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Overview for MACiE Entry M0197

Version history

General Information

EC Number: 6.1.1.1 (A member of the Ligases, Forming carbon-oxygen bonds, Ligases forming aminoacyl-tRNA and related compounds)

Enzyme Name: tyrosine-tRNA ligase

Biological Species: Bacillus stearothermophilus (Bacteria)

Catalytic Chain UniprotKB Accession Codes:

  • P00952 - Tyrosyl-tRNA synthetase

Representative PDB Code: 2ts1 - STRUCTURE OF TYROSYL-T/RNA SYNTHETASE REFINED AT 2.3 ANGSTROMSRESOLUTION. INTERACTION OF THE ENZYME WITH THE TYROSYL ADENYLATEINTERMEDIATE (Resolution = 2.30 Å).

Catalytic CATH Codes:

  • 3.40.50.620 - Tyrosyl-Transfer RNA Synthetase , subunit E, domain 1
  • 1.10.240.10 - Tyrosyl-Transfer RNA Synthetase

Display structure information

Overall Reaction:

Image of L-tyrosine

Image of ATP

Image of tRNA(Tyr)

right arrow

Image of L-tyrosyl-tRNA(Tyr)

Image of AMP

Image of diphosphate

L-tyrosine
C00082
CHEBI:58315
ATP
C00002
CHEBI:30616
tRNA(Tyr)
C00787
CHEBI:29182
L-tyrosyl-tRNA(Tyr)
C02839
CHEBI:29161
AMP
C00020
CHEBI:456215
diphosphate
C00013
CHEBI:33019

Overall Comment: The position of the Mg(II) within the active site of tyrosyl-tRNA synthetase is not apparent from the X-ray crystal structure. It also appears that substrate binding induces a conformational change that brings the residues Lys82 and Arg86 into range [1].


View similar reactions


Stepwise Description of the Reaction

Step 1The 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 2The 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.

View similar reactions (composite manual annotation)


Catalytic Residues Involved

Type Number Chain Location of Function
Thr 40 A Side Chain
His 45 A Side Chain
His 48 A Side Chain
Lys 82 A Side Chain
Arg 86 A Side Chain
Gln 173 A Side Chain
Lys 230 A Side Chain
Lys 233 A Side Chain
Thr 234 A Side Chain
Asp 194 A Side Chain

Metal Cofactors for M0197

Type Het group Number Chain
magnesium MG(not in PDB) 1 x Overview

References

  1. A. R. Fersht 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.
    Medline: 3284584
  2. Y. Xin et al. (2000), J. Mol. Biol., 303, 299-310. Stabilization of the transition state for the transfer of tyrosine to tRNA(Tyr) by tyrosyl-tRNA synthetase.
    Medline: 11023794
  3. Y. Xin et al. (2000), J. Mol. Biol., 303, 287-298. Correlating amino acid conservation with function in tyrosyl-tRNA synthetase.
    Medline: 11023793
  4. E. A. First et al. (1993), Biochemistry, 32, 13644-13650. Involvement of threonine 234 in catalysis of tyrosyl adenylate formation by tyrosyl-tRNA synthetase.
    Medline: 8257697
  5. M. G. Caprara 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 ions.
    Medline: 11327760

Homologue information for M0197 (2ts1)

CSA Homologues

MACiE Homologues (within the PDB)

MACiE Homologues (within UniprotKB/SwissProt)



Entries with at least one Catalytic CATH code in common (different mechanisms):

MACiE Entry Enzyme Name
EC Number
PDB code CATH code Composite
Reaction Similarity
Catalytic Machinery
Similarity
M0279 phosphoadenylyl-sulfate reductase (thioredoxin)
1.8.4.8
1sur 3.40.50.620
0.05880Compare
M0299 pantetheine-phosphate adenylyltransferase
2.7.7.3
1b6t 3.40.50.620
0.33330.2999Compare
M0287 sulfate adenylyltransferase
2.7.7.4
1g8f 3.40.50.620
0.36360.2598Compare
M0296 glycerol-3-phosphate cytidylyltransferase
2.7.7.39
1n1d 3.40.50.620
0.33330.2999Compare
M0309 isoleucine-tRNA ligase
6.1.1.5
1ile 3.40.50.620
0.750.3234Compare
M0235 arginine-tRNA ligase
6.1.1.19
1f7u 3.40.50.620
0.66660.3749Compare
M0229 pantoate-beta-alanine ligase
6.3.2.1
2a84 3.40.50.620
0.3750.2103Compare
M0303 (carboxyethyl)arginine beta-lactam-synthase
6.3.3.4
1mb9 3.40.50.620
0.41170.135Compare
M0316 argininosuccinate synthetase
6.3.4.5
1j21 3.40.50.620
0.42850.0428Compare
M0234 GMP synthase (glutamine-hydrolysing)
6.3.5.2
1gpm 3.40.50.620
0.17070.2571Compare
M0302 asparagine synthase (glutamine-hydrolysing)
6.3.5.4
1ct9 3.40.50.620
0.15940.1173Compare

View a comparison of the other reactions in MACiE with the CATH domain 3.40.50.620


Links to this entry in other databases

Link to EC-PDB-SUM Link to PDB-SUM Link to RCSB PDB Link to PDBe Link to CSA
Link to MetaCyc Link to KEGG Link to BRENDA Link to ExplorENZ

GOA logo
nucleotide binding (molecular function)
RNA binding (molecular function)
aminoacyl-tRNA ligase activity (molecular function)
tyrosine-tRNA ligase activity (molecular function)
ATP binding (molecular function)
cytoplasm (cellular component)
translation (biological process)
tRNA aminoacylation for protein translation (biological process)
tyrosyl-tRNA aminoacylation (biological process)
ligase activity (molecular function)
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