Structural basis for functional mimicry of long-variable-arm tRNA by transfer-messenger RNA.

PubWeight™: 1.52‹?› | Rank: Top 4%

🔗 View Article (PMC 1895943)

Published in Proc Natl Acad Sci U S A on May 08, 2007

Authors

Yoshitaka Bessho1, Rie Shibata, Shun-ichi Sekine, Kazutaka Murayama, Kyoko Higashijima, Chie Hori-Takemoto, Mikako Shirouzu, Seiki Kuramitsu, Shigeyuki Yokoyama

Author Affiliations

1: Genomic Sciences Center, Yokohama Institute, RIKEN 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan.

Articles citing this

tRNA-mRNA mimicry drives translation initiation from a viral IRES. Nat Struct Mol Biol (2007) 1.84

The crystal structure of Cpf1 in complex with CRISPR RNA. Nature (2016) 1.35

Decoding in the absence of a codon by tmRNA and SmpB in the ribosome. Science (2012) 1.24

The bacterial translation stress response. FEMS Microbiol Rev (2014) 1.14

The role of upstream sequences in selecting the reading frame on tmRNA. BMC Biol (2008) 1.10

The complex of tmRNA-SmpB and EF-G on translocating ribosomes. Nature (2012) 1.09

Visualizing the transfer-messenger RNA as the ribosome resumes translation. EMBO J (2010) 1.08

A functional interaction of SmpB with tmRNA for determination of the resuming point of trans-translation. RNA (2007) 1.07

Differential transcriptional profile of Corynebacterium pseudotuberculosis in response to abiotic stresses. BMC Genomics (2014) 1.07

tmRNA-SmpB: a journey to the centre of the bacterial ribosome. EMBO J (2010) 1.06

Functional SmpB-ribosome interactions require tmRNA. J Biol Chem (2007) 1.05

Accommodation of tmRNA-SmpB into stalled ribosomes: a cryo-EM study. RNA (2009) 1.04

HLTF's Ancient HIRAN Domain Binds 3' DNA Ends to Drive Replication Fork Reversal. Mol Cell (2015) 1.04

Ribosome hijacking: a role for small protein B during trans-translation. EMBO Rep (2009) 1.02

Role of the C-terminal tail of SmpB in the early stage of trans-translation. RNA (2010) 1.00

Structure and function of the T-loop structural motif in noncoding RNAs. Wiley Interdiscip Rev RNA (2013) 0.99

Quality control of bacterial mRNA decoding and decay. Biochim Biophys Acta (2008) 0.98

Coarse-grained model for simulation of RNA three-dimensional structures. J Phys Chem B (2010) 0.98

Resolving nonstop translation complexes is a matter of life or death. J Bacteriol (2014) 0.96

SmpB contributes to reading frame selection in the translation of transfer-messenger RNA. J Mol Biol (2009) 0.94

The highest affinity binding site of small protein B on transfer messenger RNA is outside the tRNA domain. RNA (2008) 0.92

Translational bypassing without peptidyl-tRNA anticodon scanning of coding gap mRNA. EMBO J (2008) 0.90

The role of SmpB and the ribosomal decoding center in licensing tmRNA entry into stalled ribosomes. RNA (2011) 0.90

Structural constraints identified with covariation analysis in ribosomal RNA. PLoS One (2012) 0.88

Escherichia coli tmRNA lacking pseudoknot 1 tags truncated proteins in vivo and in vitro. RNA (2008) 0.88

tmRNA-mediated trans-translation as the major ribosome rescue system in a bacterial cell. Front Genet (2014) 0.88

Ends of the line for tmRNA-SmpB. Front Microbiol (2014) 0.88

Bifunctional transfer-messenger RNA. Biochimie (2011) 0.85

Trans-translation exposed: understanding the structures and functions of tmRNA-SmpB. Front Microbiol (2014) 0.84

Active and accurate trans-translation requires distinct determinants in the C-terminal tail of SmpB protein and the mRNA-like domain of transfer messenger RNA (tmRNA). J Biol Chem (2013) 0.84

Ribosome-based quality control of mRNA and nascent peptides. Wiley Interdiscip Rev RNA (2016) 0.82

RNA-methyltransferase TrmA is a dual-specific enzyme responsible for C5-methylation of uridine in both tmRNA and tRNA. RNA Biol (2013) 0.82

An unusual mechanism for EF-Tu activation during tmRNA-mediated ribosome rescue. RNA (2013) 0.81

Biochemical aspects of bacterial strategies for handling the incomplete translation processes. Front Microbiol (2014) 0.80

mRNA modifications: Dynamic regulators of gene expression? RNA Biol (2016) 0.80

Rejection of tmRNA·SmpB after GTP hydrolysis by EF-Tu on ribosomes stalled on intact mRNA. RNA (2014) 0.80

