The solution structure of coronaviral stem-loop 2 (SL2) reveals a canonical CUYG tetraloop fold.

PubWeight™: 0.83‹?›

🔗 View Article (PMC 3086565)

Published in FEBS Lett on March 04, 2011

Authors

Chul Won Lee1, Lichun Li, David P Giedroc

Author Affiliations

1: Department of Chemistry, Indiana University, Bloomington, IN 47405, USA.

Articles cited by this

NMRPipe: a multidimensional spectral processing system based on UNIX pipes. J Biomol NMR (1995) 93.94

Structure of the 30S ribosomal subunit. Nature (2000) 23.11

Vienna RNA secondary structure server. Nucleic Acids Res (2003) 19.69

The Xplor-NIH NMR molecular structure determination package. J Magn Reson (2003) 16.23

Functional insights from the structure of the 30S ribosomal subunit and its interactions with antibiotics. Nature (2000) 11.30

Protein NMR structure determination with automated NOE assignment using the new software CANDID and the torsion angle dynamics algorithm DYANA. J Mol Biol (2002) 11.20

Automated NMR structure calculation with CYANA. Methods Mol Biol (2004) 9.31

3DNA: a versatile, integrated software system for the analysis, rebuilding and visualization of three-dimensional nucleic-acid structures. Nat Protoc (2008) 4.61

NMR spectroscopy of RNA. Chembiochem (2003) 2.49

Arterivirus discontinuous mRNA transcription is guided by base pairing between sense and antisense transcription-regulating sequences. Proc Natl Acad Sci U S A (1999) 2.42

Sequence motifs involved in the regulation of discontinuous coronavirus subgenomic RNA synthesis. J Virol (2004) 2.30

Three intergenic regions of coronavirus mouse hepatitis virus strain A59 genome RNA contain a common nucleotide sequence that is homologous to the 3' end of the viral mRNA leader sequence. J Virol (1985) 1.71

Shape-specific recognition in the structure of the Vts1p SAM domain with RNA. Nat Struct Mol Biol (2006) 1.61

Improving the accuracy of NMR structures of RNA by means of conformational database potentials of mean force as assessed by complete dipolar coupling cross-validation. J Am Chem Soc (2003) 1.29

Rewiring the severe acute respiratory syndrome coronavirus (SARS-CoV) transcription circuit: engineering a recombination-resistant genome. Proc Natl Acad Sci U S A (2006) 1.22

A U-turn motif-containing stem-loop in the coronavirus 5' untranslated region plays a functional role in replication. RNA (2007) 1.21

Stem-loop III in the 5' untranslated region is a cis-acting element in bovine coronavirus defective interfering RNA replication. J Virol (2003) 1.18

The stability of the duplex between sense and antisense transcription-regulating sequences is a crucial factor in arterivirus subgenomic mRNA synthesis. J Virol (2003) 1.15

Stem-loop IV in the 5' untranslated region is a cis-acting element in bovine coronavirus defective interfering RNA replication. J Virol (2005) 1.15

Genetic interactions between an essential 3' cis-acting RNA pseudoknot, replicase gene products, and the extreme 3' end of the mouse coronavirus genome. J Virol (2007) 1.09

Single nucleotide RNA choreography. Nucleic Acids Res (2006) 1.06

Putative cis-acting stem-loops in the 5' untranslated region of the severe acute respiratory syndrome coronavirus can substitute for their mouse hepatitis virus counterparts. J Virol (2006) 1.06

Group-specific structural features of the 5'-proximal sequences of coronavirus genomic RNAs. Virology (2010) 1.05

Structural lability in stem-loop 1 drives a 5' UTR-3' UTR interaction in coronavirus replication. J Mol Biol (2008) 1.00

Nuclear magnetic resonance structure of the Varkud satellite ribozyme stem-loop V RNA and magnesium-ion binding from chemical-shift mapping. Biochemistry (2005) 0.98

A hypervariable region within the 3' cis-acting element of the murine coronavirus genome is nonessential for RNA synthesis but affects pathogenesis. J Virol (2006) 0.96

Thermodynamic characterization of RNA triloops. Biochemistry (2010) 0.96

Mouse hepatitis virus stem-loop 2 adopts a uYNMG(U)a-like tetraloop structure that is highly functionally tolerant of base substitutions. J Virol (2009) 0.91

