Tyrosine—tRNA ligase
This article may be confusing or unclear to readers. (May 2021) |
tyrosine—tRNA ligase | |||||||||
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ExPASy | NiceZyme view | ||||||||
KEGG | KEGG entry | ||||||||
MetaCyc | metabolic pathway | ||||||||
PRIAM | profile | ||||||||
PDB structures | RCSB PDB PDBe PDBsum | ||||||||
Gene Ontology | AmiGO / QuickGO | ||||||||
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Tyrosine—tRNA ligase (EC 6.1.1.1), also known as tyrosyl-tRNA synthetase is an enzyme that is encoded by the gene YARS. Tyrosine—tRNA ligase catalyzes the chemical reaction
- ATP + L-tyrosine + tRNA(Tyr) AMP + diphosphate + L-tyrosyl-tRNA(Tyr)
The three
This enzyme belongs to the family of
Structural studies
As of late 2007, 34
The tyrosyl-tRNA synthetases (YARS) are either
Eubacteria
Tyrosyl-tRNA synthetase from
The C-terminal moiety of the eubacterial YARSs comprises two domains: (i) a proximal α-helical domain (known as Anticodon Binding Domain or α-ACB) of about 100 amino acids; (ii) a distal domain (known as S4-like) that shares high homology with the C-terminal domain of ribosomal protein S4.[10] The S4-like domain was disordered in the crystal structure of B. stearothermophilus YARS. However, biochemical and NMR experiments have shown that the S4-like domain is folded in solution, and that its structure is similar to that in the crystal structure of the T. thermophilus YARS.[10] Mutagenesis experiments have shown that the flexibility of the peptide that links the α-ACB and S4-like domains is responsible for the disorder of the latter in the structure and that elements of sequence in this linker peptide are essential for the binding of tRNA(Tyr) by YARS and its aminoacylation with tyrosine.[11] TyrRSs from eubacterial species are divided into two subgroups according to variation in their C-terminal moiety.[12]
Archaea and lower eukaryotes
The crystal structures of several archaeal tyrosyl-tRNA synthetases are available. The crystal structure of the complex between YARS from
Homo sapiens cytoplasm
The human
Homo sapiens mitochondria
The
Neurospora crassa mitochondria
The
Plasmodium falciparum
The structure of the complex between Plasmodium falciparum tyrosyl-tRNA synthetase (Pf-YARS) and tyrosyl-adenylate at 2.2 Å resolution, shows that the overall fold of Pf-YARS is typical of class I
Mimivirus
Leishmania major
The single YARS gene that is present in the genomes of trypanosomatids, codes for a protein that has twice the length of tyrosyl-tRBA synthetase from other organisms. Each half of the double-length YARS contains a catalytic domain and an anticodon-binding domain; however, the two halves retain only 17% sequence identity to each other. Crystal structures of Leishmania major YARS at 3.0 Å resolution show that the two halves of a single molecule form a pseudo-dimer that resembles the canonical YARS dimer. The C-terminal copy of the catalytic domain has lost the catalytically important HIGH and KMSKS motifs, characteristic of class I aminoacyl-tRNA synthetases. Thus, the pseudo-dimer contains only one functional active site (contributed by the N-terminal half) and only one functional anticodon recognition site (contributed by the C-terminal half). Thus, the L. major YARS pseudo-dimer is inherently asymmetric.[23]
Roles of the subunits and domains
The N-terminal domain of tyrosyl-tRNA synthetase provides the chemical groups necessary for converting the substrates tyrosine and ATP into a reactive intermediate, tyrosyl-adenylate (the first step of the aminoacylation reaction) and for transferring the amino-acid moiety from tyrosyl-adenylate to the 3'OH-CCA terminus of the cognate tRNA(Tyr) (the second step of the aminoacylation reaction).[24][25] The other domains are responsible (i) for the recognition of the anticodon bases of the cognate tRNA(Tyr); (ii) for the binding of the long variable arm of tRNA(Tyr) in eubacteria;[9] and (iii) for unrelated functions such as cytokine activity.
Recognition of tRNA(Tyr)
The tRNA(Tyr) molecule has an L-shaped structure. Its recognition involves both subunits of the tyrosyl-tRNA synthetase dimer. The acceptor arm of tRNA(Tyr) interacts with the catalytic domain of one YARS monomer whereas the anticodon arm interacts with the C-terminal moiety of the other monomer.[26][7] In most YARS structures, the monomers are related to each other by a twofold rotational symmetry. Moreover, all available crystal structures of complexes between YARS and tRNA(Tyr) are also planar, with symmetrical conformations of the two monomers in the dimer and with two tRNA(Tyr) molecules simultaneously interacting with one YARS dimer.[16] However, kinetic studies of tyrosine activation and tRNA(Tyr) charging have revealed an anticooperative behavior of the TyrRS dimer in solution: each TyrRS dimer binds and tyrosylates only one tRNA(Tyr) molecule at a time. Thus, only one of the two sites is active at any given time.[7][27]
The presence of base pair Gua1:Cyt72 in the acceptor stem of tRNA(Tyr) from eubacteria and of base pair Cyt1-Gua72 in tRNA(Tyr) from archaea and eukaryotes results in a species specific recognition of tRNATyr by tyrosyl-tRNA synthetase. This characteristic of the recognition between YARS and tRNA(Tyr) has been used to obtain aminoacyl-tRNA synthetases that can specifically charge non-sense suppressor derivatives of tRNA(Tyr) with unnatural aminoacids in vivo without interfering with the normal process of translation in the cell.[28]
Both tyrosyl-tRNA synthetases and tryptophanyl-tRNA synthetases belong to Class I of the aminoacyl-tRNA synthetases, both are dimers and both have a class II mode of tRNA recognition, i.e. they interact with their cognate tRNAs from the variable loop and major groove side of the acceptor stem.[7][8][9][29] This is in strong contrast to the other class I enzymes, which are monomeric and approach their cognate tRNA from minor groove side of the acceptor stem.[30]
Folding and stability
The unfolding reaction and stability of tyrosyl-tRNA synthetase from
References
- S2CID 4324290.
- ^ PMID 10447505.
- ^ Bedouelle, Hugues (2013). Tyrosyl-tRNA Synthetases. Austin (TX): Landes Bioscience.
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- ^ S2CID 4307998.
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- PMID 7517395.
- S2CID 26282354.
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- ^ PMID 17576676.
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- S2CID 2863728.
- PMID 16798914.
- S2CID 46222849.
- S2CID 9070841.
- PMID 4084496.
- S2CID 1824025.
External links
Further reading
- Allen EH, Glassman E, Schweet RS (April 1960). "Incorporation of amino acids into ribonucleic acid. I. The role of activating enzymes". The Journal of Biological Chemistry. 235 (4): 1061–7. PMID 13792726.
- Cowles JR, Key JL (September 1972). "Demonstration of two tyrosyl-tRNA synthetases of pea roots". Biochimica et Biophysica Acta (BBA) - Nucleic Acids and Protein Synthesis. 281 (1): 33–44. PMID 4563531.
- Holley RW, Brunngraber EF, Saad F, Williams HH (January 1961). "Partial purification of the threonine- and tyrosine-activating enzymes from rat liver, and the effect of patassium ions on the activity of the tyrosine enzyme". The Journal of Biological Chemistry. 236: 197–9. PMID 13715350.
- Schweet RS, Allen EH (November 1958). "Purification and properties of tyrosine-activating enzyme of hog pancreas". The Journal of Biological Chemistry. 233 (5): 1104–8. PMID 13598741.