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Title: Crystal Structure of RNase T, an Exoribonuclease Involved in tRNA Maturation and End Turnover

Abstract

The 3 processing of most bacterial precursor tRNAs involves exonucleolytic trimming to yield a mature CCA end. This step is carried out by RNase T, a member of the large DEDD family of exonucleases. We report the crystal structures of RNase T from Escherichia coli and Pseudomonas aeruginosa, which show that this enzyme adopts an opposing dimeric arrangement, with the catalytic DEDD residues from one monomer closely juxtaposed with a large basic patch on the other monomer. This arrangement suggests that RNase T has to be dimeric for substrate specificity, and agrees very well with prior site-directed mutagenesis studies. The dimeric architecture of RNase T is very similar to the arrangement seen in oligoribonuclease, another bacterial DEDD family exoribonuclease. The catalytic residues in these two enzymes are organized very similarly to the catalytic domain of the third DEDD family exoribonuclease in E. coli, RNase D, which is monomeric.

Authors:
; ; ; ; ; ; ; ;
Publication Date:
Research Org.:
Brookhaven National Laboratory (BNL) National Synchrotron Light Source
Sponsoring Org.:
Doe - Office Of Science
OSTI Identifier:
930365
Report Number(s):
BNL-81084-2008-JA
Journal ID: ISSN 0969-2126; TRN: US200904%%653
DOE Contract Number:
DE-AC02-98CH10886
Resource Type:
Journal Article
Resource Relation:
Journal Name: Structure; Journal Volume: 15
Country of Publication:
United States
Language:
English
Subject:
36 MATERIALS SCIENCE; CRYSTAL STRUCTURE; ENZYMES; ESCHERICHIA COLI; MONOMERS; MUTAGENESIS; PRECURSOR; PSEUDOMONAS; RESIDUES; RNA-ASE; SPECIFICITY; SUBSTRATES; national synchrotron light source

Citation Formats

Zuo,Y., Zheng, H., Wang, Y., Chruszcz, M., Cymborowski, M., Skarina, T., Savchenko, A., Malhotra, A., and Minor, W. Crystal Structure of RNase T, an Exoribonuclease Involved in tRNA Maturation and End Turnover. United States: N. p., 2007. Web. doi:10.1016/j.str.2007.02.004.
Zuo,Y., Zheng, H., Wang, Y., Chruszcz, M., Cymborowski, M., Skarina, T., Savchenko, A., Malhotra, A., & Minor, W. Crystal Structure of RNase T, an Exoribonuclease Involved in tRNA Maturation and End Turnover. United States. doi:10.1016/j.str.2007.02.004.
Zuo,Y., Zheng, H., Wang, Y., Chruszcz, M., Cymborowski, M., Skarina, T., Savchenko, A., Malhotra, A., and Minor, W. Mon . "Crystal Structure of RNase T, an Exoribonuclease Involved in tRNA Maturation and End Turnover". United States. doi:10.1016/j.str.2007.02.004.
@article{osti_930365,
title = {Crystal Structure of RNase T, an Exoribonuclease Involved in tRNA Maturation and End Turnover},
author = {Zuo,Y. and Zheng, H. and Wang, Y. and Chruszcz, M. and Cymborowski, M. and Skarina, T. and Savchenko, A. and Malhotra, A. and Minor, W.},
abstractNote = {The 3 processing of most bacterial precursor tRNAs involves exonucleolytic trimming to yield a mature CCA end. This step is carried out by RNase T, a member of the large DEDD family of exonucleases. We report the crystal structures of RNase T from Escherichia coli and Pseudomonas aeruginosa, which show that this enzyme adopts an opposing dimeric arrangement, with the catalytic DEDD residues from one monomer closely juxtaposed with a large basic patch on the other monomer. This arrangement suggests that RNase T has to be dimeric for substrate specificity, and agrees very well with prior site-directed mutagenesis studies. The dimeric architecture of RNase T is very similar to the arrangement seen in oligoribonuclease, another bacterial DEDD family exoribonuclease. The catalytic residues in these two enzymes are organized very similarly to the catalytic domain of the third DEDD family exoribonuclease in E. coli, RNase D, which is monomeric.},
doi = {10.1016/j.str.2007.02.004},
journal = {Structure},
number = ,
volume = 15,
place = {United States},
year = {Mon Jan 01 00:00:00 EST 2007},
month = {Mon Jan 01 00:00:00 EST 2007}
}
  • No abstract prepared.
  • No abstract prepared.
  • A number of archaeal organisms generate Cys-tRNA{sup Cys} in a two-step pathway, first charging phosphoserine (Sep) onto tRNA{sup Cys} and subsequently converting it to Cys-tRNA{sup Cys}. We have determined, at 3.2-{angstrom} resolution, the structure of the Methanococcus maripaludis phosphoseryl-tRNA synthetase (SepRS), which catalyzes the first step of this pathway. The structure shows that SepRS is a class II, {alpha}{sub 4} synthetase whose quaternary structure arrangement of subunits closely resembles that of the heterotetrameric ({alpha}{beta}){sub 2} phenylalanyl-tRNA synthetase (PheRS). Homology modeling of a tRNA complex indicates that, in contrast to PheRS, a single monomer in the SepRS tetramer may recognize bothmore » the acceptor terminus and anticodon of a tRNA substrate. Using a complex with tungstate as a marker for the position of the phosphate moiety of Sep, we suggest that SepRS and PheRS bind their respective amino acid substrates in dissimilar orientations by using different residues.« less
  • Yeast aspartyl-tRNA synthetase, a dimer of molecular weight 125,000, and two molecules of its cognate tRNA (Mr = 24160) cocrystallize in the cubic space group I432 (a = 354 A). The crystal structure was solved to low resolution using neutron and X-ray diffraction data. Neutron single crystal diffraction data were collected in five solvents differing by their D2O content in order to use the contrast variation method to distinguish between the protein and tRNA. The synthetase was first located at 40 A resolution using the 65% D2O neutron data (tRNA matched) tRNA molecules were found at 20 A resolution usingmore » both neutron and X-ray data. The resulting model was refined against 10 A resolution X-ray data, using density modification and least-squares refinement of the tRNA positions. The crystal structure solved without a priori phase knowledge, was confirmed later by isomorphous replacement. The molecular model of the complex is in good agreement with results obtained in solution by probing the protected part of the tRNA by chemical reagents.« less