Study of DNA binding and bending by Bacillus subtilis GabR, a PLP-dependent transcription factor.

[1]  R E Harrington,et al.  Curved DNA without A-A: experimental estimation of all 16 DNA wedge angles. , 1991, Proceedings of the National Academy of Sciences of the United States of America.

[2]  L. Ronda,et al.  Kinetic characterization of the human O‐phosphoethanolamine phospho‐lyase reveals unconventional features of this specialized pyridoxal phosphate‐dependent lyase , 2015, The FEBS journal.

[3]  B. Belitsky,et al.  Bacillus subtilis GabR, a protein with DNA-binding and aminotransferase domains, is a PLP-dependent transcriptional regulator. , 2004, Journal of molecular biology.

[4]  D. Metzler Tautomerism in pyridoxal phosphate and in enzymatic catalysis. , 1979, Advances in enzymology and related areas of molecular biology.

[5]  Paolo Facci,et al.  AFM: a versatile tool in biophysics , 2005 .

[6]  J. Allison,et al.  Determination of pyridoxal-5'-phosphate (PLP)-bonding sites in proteins: a peptide mass fingerprinting approach based on diagnostic tandem mass spectral features of PLP-modified peptides. , 2009, Rapid communications in mass spectrometry : RCM.

[7]  A. Sonenshein,et al.  GabR, a member of a novel protein family, regulates the utilization of γ‐aminobutyrate in Bacillus subtilis , 2002, Molecular microbiology.

[8]  A. Travers,et al.  RNA polymerase and an activator form discrete subcomplexes in a transcription initiation complex , 2006, The EMBO journal.

[9]  R. E. Hansen,et al.  Reaction of Pyridoxal-5-phosphate with Aminothiols , 1960 .

[10]  S. Rigali,et al.  Subdivision of the Helix-Turn-Helix GntR Family of Bacterial Regulators in the FadR, HutC, MocR, and YtrA Subfamilies* , 2002, The Journal of Biological Chemistry.

[11]  R. Heath,et al.  The FadR·DNA Complex , 2001, The Journal of Biological Chemistry.

[12]  Alexandre M. J. J. Bonvin,et al.  3D-DART: a DNA structure modelling server , 2009, Nucleic Acids Res..

[13]  E. Fischer,et al.  The site of binding of pyridoxal-5'-phosphate to heart glutamic-aspartic transaminase. , 1962, Proceedings of the National Academy of Sciences of the United States of America.

[14]  D. Maes,et al.  Insights into the architecture and stoichiometry of Escherichia coli PepA•DNA complexes involved in transcriptional control and site-specific DNA recombination by atomic force microscopy , 2009, Nucleic acids research.

[15]  Wei Wang,et al.  Crystal structure of Bacillus subtilis GabR, an autorepressor and transcriptional activator of gabT , 2013, Proceedings of the National Academy of Sciences.

[16]  C. Bustamante,et al.  Determination of heat‐shock transcription factor 2 stoichiometry at looped DNA complexes using scanning force microscopy. , 1995, The EMBO journal.

[17]  H. Rozenberg,et al.  DNA bending by an adenine–thymine tract and its role in gene regulation , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[18]  C. Rivetti A simple and optimized length estimator for digitized DNA contours , 2009, Cytometry. Part A : the journal of the International Society for Analytical Cytology.

[19]  K. Suzuki,et al.  4-Aminobutyrate:2-oxoglutarate aminotransferase of Streptomyces griseus: purification and properties. , 1985, European journal of biochemistry.

[20]  C. Bustamante,et al.  Wrapping of DNA around the E.coli RNA polymerase open promoter complex , 1999, The EMBO journal.

[21]  C. Bustamante,et al.  New insights into the regulatory mechanisms of ppGpp and DksA on Escherichia coli RNA polymerase–promoter complex , 2015, Nucleic acids research.

[22]  B. Tao,et al.  Polymerase chain reaction (PCR) techniques for site-directed mutagenesis. , 1992, Biotechnology advances.

[23]  J. F. Thompson,et al.  Empirical estimation of protein-induced DNA bending angles: applications to lambda site-specific recombination complexes. , 1988, Nucleic acids research.

[24]  H. Hemmi,et al.  Domain characterization of Bacillus subtilis GabR, a pyridoxal 5'-phosphate-dependent transcriptional regulator. , 2015, Journal of biochemistry.

