Molecular modeling study of the editing active site of Escherichia coli leucyl-tRNA synthetase: Two amino acid binding sites in the editing domain

2004 ◽  
Vol 54 (4) ◽  
pp. 693-704 ◽  
Author(s):  
Keun Woo Lee ◽  
James M. Briggs
Keyword(s):  
Escherichia Coli ◽  
Amino Acid ◽  
Molecular Modeling ◽  
Active Site ◽  
Binding Sites ◽  
Trna Synthetase ◽  
Molecular Modeling Study ◽  
Editing Domain ◽  
Amino Acid Binding ◽  
Modeling Study

scholarly journals Transcription and translation in an RNA world

2006 ◽  
Vol 361 (1474) ◽  
pp. 1751-1760 ◽  
Author(s):  
William R Taylor
Keyword(s):  
Amino Acid ◽  
Active Site ◽  
Rna World ◽  
Large Subunit ◽  
Trna Synthetase ◽  
Nucleoside Triphosphate ◽  
Amino Acid Binding ◽  
World Hypothesis ◽  
Protein Elongation ◽  
Rna World Hypothesis

The RNA world hypothesis requires a ribozyme that was an RNA-directed RNA polymerase (ribopolymerase). If such a replicase makes a reverse complementary copy of any sequence (including itself), in a simple RNA world, there is no mechanism to prevent self-hybridization. It is proposed that this can be avoided through the synthesis of a parallel complementary copy. The logical consequences of this are pursued and developed in a computer simulation, where the behaviour of the parallel copy is compared to the conventional reverse complementary copy. It is found that the parallel copy is more efficient at higher temperatures (up to 90°C). A model for the ribopolymerase, based on the core of the large subunit (LSU) of the ribosome, is described. The geometry of a potential active site for this ribopolymerase suggests that it contained a cavity (now occupied by the aminoacyl-tRNA) and that an amino acid binding in this might have ‘poisoned’ the ribopolymerase by cross-reacting with the nucleoside-triphosphate before polymerization could occur. Based on a similarity to the active site components of the class-I tRNA synthetase enzymes, it is proposed that the amino acid could become attached to the nascent RNA transcript producing a variety of aminoacylated tRNA-like products. Using base-pairing interactions, some of these molecules might cross-link two ribopolymerases, giving rise to a precursor of the modern ribosome. A hybrid dimer, half polymerase and half proto-ribosome, could account for mRNA translocation before the advent of protein elongation factors.

A Single Substitution in the Motif 1 of Escherichia coli Lysyl-tRNA Synthetase Induces Cooperativity toward Amino Acid Binding

Biochemistry ◽  
1995 ◽  
Vol 34 (25) ◽  
pp. 8180-8189 ◽  
Author(s):  
Stephane Commans ◽  
Sylvain Blanquet ◽  
Pierre Plateau
Keyword(s):  
Escherichia Coli ◽  
Amino Acid ◽  
Trna Synthetase ◽  
Amino Acid Binding ◽  
Single Substitution

scholarly journals Crystal structures of the editing domain of Escherichia coli leucyl-tRNA synthetase and its complexes with Met and Ile reveal a lock-and-key mechanism for amino acid discrimination

2006 ◽  
Vol 394 (2) ◽  
pp. 399-407 ◽  
Author(s):  
Yunqing Liu ◽  
Jing Liao ◽  
Bin Zhu ◽  
En-Duo Wang ◽  
Jianping Ding
Keyword(s):  
Escherichia Coli ◽  
Amino Acids ◽  
Crystal Structures ◽  
Active Site ◽  
Binding Pocket ◽  
Trna Synthetase ◽  
Vital Role ◽  
Common Mechanism ◽  
Trna Synthetases ◽  
Editing Domain

