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Literature summary for 6.1.1.3 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

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

Natural Substrates/ Products (Substrates)

Natural Substrates Organism Comment (Nat. Sub.) Natural Products Comment (Nat. Pro.) Rev. Reac.
ATP + L-threonine + tRNAThr Escherichia coli
-
AMP + diphosphate + L-threonyl-tRNAThr
-
?

Organism

Organism UniProt Comment Textmining
Escherichia coli P0A8M3
-
-

Reaction

Reaction Comment Organism Reaction ID
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)

Substrates Comment Substrates Organism Products Comment (Products) Rev. Reac.
ATP + L-threonine + tRNAThr
-
Escherichia coli AMP + diphosphate + L-threonyl-tRNAThr
-
?
ATP + L-threonine + tRNAThr Escherichia coli ectRNAThr Escherichia coli AMP + diphosphate + L-threonyl-tRNAThr
-
?
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 ?
-
?

Subunits

Subunits Comment Organism
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

Synonyms

Synonyms Comment Organism
ectRNAThr
-
Escherichia coli
threonyl tRNA synthetase
-
Escherichia coli

Cofactor

Cofactor Comment Organism Structure
ATP
-
Escherichia coli

General Information

General Information Comment Organism
evolution the enzyme belongs to the class II of aminoacyl-tRNA sythetases Escherichia coli
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