Published in J Biol Chem on March 04, 2009
Riboswitches: structures and mechanisms. Cold Spring Harb Perspect Biol (2011) 1.75
Ribozymes and riboswitches: modulation of RNA function by small molecules. Biochemistry (2010) 1.58
Riboswitches: discovery of drugs that target bacterial gene-regulatory RNAs. Acc Chem Res (2011) 1.52
Metabolite recognition principles and molecular mechanisms underlying riboswitch function. Annu Rev Biophys (2012) 1.47
The structure of a tetrahydrofolate-sensing riboswitch reveals two ligand binding sites in a single aptamer. Structure (2011) 1.36
Folding of a transcriptionally acting preQ1 riboswitch. Proc Natl Acad Sci U S A (2010) 1.34
Design and antimicrobial action of purine analogues that bind Guanine riboswitches. ACS Chem Biol (2009) 1.29
Riboswitch structure in the ligand-free state. Wiley Interdiscip Rev RNA (2011) 1.17
Comparison of a preQ1 riboswitch aptamer in metabolite-bound and free states with implications for gene regulation. J Biol Chem (2011) 1.14
Comparison of solution and crystal structures of preQ1 riboswitch reveals calcium-induced changes in conformation and dynamics. J Am Chem Soc (2011) 1.13
Molecular recognition and function of riboswitches. Curr Opin Struct Biol (2012) 1.13
Amino acid recognition and gene regulation by riboswitches. Biochim Biophys Acta (2009) 1.11
Structural basis for recognition of S-adenosylhomocysteine by riboswitches. RNA (2010) 1.10
Tuning a riboswitch response through structural extension of a pseudoknot. Proc Natl Acad Sci U S A (2013) 1.09
Unraveling the structural complexity in a single-stranded RNA tail: implications for efficient ligand binding in the prequeuosine riboswitch. Nucleic Acids Res (2011) 1.06
Structure and mechanism of purine-binding riboswitches. Q Rev Biophys (2012) 1.06
Biosynthesis of pyrrolopyrimidines. Bioorg Chem (2012) 1.06
Biochemical Validation of a Second Guanidine Riboswitch Class in Bacteria. Biochemistry (2017) 1.03
Recognition of S-adenosylmethionine by riboswitches. Wiley Interdiscip Rev RNA (2011) 1.03
Predicting loop-helix tertiary structural contacts in RNA pseudoknots. RNA (2010) 1.02
5-Fluoro pyrimidines: labels to probe DNA and RNA secondary structures by 1D 19F NMR spectroscopy. Nucleic Acids Res (2009) 0.99
Single transcriptional and translational preQ1 riboswitches adopt similar pre-folded ensembles that follow distinct folding pathways into the same ligand-bound structure. Nucleic Acids Res (2013) 0.98
Structural determinants for ligand capture by a class II preQ1 riboswitch. Proc Natl Acad Sci U S A (2014) 0.98
RNA pseudoknots: folding and finding. F1000 Biol Rep (2010) 0.93
The roles of metal ions in regulation by riboswitches. Met Ions Life Sci (2011) 0.92
Molecular mechanism of preQ1 riboswitch action: a molecular dynamics study. J Phys Chem B (2012) 0.90
Structure and function of preQ1 riboswitches. Biochim Biophys Acta (2014) 0.89
Photochemical control of RNA structure by disrupting π-stacking. J Am Chem Soc (2012) 0.86
Structure and function of pseudoknots involved in gene expression control. Wiley Interdiscip Rev RNA (2014) 0.85
Base ionization and ligand binding: how small ribozymes and riboswitches gain a foothold in a protein world. Curr Opin Struct Biol (2011) 0.84
Exploring ribozyme conformational changes with X-ray crystallography. Methods (2009) 0.83
Stimulation of -1 programmed ribosomal frameshifting by a metabolite-responsive RNA pseudoknot. RNA (2010) 0.82
Comparative sequence and structure analysis reveals the conservation and diversity of nucleotide positions and their associated tertiary interactions in the riboswitches. PLoS One (2013) 0.82
Recognition of the bacterial alarmone ZMP through long-distance association of two RNA subdomains. Nat Struct Mol Biol (2015) 0.80