aaRSs (aminoacyl-tRNA synthetases) are responsible for the covalent linking of amino acids to their cognate tRNAs via the aminoacylation reaction and play a vital role in maintaining the fidelity of protein synthesis. LeuRS (leucyl-tRNA synthetase) can link not only the cognate leucine but also the nearly cognate residues Ile and Met to tRNALeu. The editing domain of LeuRS deacylates the mischarged Ile–tRNALeu and Met–tRNALeu. We report here the crystal structures of ecLeuRS-ED (the editing domain of Escherichia coli LeuRS) in both the apo form and in complexes with Met and Ile at 2.0 Å, 2.4 Å, and 3.2 Å resolution respectively. The editing active site consists of a number of conserved amino acids, which are involved in the precise recognition and binding of the noncognate amino acids. The substrate-binding pocket has a rigid structure which has an optimal stereochemical fit for Ile and Met, but has steric hindrance for leucine. Based on our structural results and previously available biochemical data, we propose that ecLeuRS-ED uses a lock-and-key mechanism to recognize and discriminate between the amino acids. Structural comparison also reveals that all subclass Ia aaRSs share a conserved structure core consisting of the editing domain and conserved residues at the editing active site, suggesting that these enzymes may use a common mechanism for the editing function.

Molecular Modeling Study of Selective Recognition Between Imidazole Cyclophane and Amino Acid Esters

2012 ◽  
Vol 18 (1) ◽  
pp. 6-10
Author(s):  
Kai Lei ◽  
Yongfeng Lou ◽  
Qun Zeng ◽  
Mingli Yang ◽  
Rong Xiao ◽  
...  
Keyword(s):  
Amino Acid ◽  
Molecular Modeling ◽  
Selective Recognition ◽  
Amino Acid Esters ◽  
Molecular Modeling Study ◽  
Acid Esters ◽  
Modeling Study

Role of Zinc in tRNA-acceptor Stem Binding by Glutamyl-tRNA Synthetase FromE.coli: A Molecular Modeling Study

1997 ◽  
Vol 15 (1) ◽  
pp. 19-25
Author(s):  
Asim K. Bothra ◽  
Siddhartha Roy ◽  
Chhabinath Mandal ◽  
Chaitali Mukhophadhyay
Keyword(s):  
Molecular Modeling ◽  
Trna Synthetase ◽  
Acceptor Stem ◽  
Molecular Modeling Study ◽  
Trna Acceptor ◽  
Modeling Study

Evidence for two aromatic amino acid-binding sites, one ATP-dependent and the other ATP-independent, in the Escherichia coli regulatory protein TyrR

1995 ◽  
Vol 17 (3) ◽  
pp. 483-492 ◽  
Author(s):  
Timothy J. Wilson ◽  
Victor P. Argaet ◽  
Geoffrey J. Howlett ◽  
Barrie E. Davidson
Keyword(s):  
Escherichia Coli ◽  
Amino Acid ◽  
Binding Sites ◽  
Aromatic Amino Acid ◽  
Regulatory Protein ◽  
The Other ◽  
Amino Acid Binding

Mapping of the active site of Escherichia coli methionyl-tRNA synthetase: identification of amino acid residues labeled by periodate-oxidized tRNAfMet molecules having modified lengths at the 3'-acceptor end

Biochemistry ◽  
1990 ◽  
Vol 29 (35) ◽  
pp. 8190-8198 ◽  
Author(s):  
Codjo Hountondji ◽  
Jean Marie Schmitter ◽  
Christian Beauvallet ◽  
Sylvain Blanquet
Keyword(s):  
Escherichia Coli ◽  
Amino Acid ◽  
Active Site ◽  
Trna Synthetase ◽  
Amino Acid Residues ◽  
Methionyl Trna Synthetase

A molecular modeling study of the urease active site

1997 ◽  
Vol 419 (1-3) ◽  
pp. 33-36 ◽  
Author(s):  
B Manunza ◽  
S Deiana ◽  
M Pintore ◽  
V Solinas ◽  
C Gessa
Keyword(s):  
Molecular Modeling ◽  
Active Site ◽  
Molecular Modeling Study ◽  
Modeling Study

Protonation States of Important Acidic Residues in the Central Ca2+Ion Binding Sites of the Ca2+-ATPase: A Molecular Modeling Study

Biochemistry ◽  
2011 ◽  
Vol 50 (51) ◽  
pp. 11109-11120 ◽  
Author(s):  
Maria Musgaard ◽  
Lea Thøgersen ◽  
Birgit Schiøtt
Keyword(s):  
Molecular Modeling ◽  
Binding Sites ◽  
Ion Binding ◽  
Molecular Modeling Study ◽  
Acidic Residues ◽  
Ion Binding Sites ◽  
Modeling Study
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