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.

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

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.

scholarly journals Cloning, expression, purification, crystallization and preliminary X-ray crystallographic analyses of threonyl-tRNA synthetase editing domain fromAeropyrum pernix

2012 ◽  
Vol 68 (11) ◽  
pp. 1390-1393 ◽  
Author(s):  
Sadeem Ahmad ◽  
Antony S. K. Sravankumar ◽  
Shobha P. Kruparani ◽  
Rajan Sankaranarayanan
Keyword(s):  
Trna Synthetase ◽  
Asymmetric Unit ◽  
Crystallographic Investigation ◽  
X Ray ◽  
Trna Synthetases ◽  
Aeropyrum Pernix ◽  
Substrate Analogues ◽  
Aminoacyl Trna Synthetases ◽  
Editing Domain ◽  
Evolutionary Aspects

The proofreading function of aminoacyl-tRNA synthetases is crucial in maintaining the fidelity of protein synthesis. Most archaeal threonyl-tRNA synthetases (ThrRSs) possess a unique proofreading domain unrelated to their eukaryotic/bacterial counterpart. The crystal structure of this domain from the archaeonPyrococcus abysiiin complex with its cognate and noncognate substrate analogues had given insights into its catalytic and discriminatory mechanisms. To probe further into the mechanistic and evolutionary aspects of this domain, work has been extended to another archaeonAeropyrum pernix. The organism possesses two proteins corresponding to threonyl-tRNA synthetase,i.e.ThrRS1 and ThrRS2, encoded by two different genes,thrS1andthrS2, respectively. ThrRS1 is responsible for aminoacylation and ThrRS2 for proofreading activity. Here the purification, crystallization and preliminary X-ray crystallographic investigation of the N-terminal proofreading domain of ThrRS2 fromA. pernixis reported. The crystals belong to either theP41212 orP43212 space group and consist of one monomer per asymmetric unit.

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.

scholarly journals X‐RAY CRYSTAL STRUCTURAL STUDIES OF VP26 OF WSSV

2006 ◽  
Vol 20 (4) ◽  
Author(s):  
Xuhua Tang ◽  
Jayaraman Sivaraman ◽  
Choy‐leong Hew
Keyword(s):  
Structural Studies ◽  
X Ray ◽  
Crystal Structural

scholarly journals Heliophyllite: a discredited mineral species identical to ecdemite

2020 ◽  
Vol 32 (2) ◽  
pp. 265-273
Author(s):  
Natale Perchiazzi ◽  
Ulf Hålenius ◽  
Nicola Demitri ◽  
Pietro Vignola
Keyword(s):  
Natural History ◽  
Single Crystal ◽  
Electron Probe ◽  
Structural Studies ◽  
X Ray ◽  
Single Crystal Study ◽  
Crystal Structural ◽  
Diffraction Peaks ◽  
A Minor ◽  
Minor Quantity

Abstract. The type material for heliophyllite, preserved in the Swedish Museum of Natural History in Stockholm, was re-investigated through a combined EPMA (electron probe X-ray microanalysis), Raman, and X-ray powder diffraction (XRPD) and single-crystal study. EPMA chemical data, together with Raman and single-crystal structural studies, point to heliophyllite being identical to ecdemite. XRPD synchrotron data highlight the presence of a minor quantity of finely admixed finnemanite in the analyzed material, explaining the presence of some additional diffraction peaks, not indexable with the ecdemite unit cell, reported in the literature. The discreditation of heliophyllite has been approved by the IMA Commission on New Minerals and Mineral Names (proposal 19-H, 2019).

Structural studies of the hemocyanin active site. 1. Extended x-ray absorption fine structure (EXAFS) analysis

1980 ◽  
Vol 102 (12) ◽  
pp. 4210-4216 ◽  
Author(s):  
J. M. Brown ◽  
L. Powers ◽  
B. Kincaid ◽  
J. A. Larrabee ◽  
T. G. Spiro
Keyword(s):  
Fine Structure ◽  
Active Site ◽  
Structural Studies ◽  
X Ray ◽  
Exafs Analysis ◽  
Absorption Fine ◽  
X Ray Absorption

scholarly journals Study on the putative active site of Enterococcus faecalis prolyl- tRNA synthetase editing domain by methods of site-directed mutagenesis

2009 ◽  
Vol 25 (1) ◽  
pp. 39-42 ◽  
Author(s):  
K. S. Boyarshin ◽  
I. A. Kriklivyi ◽  
A. V. Rayevsky ◽  
A. A. Himin ◽  
A. D. Yaremchuk ◽  
...  
Keyword(s):  
Enterococcus Faecalis ◽  
Active Site ◽  
Trna Synthetase ◽  
Site Directed Mutagenesis ◽  
Directed Mutagenesis ◽  
Putative Active Site ◽  
Editing Domain
Sign in / Sign up

Export Citation Format

Share Document