Literature DB >> 23994531

Pyrrolysyl-tRNA synthetase variants reveal ancestral aminoacylation function.

Jae-hyeong Ko1, Yane-Shih Wang, Akiyoshi Nakamura, Li-Tao Guo, Dieter Söll, Takuya Umehara.   

Abstract

Pyrrolysyl-tRNA synthetase (PylRS) is a class IIc aminoacyl-tRNA synthetase that is related to phenylalanyl-tRNA synthetase (PheRS). Genetic selection provided PylRS variants with a broad range of specificity for diverse non-canonical amino acids (ncAAs). One variant is a specific phenylalanine-incorporating enzyme. Structural models of the PylRSamino acid complex show that the small pocket size and π-interaction play an important role in specific recognition of Phe and the engineered PylRS active site resembles that of Escherichia coli PheRS.
Copyright © 2013 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved.

Entities:  

Keywords:  Non-canonical amino acid; Phenylalanyl-tRNA synthetase; Pyrrolysyl-tRNA synthetase; Superfolder green fluorescent protein

Mesh：

Substances：

Year:  2013        PMID： 23994531      PMCID： PMC3778162          DOI： 10.1016/j.febslet.2013.08.018

Source DB:  PubMed          Journal:  FEBS Lett        ISSN： 0014-5793            Impact factor:   4.124


  20 in total

1.  A facile system for genetic incorporation of two different noncanonical amino acids into one protein in Escherichia coli.

Authors:  Wei Wan; Ying Huang; Zhiyong Wang; William K Russell; Pei-Jing Pai; David H Russell; Wenshe R Liu
Journal:  Angew Chem Int Ed Engl       Date:  2010-04-19       Impact factor: 15.336

2.  Engineering and characterization of a superfolder green fluorescent protein.

Authors:  Jean-Denis Pédelacq; Stéphanie Cabantous; Timothy Tran; Thomas C Terwilliger; Geoffrey S Waldo
Journal:  Nat Biotechnol       Date:  2005-12-20       Impact factor: 54.908

Review 3.  Distinct genetic code expansion strategies for selenocysteine and pyrrolysine are reflected in different aminoacyl-tRNA formation systems.

Authors:  Jing Yuan; Patrick O'Donoghue; Alex Ambrogelly; Sarath Gundllapalli; R Lynn Sherrer; Sotiria Palioura; Miljan Simonović; Dieter Söll
Journal:  FEBS Lett       Date:  2010-01-21       Impact factor: 4.124

4.  Crystallographic studies on multiple conformational states of active-site loops in pyrrolysyl-tRNA synthetase.

Authors:  Tatsuo Yanagisawa; Ryohei Ishii; Ryuya Fukunaga; Takatsugu Kobayashi; Kensaku Sakamoto; Shigeyuki Yokoyama
Journal:  J Mol Biol       Date:  2008-02-29       Impact factor: 5.469

5.  PHENIX: a comprehensive Python-based system for macromolecular structure solution.

Authors:  Paul D Adams; Pavel V Afonine; Gábor Bunkóczi; Vincent B Chen; Ian W Davis; Nathaniel Echols; Jeffrey J Headd; Li-Wei Hung; Gary J Kapral; Ralf W Grosse-Kunstleve; Airlie J McCoy; Nigel W Moriarty; Robert Oeffner; Randy J Read; David C Richardson; Jane S Richardson; Thomas C Terwilliger; Peter H Zwart
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  2010-01-22

6.  Prokaryotic and eukaryotic tetrameric phenylalanyl-tRNA synthetases display conservation of the binding mode of the tRNA(Phe) CCA end.

Authors:  Nina Moor; Olga Lavrik; Alain Favre; Mark Safro
Journal:  Biochemistry       Date:  2003-09-16       Impact factor: 3.162

7.  Structure of pyrrolysyl-tRNA synthetase, an archaeal enzyme for genetic code innovation.

Authors:  Jennifer M Kavran; Sarath Gundllapalli; Patrick O'Donoghue; Markus Englert; Dieter Söll; Thomas A Steitz
Journal:  Proc Natl Acad Sci U S A       Date:  2007-06-25       Impact factor: 11.205

8.  Specificity of pyrrolysyl-tRNA synthetase for pyrrolysine and pyrrolysine analogs.

Authors:  Wen-Tai Li; Anirban Mahapatra; David G Longstaff; Jonathan Bechtel; Gang Zhao; Patrick T Kang; Michael K Chan; Joseph A Krzycki
Journal:  J Mol Biol       Date:  2008-11-25       Impact factor: 5.469

9.  Genetic incorporation of twelve meta-substituted phenylalanine derivatives using a single pyrrolysyl-tRNA synthetase mutant.