Articles by these authors

CsoR is a novel Mycobacterium tuberculosis copper-sensing transcriptional regulator. Nat Chem Biol (2006) 3.30

Coordination chemistry of bacterial metal transport and sensing. Chem Rev (2009) 2.65

The SmtB/ArsR family of metalloregulatory transcriptional repressors: Structural insights into prokaryotic metal resistance. FEMS Microbiol Rev (2003) 2.51

Structural determinants of metal selectivity in prokaryotic metal-responsive transcriptional regulators. Biometals (2005) 1.65

A metal-ligand-mediated intersubunit allosteric switch in related SmtB/ArsR zinc sensor proteins. J Mol Biol (2003) 1.61

A nickel-cobalt-sensing ArsR-SmtB family repressor. Contributions of cytosol and effector binding sites to metal selectivity. J Biol Chem (2002) 1.47

Individual metal ligands play distinct functional roles in the zinc sensor Staphylococcus aureus CzrA. J Mol Biol (2005) 1.35

Elucidation of primary (alpha(3)N) and vestigial (alpha(5)) heavy metal-binding sites in Staphylococcus aureus pI258 CadC: evolutionary implications for metal ion selectivity of ArsR/SmtB metal sensor proteins. J Mol Biol (2002) 1.33

Solution structure of a luteoviral P1-P2 frameshifting mRNA pseudoknot. J Mol Biol (2002) 1.31

A loop 2 cytidine-stem 1 minor groove interaction as a positive determinant for pseudoknot-stimulated -1 ribosomal frameshifting. Proc Natl Acad Sci U S A (2005) 1.29

Molecular insights into the metal selectivity of the copper(I)-sensing repressor CsoR from Bacillus subtilis. Biochemistry (2009) 1.29

Interplay between manganese and zinc homeostasis in the human pathogen Streptococcus pneumoniae. Metallomics (2011) 1.26

The metalloregulatory zinc site in Streptococcus pneumoniae AdcR, a zinc-activated MarR family repressor. J Mol Biol (2010) 1.25

A U-turn motif-containing stem-loop in the coronavirus 5' untranslated region plays a functional role in replication. RNA (2007) 1.21

Structural elements of metal selectivity in metal sensor proteins. Proc Natl Acad Sci U S A (2003) 1.20

Metalloregulatory proteins: metal selectivity and allosteric switching. Biophys Chem (2011) 1.19

Solution structure of a paradigm ArsR family zinc sensor in the DNA-bound state. Proc Natl Acad Sci U S A (2009) 1.18

The CRR1 nutritional copper sensor in Chlamydomonas contains two distinct metal-responsive domains. Plant Cell (2010) 1.18

A new structural paradigm in copper resistance in Streptococcus pneumoniae. Nat Chem Biol (2013) 1.17

Unnatural amino acid substitution as a probe of the allosteric coupling pathway in a mycobacterial Cu(I) sensor. J Am Chem Soc (2009) 1.14

Control of copper resistance and inorganic sulfur metabolism by paralogous regulators in Staphylococcus aureus. J Biol Chem (2011) 1.12

Putative cis-acting stem-loops in the 5' untranslated region of the severe acute respiratory syndrome coronavirus can substitute for their mouse hepatitis virus counterparts. J Virol (2006) 1.06

A zinc(II)/lead(II)/cadmium(II)-inducible operon from the Cyanobacterium anabaena is regulated by AztR, an alpha3N ArsR/SmtB metalloregulator. Biochemistry (2005) 1.05

Simulating RNA folding kinetics on approximated energy landscapes. J Mol Biol (2008) 1.05

Dual functions of single-stranded DNA-binding protein in helicase loading at the bacteriophage T4 DNA replication fork. J Biol Chem (2004) 1.05

Crystal structure of the zinc-dependent MarR family transcriptional regulator AdcR in the Zn(II)-bound state. J Am Chem Soc (2011) 1.04

Thermodynamic analysis of conserved loop-stem interactions in P1-P2 frameshifting RNA pseudoknots from plant Luteoviridae. Biochemistry (2002) 1.04

A novel cysteine cluster in human metal-responsive transcription factor 1 is required for heavy metal-induced transcriptional activation in vivo. J Biol Chem (2003) 1.03

Predicting loop-helix tertiary structural contacts in RNA pseudoknots. RNA (2010) 1.02

Metal site occupancy and allosteric switching in bacterial metal sensor proteins. Arch Biochem Biophys (2011) 1.01

