modified bases: , pseudouridine; D, dihydrouridine; I, inosine; K, 1-methylguanosine; L, N[2]-methylguanosine; R, N[2],N[2]-dimethylguanosine; m^5C, 5-methylcytidine; m^1A, 1-methyladenosine; T, 5-methyluridine. (B) Overview of one monomer of yArgRS interacting with tRNA^Arg[ICG] (drawn with SETOR; Evans, 1993) showing the modular architecture of yArgRS: Add1 (residues 1–143) is colored in orange; the catalytic domain in red (residues 143–194, 266–293 and 345–410); Ins1 in green (residues 194–266); Ins2 (residues 293–345) in blue; and Add2 (residues 410–607) in yellow. The tRNA backbone is drawn with its phosphate chain traced as a thick cyan line. Numbering of strands and helices is according to the structure of the 'tRNA-free' yArgRS (Cavarelli et al., 1998). The water molecules are not shown. (C) A schematic representation showing the footprint of the tRNA^Arg (in pink) on the surface of yArgRS (in green) (drawn with GRASP; Nicholls and Honig, 1991). (D) The molecular surface of yArgRS showing the electrostatic potential calculated with GRASP (Nicholls and Honig, 1991): negatively charged regions are in red and positively charged areas in blue. The orientation of the yArgRS molecule is similar in all three figures. The tRNA backbone is drawn with its phosphate chain traced as a thick green line.

Figure 5.
Figure 5 Structural changes on yArgRS upon substrate binding. The yArgRS backbone (in orange, red, green, heavy blue and yellow) corresponds to the structure found in the ternary complex. The tRNA backbone is drawn with its phosphate chain traced as a thick purple line. Superpositions were carried out by superimposing the entire protein. (A) Comparison of the structure of the ternary complex with the 'tRNA-free' structure of yArgRS shows the structural movements due to the tRNA binding. Structural elements colored in light blue correspond to the 'tRNA-free' yArgRS structure. Only large movements are displayed. The conformations of two peptides are particularly altered: the first goes from strand S13 to helix H15 and the second involves strand S14, helix H17 and the loop. Structural changes of the conformation of helix H15 induce the modification of the structure of the two signature motifs characteristic of class I aaRSs; the 'H[159]A[160]G[161]H[162]' loop is located between strand S5 and helix H6, while the 'M[408]S[409]T[410]R[411]' loop is located between strand S13 and helix H15. (B) Comparison of the structure of the ternary complex with the binary complex shows the structural movements due to the L-Arg binding. Structural elements colored in light blue correspond to the conformation found in the binary complex. Conformational changes are located mainly in the two insertion modules (Ins1 and Ins2) and helices H13 and H14 of the second moiety of the Rossmann fold. The overall conformation of the tRNA is the same; however, the absence of L-Arg substrate in the active site strongly affects the conformation of the CCA end (see below). Active site of yArgRS: (C) in the ternary complex and (D) in the binary complex, illustrating the molecular switch control by Tyr347 and L-Arg. In the absence of L-Arg substrate (D), G73 extends the helical conformation of the acceptor stem, and the last three nucleotides C[74]C[75]A[76] are not visible in the electron density map and are therefore certainly disordered. The water molecules are not shown.

The above figures are reprinted from an Open Access publication published by Macmillan Publishers Ltd: EMBO J (2000, 19, 5599-5610) copyright 2000.

Figures were selected by the author.