Published in J Bacteriol on December 14, 2007
The functional role of a conserved loop in EAL domain-based cyclic di-GMP-specific phosphodiesterase. J Bacteriol (2009) 1.39
Auxiliary phosphatases in two-component signal transduction. Curr Opin Microbiol (2010) 1.11
Binding of cyclic diguanylate in the non-catalytic EAL domain of FimX induces a long-range conformational change. J Biol Chem (2010) 1.06
Action at a distance: amino acid substitutions that affect binding of the phosphorylated CheY response regulator and catalysis of dephosphorylation can be far from the CheZ phosphatase active site. J Bacteriol (2011) 0.83
Conformational barrier of CheY3 and inability of CheY4 to bind FliM control the flagellar motor action in Vibrio cholerae. PLoS One (2013) 0.75
The CCP4 suite: programs for protein crystallography. Acta Crystallogr D Biol Crystallogr (1994) 187.88
Crystallography & NMR system: A new software suite for macromolecular structure determination. Acta Crystallogr D Biol Crystallogr (1998) 169.28
Refinement of macromolecular structures by the maximum-likelihood method. Acta Crystallogr D Biol Crystallogr (1997) 137.43
Solvent content of protein crystals. J Mol Biol (1968) 106.07
New M13 vectors for cloning. Methods Enzymol (1983) 90.74
A bacteriophage T7 RNA polymerase/promoter system for controlled exclusive expression of specific genes. Proc Natl Acad Sci U S A (1985) 46.59
Calculation of protein extinction coefficients from amino acid sequence data. Anal Biochem (1989) 29.15
WHAT IF: a molecular modeling and drug design program. J Mol Graph (1990) 24.35
Likelihood-enhanced fast rotation functions. Acta Crystallogr D Biol Crystallogr (2004) 23.86
Optimal description of a protein structure in terms of multiple groups undergoing TLS motion. Acta Crystallogr D Biol Crystallogr (2006) 14.21
Matthews coefficient probabilities: Improved estimates for unit cell contents of proteins, DNA, and protein-nucleic acid complex crystals. Protein Sci (2003) 9.53
Automated refinement of protein models. Acta Crystallogr D Biol Crystallogr (1993) 7.88
Making sense of it all: bacterial chemotaxis. Nat Rev Mol Cell Biol (2004) 6.83
Four-helical-bundle structure of the cytoplasmic domain of a serine chemotaxis receptor. Nature (1999) 5.38
Phosphorylation of bacterial response regulator proteins by low molecular weight phospho-donors. Proc Natl Acad Sci U S A (1992) 4.88
Collaborative signaling by mixed chemoreceptor teams in Escherichia coli. Proc Natl Acad Sci U S A (2002) 4.64
Databases in protein crystallography. Acta Crystallogr D Biol Crystallogr (1998) 4.18
Homologies between the Salmonella typhimurium CheY protein and proteins involved in the regulation of chemotaxis, membrane protein synthesis, and sporulation. Proc Natl Acad Sci U S A (1985) 3.72
Three-dimensional structure of CheY, the response regulator of bacterial chemotaxis. Nature (1989) 3.68
Crosslinking snapshots of bacterial chemoreceptor squads. Proc Natl Acad Sci U S A (2004) 3.09
Cellular stoichiometry of the components of the chemotaxis signaling complex. J Bacteriol (2004) 3.07
CheA protein, a central regulator of bacterial chemotaxis, belongs to a family of proteins that control gene expression in response to changing environmental conditions. Proc Natl Acad Sci U S A (1988) 2.85
Signal transduction in bacterial chemotaxis. Bioessays (2006) 2.74
Structure and catalytic mechanism of the E. coli chemotaxis phosphatase CheZ. Nat Struct Biol (2002) 2.60
The receptor binding site for the methyltransferase of bacterial chemotaxis is distinct from the sites of methylation. Biochemistry (1996) 2.44
Anchor residues in protein-protein interactions. Proc Natl Acad Sci U S A (2004) 2.35
