PDBsum entry: 1r1b

Ligase

PDB id: 1r1b

Contents

Protein chain

56 a.a. *

* Residue conservation analysis

PDB id:

1r1b

Name:

Ligase

Title:

Eprs second repeated element, nmr, minimized average structure

Structure:

tRNA synthetase. Chain: a. Fragment: residues 1 - 59. Synonym: tRNA ligase. Engineered: yes

Source:

Cricetulus griseus. Chinese hamster. Organism_taxid: 10029. Organ: ovary cells. Expressed in: escherichia coli. Expression_system_taxid: 562

NMR struc:

1 models

Authors:

B.Cahuzac,E.Berthonneau,N.Birlirakis,M.Mirande,E.Guittet

Key ref:

B.Cahuzac et al. (2000). A recurrent RNA-binding domain is appended to eukaryotic aminoacyl-tRNA synthetases. EMBO J, 19, 445-452. PubMed id: 10654942 DOI: 10.1093/emboj/19.3.445

Date:

15-Dec-98 Release date: 15-Dec-99

Protein chain

Q7SIA2  (SYEP_CRIGR) -  Bifunctional aminoacyl-tRNA synthetase (Fragment)

Seq: 49 a.a.

Struc: 56 a.a.

Enzyme reactions

• Enzyme class 2: E.C.6.1.1.15 - Proline--tRNA ligase.
• Reaction: ATP + L-proline + tRNA(Pro) = AMP + diphosphate + L-prolyl-tRNA(Pro)
• Enzyme class 3: E.C.6.1.1.17 - Glutamate--tRNA ligase.
• Reaction: ATP + L-glutamate + tRNA(Glu) = AMP + diphosphate + L-glutamyl-tRNA(Glu)

Note, where more than one E.C. class is given (as above), each may correspond to a different protein domain or, in the case of polyprotein precursors, to a different mature protein.

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 (3 terms)
• Biochemical function: catalytic activity (9 terms)

reference

DOI no: 10.1093/emboj/19.3.445

EMBO J 19:445-452 (2000)

PubMed id: 10654942

A recurrent RNA-binding domain is appended to eukaryotic aminoacyl-tRNA synthetases.

B.Cahuzac, E.Berthonneau, N.Birlirakis, E.Guittet, M.Mirande.

ABSTRACT

Aminoacyl-tRNA synthetases of higher eukaryotes possess polypeptide extensions in contrast to their prokaryotic counterparts. These extra domains of poorly understood function are believed to be involved in protein-protein or protein-RNA interactions. Here we showed by gel retardation and filter binding experiments that the repeated units that build the linker region of the bifunctional glutamyl-prolyl-tRNA synthetase had a general RNA-binding capacity. The solution structure of one of these repeated motifs was also solved by NMR spectroscopy. One repeat is built around an antiparallel coiled-coil. Strikingly, the conserved lysine and arginine residues form a basic patch on one side of the structure, presenting a suitable docking surface for nucleic acids. Therefore, this repeated motif may represent a novel type of general RNA-binding domain appended to eukaryotic aminoacyl-tRNA synthetases to serve as a cis-acting tRNA-binding cofactor.

Selected figure(s)

Figure 1.
Figure 1 Alignment of the conserved RNA-binding motifs appended to eukaryotic aaRS. The first capital letters of the protein represent the amino acid substrate, while the final two letters are for the species [Hs (Homo sapiens) stands for human, Cg (Cricetulus griseus) for hamster, Dm (Drosophila melanogaster) for fly, Ce (Caenorhabditis elegans) for nematode, Bt (Bos taurus) for cow, Mm (Mus musculus) for mouse, Oc (Oryctolagus cuniculus) for rabbit, Bm (Bombyx mori) for silkworm, At (Arabidopsis thaliana) for cress, Fr (Fugu rubripes) for pufferfish and Sp (Schizosaccharomyces pombe) for yeast]. Residues that match the consensus sequence (defined as residues conserved in 80% of the repeated sequences) are boxed. Conserved hydrophobic residues are in green, basic residues are in blue. The sequence numbers given on the top line relate to the sequence of the R1b motif from hamster used to determine its solution structure. The regions that form helices in R1b are indicated above the sequence alignment.

Figure 5.
Figure 5 (A) Ribbon diagram of the lowest energy structure of R1B (3–51) (top), compared with another RNA-binding protein, S15 (24–71) (bottom). The conserved basic residues in both families are indicated. (B) Electrostatic surface potential of R1B [in front view, same orientation as in (A)] and S15 [slightly rotated compared with (A)], and 180° rotated view. Positive and negative charges are shown in blue and red, respectively. The figures were generated using GRASP (Nicholls et al., 1991).

The above figures are reprinted from an Open Access publication published by Macmillan Publishers Ltd: EMBO J (2000, 19, 445-452) copyright 2000.

Figures were selected by an automated process.