Structural analysis of a class III preQ1 riboswitch reveals an aptamer distant from a ribosome-binding site regulated by fast dynamics. Proc Natl Acad Sci U S A (2015) 0.80
Characterizing excited conformational states of RNA by NMR spectroscopy. Curr Opin Struct Biol (2015) 0.80
Structural dynamics of a single-stranded RNA-helix junction using NMR. RNA (2014) 0.80
Crystallographic analysis of small ribozymes and riboswitches. Methods Mol Biol (2012) 0.79
Progress and outlook in structural biology of large viral RNAs. Virus Res (2014) 0.79
Native purification and labeling of RNA for single molecule fluorescence studies. Methods Mol Biol (2015) 0.77
Identification and characterization of anion binding sites in RNA. RNA (2010) 0.77
Molecular prejudice: RNA discrimination against purines allows response to a cellular alarm. Nat Struct Mol Biol (2015) 0.75
Molecular mechanism for preQ1-II riboswitch function revealed by molecular dynamics. RNA (2015) 0.75
Rational design of a synthetic mammalian riboswitch as a ligand-responsive -1 ribosomal frame-shifting stimulator. Nucleic Acids Res (2016) 0.75
Conformational Rearrangements of Individual Nucleotides during RNA-Ligand Binding Are Rate-Differentiated. J Am Chem Soc (2016) 0.75
Pseudoknots in RNA folding landscapes. Bioinformatics (2015) 0.75
Biophysical properties, thermal stability and functional impact of 8-oxo-7,8-dihydroguanine on oligonucleotides of RNA-a study of duplex, hairpins and the aptamer for preQ1 as models. Nucleic Acids Res (2017) 0.75
Statistical mechanical modeling of RNA folding: from free energy landscape to tertiary structural prediction. Nucleic Acids Mol Biol (2012) 0.75
The Cambridge Structural Database: a quarter of a million crystal structures and rising. Acta Crystallogr B (2002) 234.73
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
Maximum-likelihood density modification. Acta Crystallogr D Biol Crystallogr (2000) 20.67
Thiamine derivatives bind messenger RNAs directly to regulate bacterial gene expression. Nature (2002) 8.14
High resolution structure of the large ribosomal subunit from a mesophilic eubacterium. Cell (2001) 6.97
Riboswitches control fundamental biochemical pathways in Bacillus subtilis and other bacteria. Cell (2003) 6.21
Regulation of bacterial gene expression by riboswitches. Annu Rev Microbiol (2005) 5.66
Structural basis for discriminative regulation of gene expression by adenine- and guanine-sensing mRNAs. Chem Biol (2004) 5.44
Structure of a natural guanine-responsive riboswitch complexed with the metabolite hypoxanthine. Nature (2004) 4.91
New RNA motifs suggest an expanded scope for riboswitches in bacterial genetic control. Proc Natl Acad Sci U S A (2004) 4.35
Tools for the automatic identification and classification of RNA base pairs. Nucleic Acids Res (2003) 4.12
Structural basis of glmS ribozyme activation by glucosamine-6-phosphate. Science (2006) 3.94
Riboswitches as versatile gene control elements. Curr Opin Struct Biol (2005) 3.83
Improvement of reading frame maintenance is a common function for several tRNA modifications. EMBO J (2001) 3.80
Structure of the modified nucleoside Q isolated from Escherichia coli transfer ribonucleic acid. 7-(4,5-cis-Dihydroxy-1-cyclopenten-3-ylaminomethyl)-7-deazaguanosine. Biochemistry (1975) 3.73
Cross-validated maximum likelihood enhances crystallographic simulated annealing refinement. Proc Natl Acad Sci U S A (1997) 3.64
Riboswitches as antibacterial drug targets. Nat Biotechnol (2006) 3.01
SCOR: a Structural Classification of RNA database. Nucleic Acids Res (2002) 2.79