Structural and functional characterization of Mycobacterium tuberculosis CmtR, a PbII/CdII-sensing SmtB/ArsR metalloregulatory repressor. Biochemistry (2005) 1.01

Characterization of hepatitis B virus capsids by resistive-pulse sensing. J Am Chem Soc (2011) 1.01

Coronavirus N protein N-terminal domain (NTD) specifically binds the transcriptional regulatory sequence (TRS) and melts TRS-cTRS RNA duplexes. J Mol Biol (2009) 1.00

Structural lability in stem-loop 1 drives a 5' UTR-3' UTR interaction in coronavirus replication. J Mol Biol (2008) 1.00

The global structures of a wild-type and poorly functional plant luteoviral mRNA pseudoknot are essentially identical. RNA (2006) 0.99

Solution structure of Mycobacterium tuberculosis NmtR in the apo state: insights into Ni(II)-mediated allostery. Biochemistry (2012) 0.97

Mouse hepatitis virus stem-loop 4 functions as a spacer element required to drive subgenomic RNA synthesis. J Virol (2011) 0.96

A novel cyanobacterial SmtB/ArsR family repressor regulates the expression of a CPx-ATPase and a metallothionein in response to both Cu(I)/Ag(I) and Zn(II)/Cd(II). J Biol Chem (2004) 0.95

Allosteric negative regulation of smt O/P binding of the zinc sensor, SmtB, by metal ions: a coupled equilibrium analysis. Biochemistry (2002) 0.95

Structural characterization of distinct alpha3N and alpha5 metal sites in the cyanobacterial zinc sensor SmtB. Biochemistry (2002) 0.95

Spectroscopic studies of the AppA BLUF domain from Rhodobacter sphaeroides: addressing movement of tryptophan 104 in the signaling state. Biochemistry (2009) 0.95

A Cu(I)-sensing ArsR family metal sensor protein with a relaxed metal selectivity profile. Biochemistry (2008) 0.95

Simulations of allosteric motions in the zinc sensor CzrA. J Am Chem Soc (2011) 0.93

Copper transport and trafficking at the host-bacterial pathogen interface. Acc Chem Res (2014) 0.93

Energetics of allosteric negative coupling in the zinc sensor S. aureus CzrA. J Am Chem Soc (2009) 0.93

Structural insights into homo- and heterotropic allosteric coupling in the zinc sensor S. aureus CzrA from covalently fused dimers. J Am Chem Soc (2006) 0.92

Physical characterization of the manganese-sensing pneumococcal surface antigen repressor from Streptococcus pneumoniae. Biochemistry (2013) 0.92

Mouse hepatitis virus stem-loop 2 adopts a uYNMG(U)a-like tetraloop structure that is highly functionally tolerant of base substitutions. J Virol (2009) 0.91

Characterization of a metalloregulatory bismuth(III) site in Staphylococcus aureus pI258 CadC repressor. J Biol Inorg Chem (2002) 0.91

Allosteric inhibition of a zinc-sensing transcriptional repressor: insights into the arsenic repressor (ArsR) family. J Mol Biol (2013) 0.90

Lentivirus-mediated small interfering RNA targeting VEGF-C inhibited tumor lymphangiogenesis and growth in breast carcinoma. Anat Rec (Hoboken) (2009) 0.90

Copper sensing function of Drosophila metal-responsive transcription factor-1 is mediated by a tetranuclear Cu(I) cluster. Nucleic Acids Res (2008) 0.89

Functional transcriptional regulatory sequence (TRS) RNA binding and helix destabilizing determinants of murine hepatitis virus (MHV) nucleocapsid (N) protein. J Biol Chem (2012) 0.87

Mycobacterium tuberculosis NmtR harbors a nickel sensing site with parallels to Escherichia coli RcnR. Biochemistry (2011) 0.87

The CsoR-like sulfurtransferase repressor (CstR) is a persulfide sensor in Staphylococcus aureus. Mol Microbiol (2014) 0.87

Structure of Thermotoga maritima TM0439: implications for the mechanism of bacterial GntR transcription regulators with Zn2+-binding FCD domains. Acta Crystallogr D Biol Crystallogr (2009) 0.86

Ratiometric pulse-chase amidination mass spectrometry as a probe of biomolecular complex formation. Anal Chem (2011) 0.85

