Literature DB >> 22139168

Crystallization and preliminary X-ray analysis of peptidyl-tRNA hydrolase from Escherichia coli in complex with the acceptor-TΨC domain of tRNA.

Kosuke Ito1, Hao Qi, Yoshihiro Shimizu, Ryo Murakami, Kin-ichiro Miura, Takuya Ueda, Toshio Uchiumi.   

Abstract

Peptidyl-tRNA hydrolase (Pth) cleaves the ester bond between the peptide and the tRNA of peptidyl-tRNA molecules, which are the product of aborted translation. In the present work, Pth from Escherichia coli was crystallized with the acceptor-TΨC domain of tRNA using 1,4-butanediol as a precipitant. The crystals belonged to the hexagonal space group P6(1), with unit-cell parameters a = b = 55.1, c = 413.1 Å, and diffracted X-rays beyond 2.4 Å resolution. The asymmetric unit is expected to contain two complexes of Pth and the acceptor-TΨC domain of tRNA (V(M) = 2.8 Å(3) Da(-1)), with a solvent content of 60.8%. The structure is being solved by molecular replacement.

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Year:  2011        PMID： 22139168      PMCID： PMC3232141          DOI： 10.1107/S1744309111038383

Source DB:  PubMed          Journal:  Acta Crystallogr Sect F Struct Biol Cryst Commun        ISSN： 1744-3091


  34 in total

1.  The influence of the peptide chain length on the activity of peptidyl-tRNA hydrolase from E. coli.

Authors:  J Shiloach; S Bauer; N de Groot; Y Lapidot
Journal:  Nucleic Acids Res       Date:  1975-10       Impact factor: 16.971

Review 2.  Peptidyl-tRNA hydrolase and its critical role in protein biosynthesis.

Authors:  Gautam Das; Umesh Varshney
Journal:  Microbiology       Date:  2006-08       Impact factor: 2.777

3.  Orthologs of a novel archaeal and of the bacterial peptidyl-tRNA hydrolase are nonessential in yeast.

Authors:  Guillermina Rosas-Sandoval; Alexandre Ambrogelly; Jesse Rinehart; David Wei; L Rogelio Cruz-Vera; David E Graham; Karl O Stetter; Gabriel Guarneros; Dieter Söll
Journal:  Proc Natl Acad Sci U S A       Date:  2002-12-10       Impact factor: 11.205

4.  Mutant E. coli strain with temperature sensitive peptidyl-transfer RNA hydrolase.

Authors:  A G Atherly; J R Menninger
Journal:  Nat New Biol       Date:  1972-12-20

5.  Studies on polynucleotides. LXXXVI. Enzymic hydrolysis of N-acylaminoacyl-transfer RNA.

Authors:  H Kössel; U L RajBhandary
Journal:  J Mol Biol       Date:  1968-08-14       Impact factor: 5.469

6.  Enzymatic hydrolysis of N-substituted aminoacyl-tRNA.

Authors:  F Cuzin; N Kretchmer; R E Greenberg; R Hurwitz; F Chapeville
Journal:  Proc Natl Acad Sci U S A       Date:  1967-11       Impact factor: 11.205

7.  Solvent content of protein crystals.

Authors:  B W Matthews
Journal:  J Mol Biol       Date:  1968-04-28       Impact factor: 5.469

8.  Crystal structure at 1.8 A resolution and identification of active site residues of Sulfolobus solfataricus peptidyl-tRNA hydrolase.

Authors:  Michel Fromant; Emmanuelle Schmitt; Yves Mechulam; Christine Lazennec; Pierre Plateau; Sylvain Blanquet
Journal:  Biochemistry       Date:  2005-03-22       Impact factor: 3.162

9.  Structure of Francisella tularensis peptidyl-tRNA hydrolase.

Authors:  Teresa E Clarke; Vladimir Romanov; Robert Lam; Scott A Gothe; Srinivasa R Peddi; Ekaterina B Razumova; Richard S A Lipman; Arthur A Branstrom; Nickolay Y Chirgadze
Journal:  Acta Crystallogr Sect F Struct Biol Cryst Commun       Date:  2011-03-26

10.  Role of the 1-72 base pair in tRNAs for the activity of Escherichia coli peptidyl-tRNA hydrolase.

Authors:  S Dutka; T Meinnel; C Lazennec; Y Mechulam; S Blanquet
Journal:  Nucleic Acids Res       Date:  1993-08-25       Impact factor: 16.971
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  5 in total

1.  Crystallization and preliminary X-ray analysis of peptidyl-tRNA hydrolase from Thermus thermophilus HB8.

Authors:  Ami Matsumoto; Yoshihiro Shimizu; Chie Takemoto; Takuya Ueda; Toshio Uchiumi; Kosuke Ito
Journal:  Acta Crystallogr Sect F Struct Biol Cryst Commun       Date:  2013-02-27

2.  Recombinant production, crystallization and X-ray crystallographic structure determination of peptidyl-tRNA hydrolase from Salmonella typhimurium.

Authors:  Venugopal Vandavasi; Kasey Taylor-Creel; Robert L McFeeters; Leighton Coates; Hana McFeeters
Journal:  Acta Crystallogr F Struct Biol Commun       Date:  2014-06-18       Impact factor: 1.056

3.  Release of Ubiquitinated and Non-ubiquitinated Nascent Chains from Stalled Mammalian Ribosomal Complexes by ANKZF1 and Ptrh1.

Authors:  Kazushige Kuroha; Alexandra Zinoviev; Christopher U T Hellen; Tatyana V Pestova
Journal:  Mol Cell       Date:  2018-09-20       Impact factor: 17.970

4.  Recombinant production, crystallization and X-ray crystallographic structure determination of the peptidyl-tRNA hydrolase of Pseudomonas aeruginosa.

Authors:  Ronny C Hughes; Hana McFeeters; Leighton Coates; Robert L McFeeters
Journal:  Acta Crystallogr Sect F Struct Biol Cryst Commun       Date:  2012-11-28

5.  Structural basis for the substrate recognition and catalysis of peptidyl-tRNA hydrolase.

Authors:  Kosuke Ito; Ryo Murakami; Masahiro Mochizuki; Hao Qi; Yoshihiro Shimizu; Kin-ichiro Miura; Takuya Ueda; Toshio Uchiumi
Journal:  Nucleic Acids Res       Date:  2012-08-25       Impact factor: 16.971
  5 in total

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