Fluorescence characterization of the transfer RNA-like domain of transfer messenger RNA in complex with small binding protein B. Biochemistry (2012) 0.79

The tmRNA website. Nucleic Acids Res (2014) 0.79

Structural features of the tmRNA-ribosome interaction. RNA (2009) 0.78

The SmpB C-terminal tail helps tmRNA to recognize and enter stalled ribosomes. Front Microbiol (2014) 0.76

tmRNA on its way through the ribosome: two steps of resume, and what next? RNA Biol (2011) 0.76

tRNA/mRNA Mimicry by tmRNA and SmpB in Trans-Translation. J Nucleic Acids (2011) 0.76

Making the jump: new insights into the mechanism of trans-translation. J Biol (2008) 0.76

In vivo tmRNA protection by SmpB and pre-ribosome binding conformation in solution. RNA (2014) 0.75

Requirements for resuming translation in chimeric transfer-messenger RNAs of Escherichia coli and Mycobacterium tuberculosis. BMC Mol Biol (2014) 0.75

Articles cited by this

Crystallography & NMR system: A new software suite for macromolecular structure determination. Acta Crystallogr D Biol Crystallogr (1998) 169.28

Improved methods for building protein models in electron density maps and the location of errors in these models. Acta Crystallogr A (1991) 119.63

LIGPLOT: a program to generate schematic diagrams of protein-ligand interactions. Protein Eng (1995) 19.22

Crystal structure of the ribosome at 5.5 A resolution. Science (2001) 18.21

Role of a peptide tagging system in degradation of proteins synthesized from damaged messenger RNA. Science (1996) 11.15

Ribbons. Methods Enzymol (1997) 5.83

Detecting and overcoming crystal twinning. Methods Enzymol (1997) 4.35

The SsrA-SmpB system for protein tagging, directed degradation and ribosome rescue. Nat Struct Biol (2000) 3.97

SmpB, a unique RNA-binding protein essential for the peptide-tagging activity of SsrA (tmRNA). EMBO J (1999) 3.69

The 2.9 A crystal structure of T. thermophilus seryl-tRNA synthetase complexed with tRNA(Ser). Science (1994) 3.30

The tmRNA website: reductive evolution of tmRNA in plastids and other endosymbionts. Nucleic Acids Res (2004) 2.88

Visualizing tmRNA entry into a stalled ribosome. Science (2003) 2.67

Ribosome interactions of aminoacyl-tRNA and elongation factor Tu in the codon-recognition complex. Nat Struct Biol (2002) 2.24

Class I tyrosyl-tRNA synthetase has a class II mode of cognate tRNA recognition. EMBO J (2002) 2.09

The tmRDB and SRPDB resources. Nucleic Acids Res (2006) 2.01

Synthesis of aspartyl-tRNA(Asp) in Escherichia coli--a snapshot of the second step. EMBO J (1999) 1.88

The crystal structure of leucyl-tRNA synthetase complexed with tRNALeu in the post-transfer-editing conformation. Nat Struct Mol Biol (2005) 1.87

Crystal structure of the transfer-RNA domain of transfer-messenger RNA in complex with SmpB. Nature (2003) 1.76

Presence and location of modified nucleotides in Escherichia coli tmRNA: structural mimicry with tRNA acceptor branches. EMBO J (1998) 1.56

A previously uncharacterized role for small protein B (SmpB) in transfer messenger RNA-mediated trans-translation. Proc Natl Acad Sci U S A (2005) 1.50

The crystal structure of yeast phenylalanine tRNA at 2.0 A resolution: cleavage by Mg(2+) in 15-year old crystals. J Mol Biol (2000) 1.49

SmpB functions in various steps of trans-translation. Nucleic Acids Res (2002) 1.35

Alanyl-tRNA synthetase crystal structure and design for acceptor-stem recognition. Mol Cell (2004) 1.34

The role of SmpB protein in trans-translation. FEBS Lett (2002) 1.33

Structure of small protein B: the protein component of the tmRNA-SmpB system for ribosome rescue. EMBO J (2002) 1.31

Function of the SmpB tail in transfer-messenger RNA translation revealed by a nucleus-encoded form. J Biol Chem (2004) 1.27

Solution structure of a tmRNA-binding protein, SmpB, from Thermus thermophilus. FEBS Lett (2003) 1.14

Importance of the reverse Hoogsteen base pair 54-58 for tRNA function. Nucleic Acids Res (2003) 1.11

Mapping the interaction of SmpB with ribosomes by footprinting of ribosomal RNA. Nucleic Acids Res (2005) 1.08