Crystal structure of activated CheY. Comparison with other activated receiver domains. J Biol Chem (2001) 2.17
CheZ phosphatase localizes to chemoreceptor patches via CheA-short. J Bacteriol (2003) 2.15
The molecular replacement method. Acta Crystallogr A (1990) 2.01
The response regulators CheB and CheY exhibit competitive binding to the kinase CheA. Biochemistry (1995) 1.97
Purification and characterization of the S-adenosylmethionine:glutamyl methyltransferase that modifies membrane chemoreceptor proteins in bacteria. J Biol Chem (1987) 1.94
Beryllofluoride mimics phosphorylation of NtrC and other bacterial response regulators. Proc Natl Acad Sci U S A (1999) 1.90
A molecular viewer for the analysis of TLS rigid-body motion in macromolecules. Acta Crystallogr D Biol Crystallogr (2005) 1.82
Characterization of the CheAS/CheZ complex: a specific interaction resulting in enhanced dephosphorylating activity on CheY-phosphate. Mol Microbiol (1996) 1.63
Conformational coupling in the chemotaxis response regulator CheY. Proc Natl Acad Sci U S A (2001) 1.53
Helicase from hepatitis C virus, energetics of DNA binding. J Biol Chem (2002) 1.53
Identification of the binding interfaces on CheY for two of its targets, the phosphatase CheZ and the flagellar switch protein fliM. J Mol Biol (1999) 1.42
iMolTalk: an interactive, internet-based protein structure analysis server. Nucleic Acids Res (2004) 1.41
Rapid phosphotransfer to CheY from a CheA protein lacking the CheY-binding domain. Biochemistry (2000) 1.29
Kinetic characterization of CheY phosphorylation reactions: comparison of P-CheA and small-molecule phosphodonors. Biochemistry (1999) 1.21
Crystal structures of beryllium fluoride-free and beryllium fluoride-bound CheY in complex with the conserved C-terminal peptide of CheZ reveal dual binding modes specific to CheY conformation. J Mol Biol (2006) 1.14
Kinetic characterization of phosphotransfer between CheA and CheY in the bacterial chemotaxis signal transduction pathway. Biochemistry (1997) 1.14
The CheZ-binding surface of CheY overlaps the CheA- and FliM-binding surfaces. J Biol Chem (1997) 1.13
Oligomerization of the phosphatase CheZ upon interaction with the phosphorylated form of CheY. The signal protein of bacterial chemotaxis. J Biol Chem (1996) 1.11
In vivo and in vitro characterization of Escherichia coli protein CheZ gain- and loss-of-function mutants. J Bacteriol (1996) 1.09
Systems biology of bacterial chemotaxis. Curr Opin Microbiol (2006) 1.09
Conserved C-terminus of the phosphatase CheZ is a binding domain for the chemotactic response regulator CheY. Biochemistry (1996) 1.05
High mobility of carboxyl-terminal region of bacterial chemotaxis phosphatase CheZ is diminished upon binding divalent cation or CheY-P substrate. Biochemistry (2005) 0.96
High-resolution crystal structures of human hemoglobin with mutations at tryptophan 37beta: structural basis for a high-affinity T-state,. Biochemistry (1998) 0.88
Biological insights from structures of two-component proteins. Annu Rev Microbiol (2009) 4.47
Human but not yeast CHD1 binds directly and selectively to histone H3 methylated at lysine 4 via its tandem chromodomains. J Biol Chem (2005) 4.20
Single-molecule studies reveal dynamics of DNA unwinding by the ring-shaped T7 helicase. Cell (2007) 3.09
Structural basis of RNA recognition and activation by innate immune receptor RIG-I. Nature (2011) 3.05
Molecular information processing: lessons from bacterial chemotaxis. J Biol Chem (2002) 2.72
Bacterial response regulators: versatile regulatory strategies from common domains. Trends Biochem Sci (2007) 2.45
Mechanism of activation for transcription factor PhoB suggested by different modes of dimerization in the inactive and active states. Structure (2005) 2.39
