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Literature summary extracted from

  • Dutta, S.; Nandi, N.
    Classical molecular dynamics simulation of seryl tRNA synthetase and threonyl tRNA synthetase bound with tRNA and aminoacyl adenylate (2018), J. Biomol. Struct. Dyn., 2018, 1-23 .
    View publication on PubMed

Metals/Ions

EC Number Metals/Ions Comment Organism Structure
6.1.1.3 Mg2+ required Escherichia coli
6.1.1.3 Zn2+ the presence of dynamically rigid zinc ion coordination sphere and bipartite mode of recognition of ectRNAThr are observed Escherichia coli
6.1.1.11 Mg2+ required Thermus thermophilus

Natural Substrates/ Products (Substrates)

EC Number Natural Substrates Organism Comment (Nat. Sub.) Natural Products Comment (Nat. Pro.) Rev. Reac.
6.1.1.3 ATP + L-threonine + tRNAThr Escherichia coli
-
AMP + diphosphate + L-threonyl-tRNAThr
-
?
6.1.1.11 ATP + L-serine + tRNASer Thermus thermophilus
-
AMP + diphosphate + L-seryl-tRNASer
-
?
6.1.1.11 ATP + L-serine + tRNASer Thermus thermophilus HB27 / ATCC BAA-163 / DSM 7039
-
AMP + diphosphate + L-seryl-tRNASer
-
?
6.1.1.11 ATP + L-serine + tRNASer Thermus thermophilus DSM 7039
-
AMP + diphosphate + L-seryl-tRNASer
-
?

Organism

EC Number Organism UniProt Comment Textmining
6.1.1.3 Escherichia coli P0A8M3
-
-
6.1.1.11 Thermus thermophilus P34945
-
-
6.1.1.11 Thermus thermophilus DSM 7039 P34945
-
-
6.1.1.11 Thermus thermophilus HB27 / ATCC BAA-163 / DSM 7039 P34945
-
-

Reaction

EC Number Reaction Comment Organism Reaction ID
6.1.1.3 ATP + L-threonine + tRNAThr = AMP + diphosphate + L-threonyl-tRNAThr reaction mechanism and structure-function relationship, overview. Molecular dynamics simulation study of the dynamics of the active site organization during charging step of dimeric ThrRS from Escherichia coli (ecThrRS) bound with ectRNAThr Escherichia coli

Substrates and Products (Substrate)

EC Number Substrates Comment Substrates Organism Products Comment (Products) Rev. Reac.
6.1.1.3 ATP + L-threonine + tRNAThr
-
Escherichia coli AMP + diphosphate + L-threonyl-tRNAThr
-
?
6.1.1.3 ATP + L-threonine + tRNAThr Escherichia coli ectRNAThr Escherichia coli AMP + diphosphate + L-threonyl-tRNAThr
-
?
6.1.1.3 additional information the interaction of ecRNAThr with the enzyme, interactions between the catalytically important loops and tRNA contribute to the change in dynamics of tRNA in free and bound states, respectively. Presence of bound Mg2+ ions around tRNA and dynamically slow bound water are other common features of the enzyme Escherichia coli ?
-
?
6.1.1.11 ATP + L-serine + tRNASer
-
Thermus thermophilus AMP + diphosphate + L-seryl-tRNASer
-
?
6.1.1.11 ATP + L-serine + tRNASer tttRNASer Thermus thermophilus AMP + diphosphate + L-seryl-tRNASer
-
?
6.1.1.11 ATP + L-serine + tRNASer
-
Thermus thermophilus HB27 / ATCC BAA-163 / DSM 7039 AMP + diphosphate + L-seryl-tRNASer
-
?
6.1.1.11 ATP + L-serine + tRNASer tttRNASer Thermus thermophilus HB27 / ATCC BAA-163 / DSM 7039 AMP + diphosphate + L-seryl-tRNASer
-
?
6.1.1.11 ATP + L-serine + tRNASer
-
Thermus thermophilus DSM 7039 AMP + diphosphate + L-seryl-tRNASer
-
?
6.1.1.11 ATP + L-serine + tRNASer tttRNASer Thermus thermophilus DSM 7039 AMP + diphosphate + L-seryl-tRNASer
-
?
6.1.1.11 additional information the interaction of ttRNASer with the enzyme, interactions between the catalytically important loops and tRNA contribute to the change in dynamics of tRNA in free and bound states, respectively. These interactions help in the development of catalytically effective organization of the active site. The A76 end of the tttRNASer exhibits fast dynamics in free State, which is significantly reduced down within the active site bound with adenylate. The loops change their conformation via multimodal dynamics. Presence of bound Mg2+ ions around tRNA and dynamically slow bound water are other common features of the enzyme Thermus thermophilus ?
-
?
6.1.1.11 additional information the interaction of ttRNASer with the enzyme, interactions between the catalytically important loops and tRNA contribute to the change in dynamics of tRNA in free and bound states, respectively. These interactions help in the development of catalytically effective organization of the active site. The A76 end of the tttRNASer exhibits fast dynamics in free State, which is significantly reduced down within the active site bound with adenylate. The loops change their conformation via multimodal dynamics. Presence of bound Mg2+ ions around tRNA and dynamically slow bound water are other common features of the enzyme Thermus thermophilus HB27 / ATCC BAA-163 / DSM 7039 ?
-
?
6.1.1.11 additional information the interaction of ttRNASer with the enzyme, interactions between the catalytically important loops and tRNA contribute to the change in dynamics of tRNA in free and bound states, respectively. These interactions help in the development of catalytically effective organization of the active site. The A76 end of the tttRNASer exhibits fast dynamics in free State, which is significantly reduced down within the active site bound with adenylate. The loops change their conformation via multimodal dynamics. Presence of bound Mg2+ ions around tRNA and dynamically slow bound water are other common features of the enzyme Thermus thermophilus DSM 7039 ?
-
?