SmpB triggers GTP hydrolysis of elongation factor Tu on ribosomes by compensating for the lack of codon-anticodon interaction during trans-translation initiation. J Biol Chem (2006) 1.04

Stepping transfer messenger RNA through the ribosome. J Biol Chem (2005) 1.01

The tRNA-like domains of E coli and A.aeolicus transfer-messenger RNA: structural and functional studies. J Mol Biol (2003) 1.00

Purification of histidine-tagged T4 RNA ligase from E. coli. Biotechniques (2002) 0.86

NMR structures of double loops of an RNA aptamer against mammalian initiation factor 4A. Nucleic Acids Res (2005) 0.80

Articles by these authors

Crystal structure of a bacterial RNA polymerase holoenzyme at 2.6 A resolution. Nature (2002) 6.74

Structural basis for defects of Keap1 activity provoked by its point mutations in lung cancer. Mol Cell (2006) 6.09

Structural basis for RNA unwinding by the DEAD-box protein Drosophila Vasa. Cell (2006) 5.70

Crystal structure of the complex of human epidermal growth factor and receptor extracellular domains. Cell (2002) 5.64

An open-and-shut case? Recent insights into the activation of EGF/ErbB receptors. Mol Cell (2003) 5.06

Curved EFC/F-BAR-domain dimers are joined end to end into a filament for membrane invagination in endocytosis. Cell (2007) 4.73

Let-7 microRNA-mediated mRNA deadenylation and translational repression in a mammalian cell-free system. Genes Dev (2007) 4.35

Protein production and purification. Nat Methods (2008) 3.97

Regulation through the secondary channel--structural framework for ppGpp-DksA synergism during transcription. Cell (2004) 3.39

ATP binding by glutamyl-tRNA synthetase is switched to the productive mode by tRNA binding. EMBO J (2003) 3.14

A small-molecule AdipoR agonist for type 2 diabetes and short life in obesity. Nature (2013) 2.74

Structural basis for orthogonal tRNA specificities of tyrosyl-tRNA synthetases for genetic code expansion. Nat Struct Biol (2003) 2.71

Structural basis for substrate selection by t7 RNA polymerase. Cell (2004) 2.62

Structural basis for interaction of the ribosome with the switch regions of GTP-bound elongation factors. Mol Cell (2007) 2.62

Structural basis for transcription regulation by alarmone ppGpp. Cell (2004) 2.60

Structure of a T7 RNA polymerase elongation complex at 2.9 A resolution. Nature (2002) 2.57

An unnatural hydrophobic base pair system: site-specific incorporation of nucleotide analogs into DNA and RNA. Nat Methods (2006) 2.46

Different electrostatic potentials define ETGE and DLG motifs as hinge and latch in oxidative stress response. Mol Cell Biol (2007) 2.38

Adding l-lysine derivatives to the genetic code of mammalian cells with engineered pyrrolysyl-tRNA synthetases. Biochem Biophys Res Commun (2008) 2.29

Alternative tertiary structure of tRNA for recognition by a posttranscriptional modification enzyme. Cell (2003) 2.29

Crystal structure of hypothetical protein TTHB192 from Thermus thermophilus HB8 reveals a new protein family with an RNA recognition motif-like domain. Protein Sci (2006) 2.29

Preparation of Escherichia coli cell extract for highly productive cell-free protein expression. J Struct Funct Genomics (2004) 2.14

Multistep engineering of pyrrolysyl-tRNA synthetase to genetically encode N(epsilon)-(o-azidobenzyloxycarbonyl) lysine for site-specific protein modification. Chem Biol (2008) 2.13

Reconstitution reveals the functional core of mammalian eIF3. EMBO J (2007) 2.06

A B-box 2 surface patch important for TRIM5alpha self-association, capsid binding avidity, and retrovirus restriction. J Virol (2009) 2.03

Crystal structure of bacterial RNA polymerase bound with a transcription inhibitor protein. Nature (2010) 2.01

Parkin binds the Rpn10 subunit of 26S proteasomes through its ubiquitin-like domain. EMBO Rep (2003) 2.01

A computational model on the modulation of mitogen-activated protein kinase (MAPK) and Akt pathways in heregulin-induced ErbB signalling. Biochem J (2003) 2.00

Crystal structure of the homologous-pairing domain from the human Rad52 recombinase in the undecameric form. Mol Cell (2002) 1.98

Structure of the oncoprotein gankyrin in complex with S6 ATPase of the 26S proteasome. Structure (2007) 1.97

Inference of S-system models of genetic networks using a cooperative coevolutionary algorithm. Bioinformatics (2004) 1.96

Interaction of Era with the 30S ribosomal subunit implications for 30S subunit assembly. Mol Cell (2005) 1.93

