PDBsum entry: 1n9w

Biosynthetic protein

PDB id: 1n9w

Contents

Protein chains

356 a.a. *

Waters ×159

* Residue conservation analysis

PDB id:

1n9w

Name:

Biosynthetic protein

Title:

Crystal structure of the non-discriminating and archaeal- type aspartyl-tRNA synthetase from thermus thermophilus

Structure:

Aspartyl-tRNA synthetase 2. Chain: a, b. Engineered: yes

Source:

Thermus thermophilus. Organism_taxid: 274. Expressed in: escherichia coli. Expression_system_taxid: 562

Biol. unit:

Dimer (from PQS)

Resolution:

2.30Å R-factor: 0.227 R-free: 0.262

Authors:

C.Charron,H.Roy,M.Blaise,R.Giege,D.Kern

Key ref:

C.Charron et al. (2003). Non-discriminating and discriminating aspartyl-tRNA synthetases differ in the anticodon-binding domain. EMBO J, 22, 1632-1643. PubMed id: 12660169 DOI: 10.1093/emboj/cdg148

Date:

26-Nov-02 Release date: 08-Apr-03

Protein chains

Q9LCY8  (Q9LCY8_THETH) -  Aspartyl-tRNA synthetase 2

Seq: 422 a.a.

Struc: 356 a.a.

 Gene Ontology (GO) functional annotation 

• Cellular component: cytoplasm (1 term)
• Biological process: translation (4 terms)
• Biochemical function: nucleotide binding (7 terms)

DOI no: 10.1093/emboj/cdg148

EMBO J 22:1632-1643 (2003)

PubMed id: 12660169

Non-discriminating and discriminating aspartyl-tRNA synthetases differ in the anticodon-binding domain.

C.Charron, H.Roy, M.Blaise, R.Giegé, D.Kern.

ABSTRACT

In most organisms, tRNA aminoacylation is ensured by 20 aminoacyl-tRNA synthetases (aaRSs). In eubacteria, however, synthetases can be duplicated as in Thermus thermophilus, which contains two distinct AspRSs. While AspRS-1 is specific, AspRS-2 is non-discriminating and aspartylates tRNA(Asp) and tRNA(Asn). The structure at 2.3 A resolution of AspRS-2, the first of a non-discriminating synthetase, was solved. It differs from that of AspRS-1 but has resemblance to that of discriminating and archaeal AspRS from Pyrococcus kodakaraensis. The protein presents non-conventional features in its OB-fold anticodon-binding domain, namely the absence of a helix inserted between two beta-strands of this fold and a peculiar L1 loop differing from the large loops known to interact with tRNA(Asp) identity determinant C36 in conventional AspRSs. In AspRS-2, this loop is small and structurally homologous to that in AsnRSs, including conservation of a proline. In discriminating Pyrococcus AspRS, the L1 loop, although small, lacks this proline and is not superimposable with that of AspRS-2 or AsnRS. Its particular status is demonstrated by a loop-exchange experiment that renders the Pyrococcus AspRS non-discriminating.

Selected figure(s)

Figure 1.
Figure 1 Stereoviews of the MAD electron density map (contoured at 1.0 ) of part of the catalytic site (A) and anticodon-binding (B) domains of T.thermophilus AspRS-2. In (A), the -strands A2, A3, A4, A5, and A6 are labelled as in the P.kodakaraensis AspRS structure (Schmitt et al., 1998). In (B), displaying an amino acid stretch (residues 65 -75) comprising loop L1, notice the functionally important Pro72 and the lack of density for the side chain of Lys70 (see text).

Figure 2.
Figure 2 Structure of T.thermophilus AspRS-2. (A) Ribbon representation of the dimeric synthetase. Subunit A is drawn in yellow (N-terminal domain) and in orange (catalytic domain), and subunit B is in blue (N-terminal domain) and purple (catalytic domain). The N- and C-terminal ends of each subunit are labelled. (B) Electrostatic potential mapped on the molecular surface of dimeric AspRS-2, as computed with Swiss-Pdb Viewer (Guex and Peitsch, 1997). Blue, white and red regions correspond to positive, neutral and negative electrostatic potentials, respectively. The putative location of a backbone model of tRNA^Asp, as in the complex with T.thermophilus AspRS-1 (Briand et al., 2000), covering 'blue' regions of positive potential, is indicated. The orientation of the synthetase is as in (A).

The above figures are reprinted from an Open Access publication published by Macmillan Publishers Ltd: EMBO J (2003, 22, 1632-1643) copyright 2003.

Figures were selected by an automated process.