PDBsum entry: 1bs2

Ligase

PDB id: 1bs2

Contents

Protein chain

603 a.a. *

Ligands

ARG

Waters ×271

* Residue conservation analysis

PDB id:

1bs2

Name:

Ligase

Title:

Yeast arginyl-tRNA synthetase

Structure:

Protein (arginyl-tRNA synthetase). Chain: a. Synonym: argrs, arginine - tRNA ligase. Engineered: yes

Source:

Saccharomyces cerevisiae. Baker's yeast. Organism_taxid: 4932. Atcc: ydr341c s70106. Collection: ydr341c s70106. Cellular_location: cytoplasm. Expressed in: escherichia coli. Expression_system_taxid: 562. Other_details: yeast genome, chromosome iv, open reading

Resolution:

2.75Å R-factor: 0.207 R-free: 0.269

Authors:

J.Cavarelli,B.Delagouute,G.Eriani,J.Gangloff,D.Moras

Key ref:

J.Cavarelli et al. (1998). L-arginine recognition by yeast arginyl-tRNA synthetase. EMBO J, 17, 5438-5448. PubMed id: 9736621 DOI: 10.1093/emboj/17.18.5438

Date:

31-Aug-98 Release date: 27-Aug-99

Protein chain

Q05506  (SYRC_YEAST) -  Arginyl-tRNA synthetase, cytoplasmic

Seq: 607 a.a.

Struc: 603 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/17.18.5438

EMBO J 17:5438-5448 (1998)

PubMed id: 9736621

L-arginine recognition by yeast arginyl-tRNA synthetase.

J.Cavarelli, B.Delagoutte, G.Eriani, J.Gangloff, D.Moras.

ABSTRACT

The crystal structure of arginyl-tRNA synthetase (ArgRS) from Saccharomyces cerevisiae, a class I aminoacyl-tRNA synthetase (aaRS), with L-arginine bound to the active site has been solved at 2.75 A resolution and refined to a crystallographic R-factor of 19.7%. ArgRS is composed predominantly of alpha-helices and can be divided into five domains, including the class I-specific active site. The N-terminal domain shows striking similarity to some completely unrelated proteins and defines a module which should participate in specific tRNA recognition. The C-terminal domain, which is the putative anticodon-binding module, displays an all-alpha-helix fold highly similar to that of Escherichia coli methionyl-tRNA synthetase. While ArgRS requires tRNAArg for the first step of the aminoacylation reaction, the results show that its presence is not a prerequisite for L-arginine binding. All H-bond-forming capability of L-arginine is used by the protein for the specific recognition. The guanidinium group forms two salt bridge interactions with two acidic residues, and one H-bond with a tyrosine residue; these three residues are strictly conserved in all ArgRS sequences. This tyrosine is also conserved in other class I aaRS active sites but plays several functional roles. The ArgRS structure allows the definition of a new framework for sequence alignments and subclass definition in class I aaRSs.

Selected figure(s)

Figure 1.
Figure 1 The structure of cytoplasmic ArgRS from the yeast S.cerevisae. (A) Schematic drawing (overall dimension 85 65 40 Å) (drawn with SETOR, Evans, 1993). (B) Topology diagram of the secondary structure elements. Add-1 is in orange, the catalytic domain in red, Ins-1 in green, Ins-2 (CP1) in blue and Add-2 in yellow.

Figure 4.
Figure 4 Schematic representation of the six class I aaRSs highlighting the positions of the Rossmann fold moieties (RF1, RF2 colour coded red). The anticodon-binding module whose fold is similar to that of MetRS and ArgRS is colour coded in yellow. Another inserted peptide, called connecting peptide 2 (CP2), has been identified by sequence analysis in five class I aaRSs (LeuRS, ValRS, IleRS, CysRS and MetRS) (Starzyk et al., 1987; Burbaum and Schimmel, 1991). The CP2 domain of MetRS is highlighted in grey. In ArgRS, as in GluRS, GlnRS, TyrRS and TrpRS, there is no insertion peptide corresponding to CP2.

The above figures are reprinted from an Open Access publication published by Macmillan Publishers Ltd: EMBO J (1998, 17, 5438-5448) copyright 1998.

Figures were selected by the author.