Structural basis of the substrate-specific two-step catalysis of long chain fatty acyl-CoA synthetase dimer. J Biol Chem (2004) 1.89

The crystal structure of leucyl-tRNA synthetase complexed with tRNALeu in the post-transfer-editing conformation. Nat Struct Mol Biol (2005) 1.87

Aminoacylation complex structures of leucyl-tRNA synthetase and tRNALeu reveal two modes of discriminator-base recognition. Nat Struct Mol Biol (2005) 1.82

Increased Ras expression and caspase-independent neuroblastoma cell death: possible mechanism of spontaneous neuroblastoma regression. J Natl Cancer Inst (2002) 1.78

An enzyme with a deep trefoil knot for the active-site architecture. Acta Crystallogr D Biol Crystallogr (2002) 1.72

Codon reassignment in the Escherichia coli genetic code. Nucleic Acids Res (2010) 1.68

Protein photo-cross-linking in mammalian cells by site-specific incorporation of a photoreactive amino acid. Nat Methods (2005) 1.67

UTX and UTY demonstrate histone demethylase-independent function in mouse embryonic development. PLoS Genet (2012) 1.67

Crystal structure of elongation factor P from Thermus thermophilus HB8. Proc Natl Acad Sci U S A (2004) 1.65

Real-time imaging of histone H4K12-specific acetylation determines the modes of action of histone deacetylase and bromodomain inhibitors. Chem Biol (2011) 1.65

Genetic encoding of 3-iodo-L-tyrosine in Escherichia coli for single-wavelength anomalous dispersion phasing in protein crystallography. Structure (2009) 1.64

Site-specific incorporation of an unnatural amino acid into proteins in mammalian cells. Nucleic Acids Res (2002) 1.64

DOCK8 is a Cdc42 activator critical for interstitial dendritic cell migration during immune responses. Blood (2012) 1.63

Structure, interaction and real-time monitoring of the enzymatic reaction of wild-type APOBEC3G. EMBO J (2009) 1.63

Structural evidence for loose linkage between ligand binding and kinase activation in the epidermal growth factor receptor. Mol Cell Biol (2010) 1.63

A paralog of lysyl-tRNA synthetase aminoacylates a conserved lysine residue in translation elongation factor P. Nat Struct Mol Biol (2010) 1.62

Site-specific incorporation of a photo-crosslinking component into RNA by T7 transcription mediated by unnatural base pairs. Chem Biol (2004) 1.59

Structural basis for octameric ring formation and DNA interaction of the human homologous-pairing protein Dmc1. Mol Cell (2004) 1.57

An unnatural base pair system for efficient PCR amplification and functionalization of DNA molecules. Nucleic Acids Res (2008) 1.56

Structural bases of transfer RNA-dependent amino acid recognition and activation by glutamyl-tRNA synthetase. Structure (2006) 1.56

The RAC binding domain/IRSp53-MIM homology domain of IRSp53 induces RAC-dependent membrane deformation. J Biol Chem (2006) 1.56

Expression and purification of recombinant human histones. Methods (2004) 1.54

Crystal structure of the human BRD2 bromodomain: insights into dimerization and recognition of acetylated histone H4. J Biol Chem (2006) 1.54

Structural basis of replication origin recognition by the DnaA protein. Nucleic Acids Res (2003) 1.54

Deep knot structure for construction of active site and cofactor binding site of tRNA modification enzyme. Structure (2004) 1.53

Drosophila U6 promoter-driven short hairpin RNAs effectively induce RNA interference in Schneider 2 cells. Biochem Biophys Res Commun (2005) 1.53

Transcription profile of Thermus thermophilus CRISPR systems after phage infection. J Mol Biol (2009) 1.50

Mammalian GW182 contains multiple Argonaute-binding sites and functions in microRNA-mediated translational repression. RNA (2009) 1.50

Rapid SNP diagnostics using asymmetric isothermal amplification and a new mismatch-suppression technology. Nat Methods (2007) 1.48

The antibiotic kasugamycin mimics mRNA nucleotides to destabilize tRNA binding and inhibit canonical translation initiation. Nat Struct Mol Biol (2006) 1.47

Pin1 and Par14 peptidyl prolyl isomerase inhibitors block cell proliferation. Chem Biol (2003) 1.47

A common mechanism for the ATP-DnaA-dependent formation of open complexes at the replication origin. J Biol Chem (2008) 1.46

Solution structure of an Arabidopsis WRKY DNA binding domain. Plant Cell (2005) 1.45

Cytoplasmic destruction of p53 by the endoplasmic reticulum-resident ubiquitin ligase 'Synoviolin'. EMBO J (2006) 1.45

Tertiary structure checkpoint at anticodon loop modification in tRNA functional maturation. Nat Struct Mol Biol (2009) 1.45