[25]  S. Pascarella,et al.  Molecular mechanism of PdxR – a transcriptional activator involved in the regulation of vitamin B6 biosynthesis in the probiotic bacterium Bacillus clausii , 2015, The FEBS journal.

[26]  G. Hammes,et al.  Kinetic studies of tryptophan synthetase. Interaction of L-serine, indole, and tryptophan with the native enzyme. , 1971, Biochemistry.

[27]  A. Rich,et al.  Asymmetric lateral distribution of unshielded phosphate groups in nucleosomal DNA and its role in DNA bending. , 1979, Proceedings of the National Academy of Sciences of the United States of America.

[28]  C. Bustamante,et al.  Visualizing protein-nucleic acid interactions on a large scale with the scanning force microscope. , 1996, Annual review of biophysics and biomolecular structure.

[29]  R. Zenobi,et al.  Toward an Effective Control of DNA's Submolecular Conformation on a Surface , 2016 .

[30]  K. Gaus,et al.  Binding of transcription factor GabR to DNA requires recognition of DNA shape at a location distinct from its cognate binding site , 2015, Nucleic acids research.

[31]  Paola Storici,et al.  Structures of γ-Aminobutyric Acid (GABA) Aminotransferase, a Pyridoxal 5′-Phosphate, and [2Fe-2S] Cluster-containing Enzyme, Complexed with γ-Ethynyl-GABA and with the Antiepilepsy Drug Vigabatrin* , 2003, Journal of Biological Chemistry.

[32]  C. C. Correll,et al.  Protein-nucleic acid interactions : structural biology , 2008 .

[33]  F. Narberhaus,et al.  The GntR-Like Regulator TauR Activates Expression of Taurine Utilization Genes in Rhodobacter capsulatus , 2007, Journal of bacteriology.

[34]  H. Gehring,et al.  Spectroscopic characterization of true enzyme-substrate intermediates of aspartate aminotransferase trapped at subzero temperatures. , 1991, European journal of biochemistry.

[35]  Masaru Goto,et al.  Role of the aminotransferase domain in Bacillus subtilis GabR, a pyridoxal 5′‐phosphate‐dependent transcriptional regulator , 2015, Molecular microbiology.

[36]  Rolf Boelens,et al.  Information-driven protein–DNA docking using HADDOCK: it is a matter of flexibility , 2006, Nucleic acids research.

[37]  C. Bustamante,et al.  Scanning force microscopy of DNA deposited onto mica: equilibration versus kinetic trapping studied by statistical polymer chain analysis. , 1996, Journal of molecular biology.

[38]  S. Codeluppi,et al.  Accurate length determination of DNA molecules visualized by atomic force microscopy: evidence for a partial B- to A-form transition on mica. , 2001, Ultramicroscopy.

[39]  W. Jencks,et al.  On the Mechanism of Schiff Base Formation and Hydrolysis , 1962 .

[40]  A. Kalia,et al.  A method for extraction of high-quality and high-quantity genomic DNA generally applicable to pathogenic bacteria. , 1999, Analytical biochemistry.

[41]  K. Cai,et al.  The Affinity of Pyridoxal 5′-Phosphate for Folding Intermediates of Escherichia coli Serine Hydroxymethyltransferase (*) , 1995, The Journal of Biological Chemistry.

[42]  S Pascarella,et al.  Genomic distribution and heterogeneity of MocR-like transcriptional factors containing a domain belonging to the superfamily of the pyridoxal-5'-phosphate dependent enzymes of fold type I. , 2011, Biochemical and biophysical research communications.

[43]  D. Jain Allosteric control of transcription in GntR family of transcription regulators: A structural overview , 2015, IUBMB life.

[44]  P. Hsieh,et al.  Determination of protein–DNA binding constants and specificities from statistical analyses of single molecules: MutS–DNA interactions , 2005, Nucleic acids research.

[45]  Jeff M Zimmerman,et al.  Charge neutralization and DNA bending by the Escherichia coli catabolite activator protein. , 2002, Nucleic acids research.

[46]  R. Mann,et al.  The role of DNA shape in protein-DNA recognition , 2009, Nature.

[47]  Yong Jiang,et al.  Detecting the oligomeric state of Escherichia coli MutS from its geometric architecture observed by an atomic force microscope at a single molecular level. , 2014, The journal of physical chemistry. B.