Authors:  Yane-Shih Wang; Xinqiang Fang; Hsueh-Ying Chen; Bo Wu; Zhiyong U Wang; Christian Hilty; Wenshe R Liu
Journal:  ACS Chem Biol       Date:  2012-11-19       Impact factor: 5.100

10.  Recognition of pyrrolysine tRNA by the Desulfitobacterium hafniense pyrrolysyl-tRNA synthetase.

Authors:  Stephanie Herring; Alexandre Ambrogelly; Carla R Polycarpo; Dieter Söll
Journal:  Nucleic Acids Res       Date:  2007-01-31       Impact factor: 16.971
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  19 in total

1.  A Strategy for Creating Organisms Dependent on Noncanonical Amino Acids.

Authors:  Weimin Xuan; Peter G Schultz
Journal:  Angew Chem Int Ed Engl       Date:  2017-06-27       Impact factor: 15.336

Review 2.  Pyrrolysyl-tRNA synthetase: an ordinary enzyme but an outstanding genetic code expansion tool.

Authors:  Wei Wan; Jeffery M Tharp; Wenshe R Liu
Journal:  Biochim Biophys Acta       Date:  2014-03-12

3.  On how many fundamental kinds of cells are present on Earth: looking for phylogenetic traits that would allow the identification of the primary lines of descent.

Authors:  Massimo Di Giulio
Journal:  J Mol Evol       Date:  2014-06-12       Impact factor: 2.395

4.  A genomically modified Escherichia coli strain carrying an orthogonal E. coli histidyl-tRNA synthetase•tRNAHis pair.

Authors:  Markus Englert; Oscar Vargas-Rodriguez; Noah M Reynolds; Yane-Shih Wang; Dieter Söll; Takuya Umehara
Journal:  Biochim Biophys Acta Gen Subj       Date:  2017-03-10       Impact factor: 3.770

5.  In Vivo Biosynthesis of a β-Amino Acid-Containing Protein.

Authors:  Clarissa Melo Czekster; Wesley E Robertson; Allison S Walker; Dieter Söll; Alanna Schepartz
Journal:  J Am Chem Soc       Date:  2016-04-18       Impact factor: 15.419

Review 6.  Upgrading aminoacyl-tRNA synthetases for genetic code expansion.

Authors:  Oscar Vargas-Rodriguez; Anastasia Sevostyanova; Dieter Söll; Ana Crnković
Journal:  Curr Opin Chem Biol       Date:  2018-07-27       Impact factor: 8.822

7.  Polyspecific pyrrolysyl-tRNA synthetases from directed evolution.

Authors:  Li-Tao Guo; Yane-Shih Wang; Akiyoshi Nakamura; Daniel Eiler; Jennifer M Kavran; Margaret Wong; Laura L Kiessling; Thomas A Steitz; Patrick O'Donoghue; Dieter Söll
Journal:  Proc Natl Acad Sci U S A       Date:  2014-11-10       Impact factor: 11.205

8.  Evolution of translation machinery in recoded bacteria enables multi-site incorporation of nonstandard amino acids.

Authors:  Miriam Amiram; Adrian D Haimovich; Chenguang Fan; Yane-Shih Wang; Hans-Rudolf Aerni; Ioanna Ntai; Daniel W Moonan; Natalie J Ma; Alexis J Rovner; Seok Hoon Hong; Neil L Kelleher; Andrew L Goodman; Michael C Jewett; Dieter Söll; Jesse Rinehart; Farren J Isaacs
Journal:  Nat Biotechnol       Date:  2015-11-16       Impact factor: 54.908

9.  Exploring the substrate range of wild-type aminoacyl-tRNA synthetases.

Authors:  Chenguang Fan; Joanne M L Ho; Napon Chirathivat; Dieter Söll; Yane-Shih Wang
Journal:  Chembiochem       Date:  2014-05-30       Impact factor: 3.164

10.  Efficient Reassignment of a Frequent Serine Codon in Wild-Type Escherichia coli.

Authors:  Joanne M Ho; Noah M Reynolds; Keith Rivera; Morgan Connolly; Li-Tao Guo; Jiqiang Ling; Darryl J Pappin; George M Church; Dieter Söll
Journal:  ACS Synth Biol       Date:  2015-11-20       Impact factor: 5.110
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