New paradigm for macromolecular crystallography experiments at SSRL: automated crystal screening and remote data collection. Acta Crystallogr D Biol Crystallogr (2008) 2.79
A riboswitch selective for the queuosine precursor preQ1 contains an unusually small aptamer domain. Nat Struct Mol Biol (2007) 2.52
Genetic control by metabolite-binding riboswitches. Chembiochem (2003) 2.32
Pound-wise but penny-foolish: How well do micromolecules fare in macromolecular refinement? Structure (2003) 2.14
Biosynthesis of the 7-deazaguanosine hypermodified nucleosides of transfer RNA. Bioorg Chem (2003) 1.66
Thermoanaerobacter tengcongensis sp. nov., a novel anaerobic, saccharolytic, thermophilic bacterium isolated from a hot spring in Tengcong, China. Int J Syst Evol Microbiol (2001) 1.64
From cyclohydrolase to oxidoreductase: discovery of nitrile reductase activity in a common fold. Proc Natl Acad Sci U S A (2005) 1.55
Queuosine modification of the wobble base in tRNAHis influences 'in vivo' decoding properties. EMBO J (1985) 1.30
Structural features of metabolite-sensing riboswitches. Trends Biochem Sci (2007) 1.26
Crystal structure of a lead-dependent ribozyme revealing metal binding sites relevant to catalysis. Nat Struct Biol (1999) 1.25
Flipping riboswitches. Cell (2006) 1.17
The copper-inducible cin operon encodes an unusual methionine-rich azurin-like protein and a pre-Q0 reductase in Pseudomonas putida KT2440. J Bacteriol (2007) 1.14
Purification, crystallization, and X-ray diffraction analysis of small ribozymes. Methods Enzymol (2000) 1.14
Multiwavelength anomalous diffraction phasing of macromolecular structures: analysis of MAD data as single isomorphous replacement with anomalous scattering data using the MADMRG Program. Methods Enzymol (1997) 1.12
Conformational heterogeneity at position U37 of an all-RNA hairpin ribozyme with implications for metal binding and the catalytic structure of the S-turn. Biochemistry (2005) 1.06
Energetics of hydrogen bond networks in RNA: hydrogen bonds surrounding G+1 and U42 are the major determinants for the tertiary structure stability of the hairpin ribozyme. Biochemistry (2002) 0.94
Riboswitch effectors as protein enzyme cofactors. RNA (2008) 0.91
'Turning on' riboswitches to their antibacterial potential. Nat Chem Biol (2007) 0.85
Diphthamide biosynthesis requires an organic radical generated by an iron-sulphur enzyme. Nature (2010) 1.85
Structure-based design of novel HIV-1 protease inhibitors to combat drug resistance. J Med Chem (2006) 1.75
Nanostructures of APOBEC3G support a hierarchical assembly model of high molecular mass ribonucleoprotein particles from dimeric subunits. J Biol Chem (2006) 1.50
Deciphering deazapurine biosynthesis: pathway for pyrrolopyrimidine nucleosides toyocamycin and sangivamycin. Chem Biol (2008) 1.42
Water in the active site of an all-RNA hairpin ribozyme and effects of Gua8 base variants on the geometry of phosphoryl transfer. Biochemistry (2006) 1.41
A comparison of vanadate to a 2'-5' linkage at the active site of a small ribozyme suggests a role for water in transition-state stabilization. RNA (2007) 1.27
The deazapurine biosynthetic pathway revealed: in vitro enzymatic synthesis of PreQ(0) from guanosine 5'-triphosphate in four steps. Biochemistry (2009) 1.27
The structure of a yeast RNA-editing deaminase provides insight into the fold and function of activation-induced deaminase and APOBEC-1. Proc Natl Acad Sci U S A (2004) 1.24
APOBEC3G subunits self-associate via the C-terminal deaminase domain. J Biol Chem (2008) 1.24
Reduced dNTP binding affinity of 3TC-resistant M184I HIV-1 reverse transcriptase variants responsible for viral infection failure in macrophage. J Biol Chem (2008) 1.23
