PDBsum entry: 1jh3

Ligase

PDB id: 1jh3

Contents

Protein chain

99 a.a. *

* Residue conservation analysis

PDB id:

1jh3

Name:

Ligase

Title:

Solution structure of tyrosyl-tRNA synthetasE C-terminal domain.

Structure:

Tyrosyl-tRNA synthetase. Chain: a. Fragment: c-terminal domain (residues 321-419). Engineered: yes

Source:

Geobacillus stearothermophilus. Organism_taxid: 1422. Gene: tyrs. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.

NMR struc:

20 models

Authors:

J.I.Guijarro,A.Pintar,A.Prochnicka-Chalufour,V.Guez, B.Gilquin,H.Bedouelle,M.Delepierre

Key ref:

J.I.Guijarro et al. (2002). Structure and dynamics of the anticodon arm binding domain of Bacillus stearothermophilus Tyrosyl-tRNA synthetase. Structure, 10, 311-317. PubMed id: 12005430 DOI: 10.1016/S0969-2126(02)00699-8

Date:

27-Jun-01 Release date: 20-Mar-02

Protein chain

P00952  (SYY_GEOSE) -  Tyrosyl-tRNA synthetase

Seq: 419 a.a.

Struc: 99 a.a.

Enzyme reactions

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

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

 Gene Ontology (GO) functional annotation 

• Cellular component: cytoplasm (1 term)
• Biological process: translation (2 terms)
• Biochemical function: nucleotide binding (4 terms)

reference

DOI no: 10.1016/S0969-2126(02)00699-8

Structure 10:311-317 (2002)

PubMed id: 12005430

Structure and dynamics of the anticodon arm binding domain of Bacillus stearothermophilus Tyrosyl-tRNA synthetase.

J.I.Guijarro, A.Pintar, A.Prochnicka-Chalufour, V.Guez, B.Gilquin, H.Bedouelle, M.Delepierre.

ABSTRACT

The structure of a recombinant protein, TyrRS(delta4), corresponding to the anticodon arm binding domain of Bacillus stearothermophilus tyrosyl-tRNA synthetase, has been solved, and its dynamics have been studied by nuclear magnetic resonance (NMR). It is the first structure described for such a domain of a tyrosyl-tRNA synthetase. It consists of a five-stranded beta sheet, packed against two alpha helices on one side and one alpha helix on the other side. A large part of the domain is structurally similar to other functionally unrelated RNA binding proteins. The basic residues known to be essential for tRNA binding and charging are exposed to the solvent on the same face of the molecule. The structure of TyrRS(delta4), together with previous mutagenesis data, allows one to delineate the region of interaction with tRNATyr.

Selected figure(s)

Figure 4.
Figure 4. Surface Representations of the Structure of TyrRS(D4)Residues 330-418. A ribbon diagram is displayed at the center of the figure to show the orientation of the molecule used in the surface representations.(A) The six basic residues identified by mutagenesis as essential for interaction with tRNA^Tyr are shown in blue, while mutated residues that are not relevant to tRNA interaction as assessed by an in vivo genetic complementation assay [7] are represented in orange. Different blues are used for clarity.(B and C) Surface electrostatic potential of TyrRS(D4) in the same orientation as in (A) and after a 180° y rotation, respectively. Positive and negative potentials are represented in blue and red, respectively. Electrostatic potentials were calculated with MOLMOL [39].(D) Analysis of the putative binding surface. The basic residues known to be important (blue) or irrelevant for tRNA binding (orange) shown in (A) are displayed without label. The remaining residues on the tRNA binding face are labeled and colored: red, negatively charged residues that most probably do not interact with tRNA; cyan, positively charged residues that could in principle interact with tRNA phosphates; dark purple and violet, polar residues (purple) and glycines (violet) with an exposed amide group that could form hydrogen bonds with tRNA bases or ribose; yellow, exposed aromatic residues that could stack with tRNA bases; purple, A[378].

The above figure is reprinted by permission from Cell Press: Structure (2002, 10, 311-317) copyright 2002.

Figure was selected by an automated process.