Structure of a cholesterol-binding protein deficient in Niemann-Pick type C2 disease. Proc Natl Acad Sci U S A (2003) 2.21
Coordinating DNA replication by means of priming loop and differential synthesis rate. Nature (2009) 2.16
DNA synthesis provides the driving force to accelerate DNA unwinding by a helicase. Nature (2005) 1.91
Molecular strategies for phosphorylation-mediated regulation of response regulator activity. Curr Opin Microbiol (2010) 1.90
Regulation of response regulator autophosphorylation through interdomain contacts. J Biol Chem (2010) 1.85
Structural basis of sterol binding by NPC2, a lysosomal protein deficient in Niemann-Pick type C2 disease. J Biol Chem (2007) 1.83
Mechanochemistry of transcription termination factor Rho. Mol Cell (2006) 1.79
The functional interaction of the hepatitis C virus helicase molecules is responsible for unwinding processivity. J Biol Chem (2004) 1.76
Structural analysis and solution studies of the activated regulatory domain of the response regulator ArcA: a symmetric dimer mediated by the alpha4-beta5-alpha5 face. J Mol Biol (2005) 1.76
Universally applicable methods for monitoring response regulator aspartate phosphorylation both in vitro and in vivo using Phos-tag-based reagents. Anal Biochem (2008) 1.76
Structural analysis of the domain interface in DrrB, a response regulator of the OmpR/PhoB subfamily. J Bacteriol (2003) 1.71
Evidence of intradomain and interdomain flexibility in an OmpR/PhoB homolog from Thermotoga maritima. Structure (2002) 1.68
A Brownian motor mechanism of translocation and strand separation by hepatitis C virus helicase. Nat Struct Mol Biol (2005) 1.60
Helicase from hepatitis C virus, energetics of DNA binding. J Biol Chem (2002) 1.53
T7 DNA helicase: a molecular motor that processively and unidirectionally translocates along single-stranded DNA. J Mol Biol (2002) 1.50
Structure of the Staphylococcus aureus AgrA LytTR domain bound to DNA reveals a beta fold with an unusual mode of binding. Structure (2008) 1.50
The DNA-unwinding mechanism of the ring helicase of bacteriophage T7. Proc Natl Acad Sci U S A (2004) 1.49
A common dimerization interface in bacterial response regulators KdpE and TorR. Protein Sci (2005) 1.42
Mechanochemistry of t7 DNA helicase. J Mol Biol (2005) 1.40
Domain arrangement of Der, a switch protein containing two GTPase domains. Structure (2002) 1.39
ATP binding modulates the nucleic acid affinity of hepatitis C virus helicase. J Biol Chem (2003) 1.33
NPC2, the protein deficient in Niemann-Pick C2 disease, consists of multiple glycoforms that bind a variety of sterols. J Biol Chem (2006) 1.32
Crystal structures of the receiver domain of the response regulator PhoP from Escherichia coli in the absence and presence of the phosphoryl analog beryllofluoride. J Bacteriol (2007) 1.32
Histone chaperone FACT action during transcription through chromatin by RNA polymerase II. Proc Natl Acad Sci U S A (2013) 1.32
T7 RNA polymerase-induced bending of promoter DNA is coupled to DNA opening. Biochemistry (2006) 1.31
Domain orientation in the inactive response regulator Mycobacterium tuberculosis MtrA provides a barrier to activation. Biochemistry (2007) 1.27
Mechanisms of a ring shaped helicase. Nucleic Acids Res (2006) 1.26
System-level mapping of Escherichia coli response regulator dimerization with FRET hybrids. Mol Microbiol (2008) 1.23
Nucleic acid unwinding by hepatitis C virus and bacteriophage t7 helicases is sensitive to base pair stability. J Biol Chem (2007) 1.21
Real-time observation of the transition from transcription initiation to elongation of the RNA polymerase. Proc Natl Acad Sci U S A (2009) 1.16