Direct Raman measurement of an elevated base pKa in the active site of a small ribozyme in a precatalytic conformation. J Am Chem Soc (2009) 1.20
Riboswitch structure in the ligand-free state. Wiley Interdiscip Rev RNA (2011) 1.17
The copper-inducible cin operon encodes an unusual methionine-rich azurin-like protein and a pre-Q0 reductase in Pseudomonas putida KT2440. J Bacteriol (2007) 1.14
Comparison of a preQ1 riboswitch aptamer in metabolite-bound and free states with implications for gene regulation. J Biol Chem (2011) 1.14
Nuclear Exclusion of the HIV-1 host defense factor APOBEC3G requires a novel cytoplasmic retention signal and is not dependent on RNA binding. J Biol Chem (2007) 1.13
Revealing the quaternary structure of a heterogeneous noncovalent protein complex through surface-induced dissociation. Anal Chem (2011) 1.13
Discovery of epoxyqueuosine (oQ) reductase reveals parallels between halorespiration and tRNA modification. Proc Natl Acad Sci U S A (2011) 1.12
Conformational heterogeneity at position U37 of an all-RNA hairpin ribozyme with implications for metal binding and the catalytic structure of the S-turn. Biochemistry (2005) 1.06
Biosynthesis of pyrrolopyrimidines. Bioorg Chem (2012) 1.06
Spectroscopic, steady-state kinetic, and mechanistic characterization of the radical SAM enzyme QueE, which catalyzes a complex cyclization reaction in the biosynthesis of 7-deazapurines. Biochemistry (2012) 1.05
Structure of a class II preQ1 riboswitch reveals ligand recognition by a new fold. Nat Chem Biol (2013) 1.03
A hydrodynamic analysis of APOBEC3G reveals a monomer-dimer-tetramer self-association that has implications for anti-HIV function. Biochemistry (2009) 1.01
Structural effects of nucleobase variations at key active site residue Ade38 in the hairpin ribozyme. RNA (2008) 1.00
Escherichia coli QueD is a 6-carboxy-5,6,7,8-tetrahydropterin synthase. Biochemistry (2009) 1.00
Single transcriptional and translational preQ1 riboswitches adopt similar pre-folded ensembles that follow distinct folding pathways into the same ligand-bound structure. Nucleic Acids Res (2013) 0.98
Mechanistic understanding of Pyrococcus horikoshii Dph2, a [4Fe-4S] enzyme required for diphthamide biosynthesis. Mol Biosyst (2010) 0.97
Identification of an imino group indispensable for cleavage by a small ribozyme. J Am Chem Soc (2009) 0.97
Pyruvate is the source of the two carbons that are required for formation of the imidazoline ring of 4-demethylwyosine. Biochemistry (2011) 0.96
Ornithine cyclodeaminase: structure, mechanism of action, and implications for the mu-crystallin family. Biochemistry (2004) 0.96
Core-binding factor β increases the affinity between human Cullin 5 and HIV-1 Vif within an E3 ligase complex. Biochemistry (2012) 0.95
A posteriori design of crystal contacts to improve the X-ray diffraction properties of a small RNA enzyme. Acta Crystallogr D Biol Crystallogr (2007) 0.94
APOBEC-1 and AID are nucleo-cytoplasmic trafficking proteins but APOBEC3G cannot traffic. Biochem Biophys Res Commun (2006) 0.94
The alpha subunit of nitrile hydratase is sufficient for catalytic activity and post-translational modification. Biochemistry (2014) 0.90
Crystallization and X-ray diffraction analysis of an all-RNA U39C mutant of the minimal hairpin ribozyme. Acta Crystallogr D Biol Crystallogr (2002) 0.90
Kinetic evidence for interaction of human immunodeficiency virus type 1 reverse transcriptase with the 3'-OH of the incoming dTTP substrate. Biochemistry (2005) 0.90
Molecular mechanism of preQ1 riboswitch action: a molecular dynamics study. J Phys Chem B (2012) 0.90
Structural phylogenetic analysis of activation-induced deaminase function. J Immunol (2006) 0.89
Radical mediated ring formation in the biosynthesis of the hypermodified tRNA base wybutosine. Curr Opin Chem Biol (2013) 0.88
