Tyrosine-tRNA ligase

 

Tyrosine-tRNA ligases (TyrRS; also known as Tyrosyl-tRNA synthetases, EC:6.1.1.1) are widely distributed, being found in archaea, bacteria and eukaryotes. TyrRS is a homodimer which attaches Tyr to the appropriate tRNA. TyrRS is a class I tRNA synthetases, so it aminoacylates the 2'-OH of the nucleotide at the 3' end of the tRNA.

 

Reference Protein and Structure

Sequence
P00952 UniProt (6.1.1.1) IPR024107 (Sequence Homologues) (PDB Homologues)
Biological species
Geobacillus stearothermophilus (Bacteria) Uniprot
PDB
2ts1 - STRUCTURE OF TYROSYL-T/RNA SYNTHETASE REFINED AT 2.3 ANGSTROMS RESOLUTION. INTERACTION OF THE ENZYME WITH THE TYROSYL ADENYLATE INTERMEDIATE (2.3 Å) PDBe PDBsum 2ts1
Catalytic CATH Domains
1.10.240.10 CATHdb 3.40.50.620 CATHdb (see all for 2ts1)
Cofactors
Magnesium(2+) (1) Metal MACiE
Click To Show Structure

Enzyme Reaction (EC:6.1.1.1)

ATP(4-)
CHEBI:30616ChEBI
+
L-tyrosine zwitterion
CHEBI:58315ChEBI
+
AMP 3'-end(1-) residue
CHEBI:78442ChEBI
→
3'-(L-tyrosyl)adenylyl(1-) group
CHEBI:78536ChEBI
+
adenosine 5'-monophosphate(2-)
CHEBI:456215ChEBI
+
hydron
CHEBI:15378ChEBI
+
diphosphate(3-)
CHEBI:33019ChEBI
Alternative enzyme names: L-tyrosine-tRNA(Tyr) ligase (AMP-forming), Tyrosine tRNA synthetase, Tyrosine translase, Tyrosine-transfer RNA ligase, Tyrosine-transfer ribonucleate synthetase, Tyrosyl-tRNA ligase, Tyrosyl-tRNA synthetase, Tyrosyl-transfer RNA synthetase, Tyrosyl-transfer ribonucleate synthetase, Tyrosyl-transfer ribonucleic acid synthetase,

Enzyme Mechanism

Introduction

Substrate binding induces a conformational change that brings the residues Lys82 and Arg86 into catalytic range [PMID:3284584]. The carboxylate group of the substrate L-tyrosine acts as a nucleophile and attacks the alpha-phosphate of the ATP in a substitution reaction that liberates pyrophosphate. The phosphate of the tyrosine-AMP complex deprotonates the OH of the ribose ring, which acts as a nucleophile to attack the carbonyl group of the tyrosine in the tyrosine-AMP complex in a substitution reaction, liberating AMP.

Catalytic Residues Roles

UniProt PDB* (2ts1)
Thr234 Thr234A Helps to stabilise the negatively charged intermediates and transition states formed during the course of the reaction. Also affects the steric outcome of the reaction. hydrogen bond acceptor, hydrogen bond donor, metal ligand, electrostatic stabiliser
His48, Asp194, Lys230, Lys233, Gln173, Thr40, His45, Lys82, Arg86 His48A, Asp194A, Lys230A, Lys233A, Gln173A, Thr40A, His45A, Lys82A, Arg86A Act to stabilise the negatively charged intermediates and transition states formed during the course of the reaction. hydrogen bond donor, electrostatic stabiliser
*PDB label guide - RESx(y)B(C) - RES: Residue Name; x: Residue ID in PDB file; y: Residue ID in PDB sequence if different from PDB file; B: PDB Chain; C: Biological Assembly Chain if different from PDB. If label is "Not Found" it means this residue is not found in the reference PDB.

