Active Site of Lysyl-tRNA Synthetase:  Structural Studies of the Adenylation Reaction†

Biochemistry ◽  
2000 ◽  
Vol 39 (29) ◽  
pp. 8418-8425 ◽  
Author(s):  
Gianluigi Desogus ◽  
Flavia Todone ◽  
Peter Brick ◽  
Silvia Onesti
Keyword(s):  
Active Site ◽  
Trna Synthetase ◽  
Structural Studies

Interdomain communication modulates the tRNA-dependent pre-transfer editing of leucyl-tRNA synthetase

2012 ◽  
Vol 449 (1) ◽  
pp. 123-131 ◽  
Author(s):  
Min Tan ◽  
Bin Zhu ◽  
Ru-Juan Liu ◽  
Xin Chen ◽  
Xiao-Long Zhou ◽  
...  
Keyword(s):  
Active Site ◽  
Control Mechanism ◽  
Trna Synthetase ◽  
Structural Studies ◽  
Conformational Rearrangement ◽  
X Ray ◽  
Editing Domain ◽  
Crystal Structural ◽  
Quality Control Mechanism ◽  
Interdomain Communication

EcLeuRS [Escherichia coli LeuRS (leucyl-tRNA synthetase)] has evolved both tRNA-dependent pre- and post-transfer editing capabilities to ensure catalytic specificity. Both editing functions rely on the entry of the tRNA CCA tail into the editing domain of the LeuRS enzyme, which, according to X-ray crystal structural studies, leads to a dynamic disordered orientation of the interface between the synthetic and editing domains. The results of the present study show that this tRNA-triggered conformational rearrangement leads to interdomain communication between the editing and synthetic domains through their interface, and this communication mechanism modulates the activity of tRNA-dependent pre-transfer editing. Furthermore, tRNA-dependent editing reaction inhibits misactivating non-cognate amino acids from the synthetic active site. These results also suggested a novel quality control mechanism of EcLeuRS which is achieved through the co-ordination between the synthetic and editing domains.

Mutational and structural studies of the active-site residues in truncatedFibrobacter succinogenes1,3–1,4-β-D-glucanase

2008 ◽  
Vol 64 (12) ◽  
pp. 1259-1266 ◽  
Author(s):  
Li-Chu Tsai ◽  
Hsiao-Chuan Huang ◽  
Ching-Hua Hsiao ◽  
Yuan-Neng Chiang ◽  
Lie-Fen Shyur ◽  
...  
Keyword(s):  
Active Site ◽  
Structural Studies ◽  
Active Site Residues

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.

RNA Splicing by the Spliceosome

2020 ◽  
Vol 89 (1) ◽  
pp. 359-388 ◽  
Author(s):  
Max E. Wilkinson ◽  
Clément Charenton ◽  
Kiyoshi Nagai
Keyword(s):  
Splice Site ◽  
Active Site ◽  
Rna Splicing ◽  
Messenger Rna ◽  
Structural Studies ◽  
U2 Snrna ◽  
U6 Snrna ◽  
Mature Mrna ◽  
Catalytic Metal ◽  
Small Nuclear Ribonucleoproteins

The spliceosome removes introns from messenger RNA precursors (pre-mRNA). Decades of biochemistry and genetics combined with recent structural studies of the spliceosome have produced a detailed view of the mechanism of splicing. In this review, we aim to make this mechanism understandable and provide several videos of the spliceosome in action to illustrate the intricate choreography of splicing. The U1 and U2 small nuclear ribonucleoproteins (snRNPs) mark an intron and recruit the U4/U6.U5 tri-snRNP. Transfer of the 5′ splice site (5′SS) from U1 to U6 snRNA triggers unwinding of U6 snRNA from U4 snRNA. U6 folds with U2 snRNA into an RNA-based active site that positions the 5′SS at two catalytic metal ions. The branch point (BP) adenosine attacks the 5′SS, producing a free 5′ exon. Removal of the BP adenosine from the active site allows the 3′SS to bind, so that the 5′ exon attacks the 3′SS to produce mature mRNA and an excised lariat intron.

scholarly journals The relationship between synthetic and editing functions of the active site of an aminoacyl-tRNA synthetase.

1993 ◽  
Vol 90 (24) ◽  
pp. 11553-11557 ◽  
Author(s):  
H. Y. Kim ◽  
G. Ghosh ◽  
L. H. Schulman ◽  
S. Brunie ◽  
H. Jakubowski
Keyword(s):  
Active Site ◽  
Trna Synthetase ◽  
Aminoacyl Trna Synthetase ◽  
The Relationship

scholarly journals Crystallization and preliminary X-ray diffraction analysis of human DNA primase

2014 ◽  
Vol 70 (2) ◽  
pp. 206-210 ◽  
Author(s):  
Andrey G. Baranovskiy ◽  
Jianyou Gu ◽  
Nigar D. Babayeva ◽  
Vinod B. Agarkar ◽  
Yoshiaki Suwa ◽  
...  
Keyword(s):  
Active Site ◽  
Large Subunit ◽  
Structural Studies ◽  
Asymmetric Unit ◽  
X Ray Diffraction ◽  
Unit Cell Parameters ◽  
X Ray ◽  
Cell Parameters ◽  
Human Dna ◽  
Structural Details

Human primase synthesizes RNA primers and transfers them to the active site of Pol α with subsequent extension with dNTPs. Human primase is a heterodimer of two subunits: a small catalytic subunit (p49) and a large subunit (p58). The structural details of the initiation and elongation steps of primer synthesis, as well as primer length counting, are not known. To address these questions, structural studies of human primase were initiated. Two types of crystals were obtained. The best diffracting crystals belonged to space groupP1, with unit-cell parametersa= 86.2,b= 88.9,c= 94.68 Å, α = 93.82, β = 96.57, γ = 111.72°, and contained two heterodimers of full-length p49 and p59 subunits in the asymmetric unit.

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