PDBsum entry 1krs

Aminoacyl-tRNA synthetase

PDB id: 1krs

Contents

Protein chain

110 a.a. *

* Residue conservation analysis

PDB id:

1krs

Name:

Aminoacyl-tRNA synthetase

Title:

Solution structure of the anticodon binding domain of escherichia coli lysyl-tRNA synthetase and studies of its interactions with tRNA-lys

Structure:

Lysyl-tRNA synthetase (product of lyss gene). Chain: a. Engineered: yes

Source:

Escherichia coli. Organism_taxid: 562. Strain: jm101tr. Gene: lyss codons 40 - 149. Expressed in: escherichia coli. Expression_system_taxid: 562. Other_details: ptrc99a (iptg-inducible lac promoter)

NMR struc:

1 models

Authors:

S.Commans,F.Dardel

Key ref:

S.Commans et al. (1995). Solution structure of the anticodon-binding domain of Escherichia coli lysyl-tRNA synthetase and studies of its interaction with tRNA(Lys). J Mol Biol, 253, 100-113. PubMed id: 7473706 DOI: 10.1006/jmbi.1995.0539

Date:

09-Jun-95 Release date: 15-Sep-95

Protein chain

P0A8N3  (SYK1_ECOLI) -  Lysine--tRNA ligase from Escherichia coli (strain K12)

Seq: 505 a.a.

Struc: 110 a.a.

Enzyme reactions

• Enzyme class: E.C.6.1.1.6 - lysine--tRNA ligase.
• Reaction: tRNA(Lys) + L-lysine + ATP = L-lysyl-tRNA(Lys) + AMP + diphosphate

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

reference

DOI no: 10.1006/jmbi.1995.0539

J Mol Biol 253:100-113 (1995)

PubMed id: 7473706

Solution structure of the anticodon-binding domain of Escherichia coli lysyl-tRNA synthetase and studies of its interaction with tRNA(Lys).

S.Commans, P.Plateau, S.Blanquet, F.Dardel.

ABSTRACT

A protein domain corresponding to residues 31 to 149 of the E. coli Lysyl-tRNA synthetase species corresponding to the lysS gene was expressed and 15N-labelled. 1H and 15N NMR resonance assignments for this domain were obtained by two-dimensional and three-dimensional homonuclear and heteronuclear spectroscopy. Using distance geometry and simulated annealing, a three-dimensional structure could be calculated using 701 NOE and 86 dihedral angle restraints. It is composed of a five-stranded antiparallel beta-barrel capped by three alpha-helices at its ends. This structure closely resembles that of the N-terminal domain of the other E. coli lysyl-tRNA synthetase species expressed from the lysU gene and is highly homologous to the fold observed for the corresponding region of aspartyl-tRNA synthetase. It is shown that the isolated N-terminal fragment of lysyl-tRNA synthetase can interact with tRNA(Lys) as well as with poly (U), which mimics the anticodon sequence. Amino acid residues involved in these interactions were identified and, in the case of poly-U, a number of specific protein-RNA contacts were characterized. Specific recognition of tRNA(Lys) involves a cluster of four structurally well-defined aromatic residues, anchored on the beta-strands, and basic residues located on the surrounding loops. This organization is reminiscent of other RNA binding proteins, such as the U1A small nuclear ribonucleoprotein.

Selected figure(s)

Figure 3.
Figure 3. LysN structure contains a five-stranded b-barrel. One face of the b-barrel features a cluster of aromatic residues the side-chains of which are reasonably well-defined in the solution structure. Shown are the backbones of the 16 best conformers (red) and the minimized mean structure (yellow), together with the side-chains (in blue and white) of Phe85, Tyr98, His139 and Phe129, from top to bottom. The side-chain of Gln96, which is correctly defined, is also indicated.

Figure 4.
Figure 4. Superposition of the 1 H- 15 N HSQC spectrum of LysN (black) with that of a tRNA Lys /LysN mixture of (0.25/1 stoichiometry; red), at 298 K, in 40 mM potassium phosphate (pH 7.0). Only peaks which show a significant broadening and/or shift are labelled.

The above figures are reprinted by permission from Elsevier: J Mol Biol (1995, 253, 100-113) copyright 1995.

Figures were selected by an automated process.