A transition-state interaction shifts nucleobase ionization toward neutrality to facilitate small ribozyme catalysis. J Am Chem Soc (2012) 0.88
Phospholipase D toxins of brown spider venom convert lysophosphatidylcholine and sphingomyelin to cyclic phosphates. PLoS One (2013) 0.88
Shared traits on the reaction coordinates of ribonuclease and an RNA enzyme. Biochem Biophys Res Commun (2008) 0.87
Single-atom imino substitutions at A9 and A10 reveal distinct effects on the fold and function of the hairpin ribozyme catalytic core. Biochemistry (2009) 0.85
Structure of phosphorylated SF1 bound to U2AF⁶⁵ in an essential splicing factor complex. Structure (2012) 0.84
Base ionization and ligand binding: how small ribozymes and riboswitches gain a foothold in a protein world. Curr Opin Struct Biol (2011) 0.84
Evolution of new function in the GTP cyclohydrolase II proteins of Streptomyces coelicolor. Biochemistry (2006) 0.84
Structural characterization of nitrosomonas europaea cytochrome c-552 variants with marked differences in electronic structure. Chembiochem (2013) 0.84
Evidence for the role of active site residues in the hairpin ribozyme from molecular simulations along the reaction path. J Am Chem Soc (2014) 0.84
Probing nitrogen-sensitive steps in the free-radical-mediated deamination of amino alcohols by ethanolamine ammonia-lyase. J Am Chem Soc (2006) 0.83
Exploring ribozyme conformational changes with X-ray crystallography. Methods (2009) 0.83
Functional characterization of APOBEC-1 complementation factor phosphorylation sites. Biochim Biophys Acta (2006) 0.82
Coupling of MBP fusion protein cleavage with sparse matrix crystallization screens to overcome problematic protein solubility. Biotechniques (2005) 0.79
Understanding functional divergence in proteins by studying intragenomic homologues. Biochemistry (2008) 0.79
Crystallographic analysis of small ribozymes and riboswitches. Methods Mol Biol (2012) 0.79
Crystallization and X-ray diffraction analysis of the Trp/amber editing site of hepatitis delta virus (+)RNA: a case of rational design. Acta Crystallogr Sect F Struct Biol Cryst Commun (2005) 0.78
Crystallization and X-ray diffraction analysis of ornithine cyclodeaminase from Pseudomonas putida. Acta Crystallogr D Biol Crystallogr (2004) 0.77
Activation induced deaminase: the importance of being specific. Trends Genet (2004) 0.77
Crystallographic analysis of the NNA7 Fab and proposal for the mode of human blood-group recognition. Acta Crystallogr D Biol Crystallogr (2005) 0.76
Structure of a 6-pyruvoyltetrahydropterin synthase homolog from Streptomyces coelicolor. Acta Crystallogr Sect F Struct Biol Cryst Commun (2008) 0.76
A new use for a familiar fold: the X-ray crystal structure of GTP-bound GTP cyclohydrolase III from Methanocaldococcus jannaschii reveals a two metal ion catalytic mechanism. Biochemistry (2007) 0.76
Purification, crystallization and X-ray diffraction analysis of a recombinant Fab that recognizes a human blood-group antigen. Acta Crystallogr D Biol Crystallogr (2004) 0.75
Delivery of tailor-made cobalamin to methylmalonyl-CoA mutase. Nat Chem Biol (2008) 0.75
Efficient syntheses of 5'-deoxy-5'-fluoroguanosine and -inosine. J Org Chem (2007) 0.75
Correction to Chemical and Biological Reduction of the Radical SAM Enzyme 7-Carboxy-7-deazaguanine Synthase. Biochemistry (2016) 0.75
Toward Broad Spectrum DHFR inhibitors Targeting Trimethoprim Resistant Enzymes Identified in Clinical Isolates of Methicillin-Resistant Staphylococcus aureus. ACS Infect Dis (2019) 0.75
Comparison of the response of bacterial IscU and SufU to Zn2+ and select transition-metal ions. ACS Chem Biol (2017) 0.75