Chemical Components

bimolecular nucleophilic substitution, overall reactant used, intermediate formation, overall product formed, proton transfer, intermediate terminated

References

  1. Fersht AR et al. (1988), Biochemistry, 27, 1581-1587. Reconstruction by site-directed mutagenesis of the transition state for the activation of tyrosine by the tyrosyl-tRNA synthetase: a mobile loop envelopes the transition state in an induced-fit mechanism. DOI:10.1021/bi00405a028. PMID:3284584.
  2. Caprara MG et al. (2001), J Mol Biol, 308, 165-190. Interaction of the Neurospora crassa mitochondrial tyrosyl-tRNA synthetase (CYT-18 protein) with the group I intron P4-P6 domain. thermodynamic analysis and the role of metal ions1 1Edited by D. E. Draper. DOI:10.1006/jmbi.2001.4581. PMID:11327760.
  3. Xin Y et al. (2000), J Mol Biol, 303, 299-310. Stabilization of the transition state for the transfer of tyrosine to tRNATyr by tyrosyl-tRNA synthetase. DOI:10.1006/jmbi.2000.4126. PMID:11023794.
  4. Xin Y et al. (2000), J Mol Biol, 303, 287-298. Correlating amino acid conservation with function in tyrosyl-tRNA synthetase. DOI:10.1006/jmbi.2000.4125. PMID:11023793.
  5. First EA et al. (1993), Biochemistry, 32, 13644-13650. Involvement of threonine 234 in catalysis of tyrosyl adenylate formation by tyrosyl-tRNA synthetase. DOI:10.1021/bi00212a032. PMID:8257697.

Step 1. The carboxylate group of the substrate L-tyrosine acts as a nucleophile and attacks the alpha-phosphate of the ATP in a substitution reaction that liberates pyrophosphate. Mg(II) and all catalytic residues stabilise the intermediates formed. Thr234 also affects the steric outcome of the reaction.

Download: Image, Marvin File

Catalytic Residues Roles

Residue Roles
Thr40A hydrogen bond donor, electrostatic stabiliser
His45A hydrogen bond donor, electrostatic stabiliser
His48A hydrogen bond donor, electrostatic stabiliser
Lys82A hydrogen bond donor, electrostatic stabiliser
Arg86A hydrogen bond donor, electrostatic stabiliser
Gln173A hydrogen bond acceptor, electrostatic stabiliser
Lys230A hydrogen bond donor, electrostatic stabiliser
Lys233A hydrogen bond donor, electrostatic stabiliser
Thr234A hydrogen bond donor, electrostatic stabiliser, metal ligand, hydrogen bond acceptor
Asp194A hydrogen bond acceptor, electrostatic stabiliser

Chemical Components

ingold: bimolecular nucleophilic substitution, overall reactant used, intermediate formation, overall product formed

Step 2. The phosphate of the tyrosine-AMP complex deprotonates the OH of the ribose ring, which acts as a nucleophile to attack the carbonyl group of the tyrosine in the tyrosine-AMP complex in a substitution reaction, liberating AMP. Mg(II), Thr40, His48, Lys82, Arg86 and Gln173 all stabilise the intermediates formed.

Download: Image, Marvin File

Catalytic Residues Roles

Residue Roles
Thr40A hydrogen bond donor, electrostatic stabiliser
His48A hydrogen bond donor, electrostatic stabiliser
Lys82A hydrogen bond donor, electrostatic stabiliser
Arg86A hydrogen bond donor, electrostatic stabiliser
Gln173A hydrogen bond acceptor, electrostatic stabiliser
Asp194A hydrogen bond acceptor, electrostatic stabiliser

Chemical Components

ingold: bimolecular nucleophilic substitution, proton transfer, overall reactant used, intermediate terminated, overall product formed
Download: Image, Marvin File

Step 1. The carboxylate group of the substrate L-tyrosine acts as a nucleophile and attacks the alpha-phosphate of the ATP in a substitution reaction that liberates pyrophosphate. Mg(II) and all catalytic residues stabilise the intermediates formed. Thr234 also affects the steric outcome of the reaction.

Step 2. The phosphate of the tyrosine-AMP complex deprotonates the OH of the ribose ring, which acts as a nucleophile to attack the carbonyl group of the tyrosine in the tyrosine-AMP complex in a substitution reaction, liberating AMP. Mg(II), Thr40, His48, Lys82, Arg86 and Gln173 all stabilise the intermediates formed.

Products.

Contributors

Gemma L. Holliday, Gail J. Bartlett, Daniel E. Almonacid, Craig Porter