ATP-induced helicase slippage reveals highly coordinated subunits. Nature (2011) 1.16
Crystal structures of beryllium fluoride-free and beryllium fluoride-bound CheY in complex with the conserved C-terminal peptide of CheZ reveal dual binding modes specific to CheY conformation. J Mol Biol (2006) 1.14
Probing kinase and phosphatase activities of two-component systems in vivo with concentration-dependent phosphorylation profiling. Proc Natl Acad Sci U S A (2012) 1.14
Transient state kinetics of transcription elongation by T7 RNA polymerase. J Biol Chem (2006) 1.12
Coupling of DNA unwinding to nucleotide hydrolysis in a ring-shaped helicase. EMBO J (2008) 1.10
Fluorescent lifetime trajectories of a single fluorophore reveal reaction intermediates during transcription initiation. J Am Chem Soc (2009) 1.10
Rapid binding of T7 RNA polymerase is followed by simultaneous bending and opening of the promoter DNA. Biochemistry (2006) 1.10
Transcription initiation in a single-subunit RNA polymerase proceeds through DNA scrunching and rotation of the N-terminal subdomains. Mol Cell (2008) 1.10
Extended upstream A-T sequence increases T7 promoter strength. J Biol Chem (2005) 1.08
Probing the roles of the two different dimers mediated by the receiver domain of the response regulator PhoB. J Mol Biol (2009) 1.08
Bright lights, abundant operons--fluorescence and genomic technologies advance studies of bacterial locomotion and signal transduction: review of the BLAST meeting, Cuernavaca, Mexico, 14 to 19 January 2001. J Bacteriol (2002) 1.07
The protease domain increases the translocation stepping efficiency of the hepatitis C virus NS3-4A helicase. J Biol Chem (2010) 1.06
The +2 NTP binding drives open complex formation in T7 RNA polymerase. J Biol Chem (2002) 1.05
Production of high-quality carbon nanoscrolls with microwave spark assistance in liquid nitrogen. Adv Mater (2011) 1.02
Fluorescence mapping of the open complex of yeast mitochondrial RNA polymerase. J Biol Chem (2008) 1.01
Human mitochondrial DNA helicase TWINKLE is both an unwinding and annealing helicase. J Biol Chem (2012) 0.99
Participation of the fingers subdomain of Escherichia coli DNA polymerase I in the strand displacement synthesis of DNA. J Biol Chem (2007) 0.99
Phosphorylation-dependent conformational changes and domain rearrangements in Staphylococcus aureus VraR activation. Proc Natl Acad Sci U S A (2013) 0.98
Inhibition of bacterial virulence: drug-like molecules targeting the Salmonella enterica PhoP response regulator. Chem Biol Drug Des (2012) 0.98
Mitochondrial transcription factor Mtf1 traps the unwound non-template strand to facilitate open complex formation. J Biol Chem (2009) 0.98
Kinetic and thermodynamic basis of promoter strength: multiple steps of transcription initiation by T7 RNA polymerase are modulated by the promoter sequence. Biochemistry (2002) 0.97
Kinetics of transcription initiation at lacP1. Multiple roles of cyclic AMP receptor protein. J Biol Chem (2003) 0.97
Yeast Pif1 helicase exhibits a one-base-pair stepping mechanism for unwinding duplex DNA. J Biol Chem (2013) 0.96
T7 lysozyme represses T7 RNA polymerase transcription by destabilizing the open complex during initiation. J Biol Chem (2004) 0.95
Sequential release of promoter contacts during transcription initiation to elongation transition. J Mol Biol (2006) 0.94
Kinetic basis for the stimulatory effect of phosphorylation on the methylesterase activity of CheB. Biochemistry (2002) 0.94
Crystal structure and autoactivation pathway of the precursor form of human tripeptidyl-peptidase 1, the enzyme deficient in late infantile ceroid lipofuscinosis. J Biol Chem (2008) 0.94