Subunits

EC Number Subunits Comment Organism
6.1.1.3 dimer the dimeric ecThrRS composed of two noncovalently bound monomers bound with ectRNAThr. The anticodon arm of the bound tRNA recognizes the C-terminal anticodon binding domain and acceptor arm interacts with both N-terminal domain and catalytic domain of monomer Escherichia coli
6.1.1.11 dimer
-
Thermus thermophilus
6.1.1.11 homodimer
-
Thermus thermophilus

Synonyms

EC Number Synonyms Comment Organism
6.1.1.3 ectRNAThr
-
Escherichia coli
6.1.1.3 threonyl tRNA synthetase
-
Escherichia coli
6.1.1.11 SerRS
-
Thermus thermophilus
6.1.1.11 serS
-
Thermus thermophilus
6.1.1.11 seryl tRNA synthetase
-
Thermus thermophilus
6.1.1.11 subclass IIa dimeric SerRS
-
Thermus thermophilus
6.1.1.11 ttSerRS
-
Thermus thermophilus
6.1.1.11 TT_C0520
-
Thermus thermophilus

Cofactor

EC Number Cofactor Comment Organism Structure
6.1.1.3 ATP
-
Escherichia coli
6.1.1.11 ATP
-
Thermus thermophilus

General Information

EC Number General Information Comment Organism
6.1.1.3 evolution the enzyme belongs to the class II of aminoacyl-tRNA sythetases Escherichia coli
6.1.1.3 additional information molecular dynamics simulation study of the dynamics of the active site organization during charging step of dimeric ThrRS from Escherichia coli (ecThrRS) bound with ectRNAThr. The active site residues of the motif 2 loop approach the proximal bases of tRNA and adenylate by slow diffusive motion (in nanosecond time scale) and make conformational changes of the respective side chains via ultrafast librational motion to develop precise hydrogen bond geometry. Presence of bound Mg2+ ions around tRNA and dynamically slow bound water are other common features of the enzyme. The presence of dynamically rigid zinc ion coordination sphere and bipartite mode of recognition of ectRNAThr are observed. Molecular dynamic simulation, overview Escherichia coli
6.1.1.11 evolution the enzyme belongs to the class II, subclass IIa, of aminoacyl-tRNA sythetases Thermus thermophilus
6.1.1.11 additional information the interactions between the catalytically important loops and tRNA contribute to the change in dynamics of tRNA in free and bound states, respectively. These interactions help in the development of catalytically effective organization of the active site. The A76 end of the tttRNASer exhibits fast dynamics in free state, which is significantly reduced within the active site bound with adenylate. Presence of bound Mg2+ ions around tRNA and dynamically slow bound water are other common features of the enzyme, dynamics of dimeric ttSerRS bound with adenylate and tttRNASer with a focus to the molecular process of the dynamic development of the catalytically competent active site organization essential for the second step, molecular dynamic simulations, overview Thermus thermophilus