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PROSITE documentation PDOC50886 [for PROSITE entry PS50886]

tRNA-binding domain profile





Description

The tRNA-binding domain (TRBD) [1] is a domain of ~110 amino acids which is widespread among all living organisms, from eubacteria, archaea or eukarya. The TRBD domain, which is also called Trbp111-like domain or EMAP II-like domain, is widely distributed among different tRNA synthetases and their association factors (such as p43, ARC1, and Trbp111 isolated from various species). The TRBD domain has been shown to possess a general tRNA-binding capacity with recognition of the L shape of tRNA and it has been proposed that the TRBD domain might be a non-specific binder of tRNAs acting in cis or in trans to enhance the catalytic efficiency or substrate specificity of aminoacyl-tRNA synthetases [1,2,3,4].

The resolution of the structure of the TRBD domain has shown that part of it adopts the oligonucleotide/oligosaccharide-binding (OB)-fold (see <PDB:1FL0>). The OB-fold of the TRBD domain consists of a five-stranded Greek-key β-barrel capped by a short α-helix located between the third and fourth strands [3,4,5,6].

Some proteins known to contain a TRBD domain are listed below:

  • Mammalian endothelial-monocyte activating polypeptide II (EMAP-II). EMAP-II is an inflammatory cytokine produced after apoptotic cleavage of the multisynthetase complex auxiliary component p43.
  • Yeast GU4 nucleic-binding protein 1 or ARC1 protein. It binds to tRNA and functions as a cofactor for the methionyl- and glutamyl-tRNA synthetases.
  • Bacterial proteins of the Trb11/CsaA family, which consist only of a TRBD domain.

The profile we developed covers the entire TRBD domain.

PROSITE is copyrighted by the SIB Swiss Institute of Bioinformatics and distributed under the Creative Commons Attribution-NonCommercial-NoDerivatives (CC BY-NC-ND 4.0) License, see https://prosite.expasy.org/prosite_license.html --------------------------------------------------------------------------------.

Last update:

November 2002 / First entry.

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Technical section

PROSITE method (with tools and information) covered by this documentation:

TRBD, PS50886; tRNA-binding domain profile  (MATRIX)


References

1AuthorsKaminska M. Deniziak M. Kerjan P. Barciszewski J. Mirande M.
TitleA recurrent general RNA binding domain appended to plant methionyl-tRNA synthetase acts as a cis-acting cofactor for aminoacylation.
SourceEMBO J. 19:6908-6917(2000).
PubMed ID11118226
DOI10.1093/emboj/19.24.6908

2AuthorsGalani K. Grosshans H. Deinert K. Hurt E.C. Simos G.
TitleThe intracellular location of two aminoacyl-tRNA synthetases depends on complex formation with Arc1p.
SourceEMBO J. 20:6889-6898(2001).
PubMed ID11726524
DOI10.1093/emboj/20.23.6889

3AuthorsKim Y. Shin J. Li R. Cheong C. Kim K. Kim S.
TitleA novel anti-tumor cytokine contains an RNA binding motif present in aminoacyl-tRNA synthetases.
SourceJ. Biol. Chem. 275:27062-27068(2000).
PubMed ID10852899
DOI10.1074/jbc.C000216200

4AuthorsCrepin T. Schmitt E. Blanquet S. Mechulam Y.
TitleStructure and function of the C-terminal domain of methionyl-tRNA synthetase.
SourceBiochemistry 41:13003-13011(2002).
PubMed ID12390027
DOI10.1021/bi026343m

5AuthorsRenault L. Kerjan P. Pasqualato S. Menetrey J. Robinson J.-C. Kawaguchi S. Vassylyev D.G. Yokoyama S. Mirande M. Cherfils J.
TitleStructure of the EMAPII domain of human aminoacyl-tRNA synthetase complex reveals evolutionary dimer mimicry.
SourceEMBO J. 20:570-578(2001).
PubMed ID11157763
DOI10.1093/emboj/20.3.570

6AuthorsKawaguchi S. Mueller J. Linde D. Kuramitsu S. Shibata T. Inoue Y. Vassylyev D.G. Yokoyama S.
TitleThe crystal structure of the ttCsaA protein: an export-related chaperone from Thermus thermophilus.
SourceEMBO J. 20:562-569(2001).
PubMed ID11157762
DOI10.1093/emboj/20.3.562



PROSITE is copyrighted by the SIB Swiss Institute of Bioinformatics and distributed under the Creative Commons Attribution-NonCommercial-NoDerivatives (CC BY-NC-ND 4.0) License, see prosite_license.html.

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