Branch migration enzyme as a Brownian ratchet. EMBO J (2008) 0.94
Mechanism of transcription initiation by the yeast mitochondrial RNA polymerase. Biochim Biophys Acta (2012) 0.93
The transition to an elongation complex by T7 RNA polymerase is a multistep process. J Biol Chem (2007) 0.93
Single strand binding proteins increase the processivity of DNA unwinding by the hepatitis C virus helicase. J Mol Biol (2007) 0.93
Do mammalian NPC1 and NPC2 play a role in intestinal cholesterol absorption? Biochem J (2007) 0.92
Identification of methylation sites in Thermotoga maritima chemotaxis receptors. J Bacteriol (2006) 0.92
Discrimination between different methylation states of chemotaxis receptor Tar by receptor methyltransferase CheR. Biochemistry (2004) 0.91
The role of the C-terminal domain of protein tyrosine phosphatase-1B in phosphatase activity and substrate binding. J Biol Chem (2006) 0.91
The intercalating beta-hairpin of T7 RNA polymerase plays a role in promoter DNA melting and in stabilizing the melted DNA for efficient RNA synthesis. J Mol Biol (2002) 0.91
The N-terminal domain of the yeast mitochondrial RNA polymerase regulates multiple steps of transcription. J Biol Chem (2011) 0.91
Evolutionary tuning of protein expression levels of a positively autoregulated two-component system. PLoS Genet (2013) 0.90
Production of graphite chloride and bromide using microwave sparks. Sci Rep (2012) 0.90
Comprehensive analysis of OmpR phosphorylation, dimerization, and DNA binding supports a canonical model for activation. J Mol Biol (2013) 0.90
Opening-closing dynamics of the mitochondrial transcription pre-initiation complex. Nucleic Acids Res (2011) 0.89
Large-area, flexible imaging arrays constructed by light-charge organic memories. Sci Rep (2013) 0.88
Loss of Niemann-Pick C1 or C2 protein results in similar biochemical changes suggesting that these proteins function in a common lysosomal pathway. PLoS One (2011) 0.88
Transcription factor-dependent DNA bending governs promoter recognition by the mitochondrial RNA polymerase. J Biol Chem (2011) 0.87
Mechanistic and kinetic analysis of the DcpS scavenger decapping enzyme. J Biol Chem (2008) 0.87
Experimental and computational analysis of DNA unwinding and polymerization kinetics. Methods Mol Biol (2010) 0.87
Model-based global analysis of heterogeneous experimental data using gfit. Methods Mol Biol (2009) 0.85
Identification of a hydrophobic cleft in the LytTR domain of AgrA as a locus for small molecule interactions that inhibit DNA binding. Biochemistry (2012) 0.85
Structural biology: Steps in the right direction. Nature (2009) 0.84
Direct measurements of torque during Holliday junction migration. Biophys J (2011) 0.83
Kinetic pathway of dTTP hydrolysis by hexameric T7 helicase-primase in the absence of DNA. J Biol Chem (2002) 0.83
The energetics of consensus promoter opening by T7 RNA polymerase. J Mol Biol (2002) 0.82
A257T linker region mutant of T7 helicase-primase protein is defective in DNA loading and rescued by T7 DNA polymerase. J Biol Chem (2011) 0.82
Characterization of the Thermotoga maritima chemotaxis methylation system that lacks pentapeptide-dependent methyltransferase CheR:MCP tethering. Mol Microbiol (2006) 0.82
Fluorescence-based assay to measure the real-time kinetics of nucleotide incorporation during transcription elongation. J Mol Biol (2010) 0.81
Switching from single-stranded to double-stranded DNA limits the unwinding processivity of ring-shaped T7 DNA helicase. Nucleic Acids Res (2013) 0.81
Nucleotide binding induces conformational changes in Escherichia coli transcription termination factor Rho. J Biol Chem (2004) 0.81
Transmembrane signaling by asymmetry. Nat Struct Mol Biol (2006) 0.79