Kinetics of metal binding by the toxic metal-sensing transcriptional repressor Staphylococcus aureus pI258 CadC. J Inorg Biochem (2006) 0.85

Resonance assignments of the metal sensor CzrA in the apo-, Zn2- and DNA-bound (42 kDa) states. Biomol NMR Assign (2007) 0.85

Co-ordinate synthesis and protein localization in a bacterial organelle by the action of a penicillin-binding-protein. Mol Microbiol (2013) 0.84

A conserved RNA pseudoknot in a putative molecular switch domain of the 3'-untranslated region of coronaviruses is only marginally stable. RNA (2011) 0.84

Ratiometric pulsed alkylation mass spectrometry as a probe of thiolate reactivity in different metalloderivatives of Staphylococcus aureus pI258 CadC. Biochemistry (2004) 0.84

Staphylococcus aureus CstB Is a Novel Multidomain Persulfide Dioxygenase-Sulfurtransferase Involved in Hydrogen Sulfide Detoxification. Biochemistry (2015) 0.84

Elucidation of the functional metal binding profile of a Cd(II)/Pb(II) sensor CmtR(Sc) from Streptomyces coelicolor. Biochemistry (2010) 0.83

Selenite and tellurite form mixed seleno- and tellurotrisulfides with CstR from Staphylococcus aureus. Metallomics (2013) 0.82

Stem-loop 1 in the 5' UTR of the SARS coronavirus can substitute for its counterpart in mouse hepatitis virus. Adv Exp Med Biol (2006) 0.81

Solution structure of mouse hepatitis virus (MHV) nsp3a and determinants of the interaction with MHV nucleocapsid (N) protein. J Virol (2013) 0.81

Multiple metal binding domains enhance the Zn(II) selectivity of the divalent metal ion transporter AztA. Biochemistry (2007) 0.81

Energetics of zinc-mediated interactions in the allosteric pathways of metal sensor proteins. J Am Chem Soc (2012) 0.81

A Q63E Rhodobacter sphaeroides AppA BLUF domain mutant is locked in a pseudo-light-excited signaling state. Biochemistry (2010) 0.81

A previously unrecognized UNR stem-loop structure in the coronavirus 5' untranslated region plays a functional role in replication. Adv Exp Med Biol (2006) 0.81

Pairwise coupling analysis of helical junction hydrogen bonding interactions in luteoviral RNA pseudoknots. Biochemistry (2006) 0.81

Backbone resonance assignments of the homotetrameric (48 kD) copper sensor CsoR from Geobacillus thermodenitrificans in the apo- and Cu(I)-bound states: insights into copper-mediated allostery. Biomol NMR Assign (2012) 0.80

Solution NMR refinement of a metal ion bound protein using metal ion inclusive restrained molecular dynamics methods. J Biomol NMR (2013) 0.79

Dissecting non-canonical interactions in frameshift-stimulating mRNA pseudoknots. J Biomol NMR (2006) 0.79

Illuminating allostery in metal sensing transcriptional regulators. Methods Mol Biol (2012) 0.78

Allosteric coupling between transition metal-binding sites in homooligomeric metal sensor proteins. Methods Mol Biol (2012) 0.78

¹H, ¹³C, ¹⁵N resonance assignments of murine hepatitis virus nonstructural protein 3a. Biomol NMR Assign (2012) 0.77

¹H, ¹³C, and ¹⁵N resonance assignments of NmtR, a Ni(II)/Co(II) metalloregulatory protein of Mycobacterium tuberculosis. Biomol NMR Assign (2012) 0.76

Backbone and sterospecific methyl side chain resonance assignments of the homodimeric zinc sensor AdcR (32 kDa) in the apo- and Zn(II)-bound states. Biomol NMR Assign (2012) 0.75

Inhibition of lipopolysaccharide-induced iNOS and COX-2 expression by indole alkaloid, 3-(hydroxymethyl)-6,7-dihydroindolo[2,3-a]quinolizin-(12H)-one, via NF-κB inactivation in RAW 264.7 macrophages. Planta Med (2013) 0.75

Insights Into the Chemical Mechanism for CO2(aq) and H+ in Aqueous Di-amine Solutions - An Experimental Stopped-flow Kinetic and 1H/13C NMR Study of Aqueous solutions of N,N-dimethylethylenediamine (DMEDA) for Post Combustion CO2 Capture. Environ Sci Technol (2017) 0.75