The TATA-binding protein core domain in solution variably bends TATA sequences via a three-step binding mechanism. 2009

Roberto F Delgadillo, and Jodell E Whittington, and Laura K Parkhurst, and Lawrence J Parkhurst
Department of Chemistry, University of Nebraska, Lincoln, Nebraska 68588-0304, USA.

Studies of the binding and bending of the AdMLP TATA sequence (TATAAAAG) by the core domain of yeast TBP allow quantitation of the roles of the N-terminal domains of yeast and human TBP. All three proteins bind DNA via a three-step mechanism with no evidence for an initially bound but unbent DNA. The large enthalpy and entropy of activation for the first step in yTBP binding can now be assigned to movement of the NTD from the DNA binding pocket and not to energetics of DNA bending. The energetic patterns for hTBP and cTBP suggest that the 158-amino acid NTD in hTBP does not initially occupy the DNA binding pocket. Despite the appearance of similar energetics for hTBP and cTBP, order of magnitude differences in rate constants lead to differing populations of intermediates during DNA binding. We find that the NTDs destabilize the three bound forms of DNA for both yTBP and hTBP. For all three proteins, the DNA bend angle (theta) depends on the TATA sequence, with theta for cTBP and hTBP being greater than that for yTBP. For all three proteins, theta for the G6 variant (TATAAGAG) varies with temperature and increases in the presence of osmolyte to be similar to that of AdMLP. Crystallographic studies of cTBP binding to a number of variants had shown no dependence of DNA bending on sequence. The results reported here reveal a clear structural difference for the bound DNA in solution versus the crystal; we attribute the difference to the presence of osmolytes in the crystals.

UI MeSH Term Description Entries
D007700 Kinetics The rate dynamics in chemical or physical systems.
D009690 Nucleic Acid Conformation The spatial arrangement of the atoms of a nucleic acid or polynucleotide that results in its characteristic 3-dimensional shape. DNA Conformation,RNA Conformation,Conformation, DNA,Conformation, Nucleic Acid,Conformation, RNA,Conformations, DNA,Conformations, Nucleic Acid,Conformations, RNA,DNA Conformations,Nucleic Acid Conformations,RNA Conformations
D011485 Protein Binding The process in which substances, either endogenous or exogenous, bind to proteins, peptides, enzymes, protein precursors, or allied compounds. Specific protein-binding measures are often used as assays in diagnostic assessments. Plasma Protein Binding Capacity,Binding, Protein
D006801 Humans Members of the species Homo sapiens. Homo sapiens,Man (Taxonomy),Human,Man, Modern,Modern Man
D001483 Base Sequence The sequence of PURINES and PYRIMIDINES in nucleic acids and polynucleotides. It is also called nucleotide sequence. DNA Sequence,Nucleotide Sequence,RNA Sequence,DNA Sequences,Base Sequences,Nucleotide Sequences,RNA Sequences,Sequence, Base,Sequence, DNA,Sequence, Nucleotide,Sequence, RNA,Sequences, Base,Sequences, DNA,Sequences, Nucleotide,Sequences, RNA
D012441 Saccharomyces cerevisiae A species of the genus SACCHAROMYCES, family Saccharomycetaceae, order Saccharomycetales, known as "baker's" or "brewer's" yeast. The dried form is used as a dietary supplement. Baker's Yeast,Brewer's Yeast,Candida robusta,S. cerevisiae,Saccharomyces capensis,Saccharomyces italicus,Saccharomyces oviformis,Saccharomyces uvarum var. melibiosus,Yeast, Baker's,Yeast, Brewer's,Baker Yeast,S cerevisiae,Baker's Yeasts,Yeast, Baker
D012996 Solutions The homogeneous mixtures formed by the mixing of a solid, liquid, or gaseous substance (solute) with a liquid (the solvent), from which the dissolved substances can be recovered by physical processes. (From Grant & Hackh's Chemical Dictionary, 5th ed) Solution
D013997 Time Factors Elements of limited time intervals, contributing to particular results or situations. Time Series,Factor, Time,Time Factor
D016385 TATA Box A conserved A-T rich sequence which is contained in promoters for RNA polymerase II. The segment is seven base pairs long and the nucleotides most commonly found are TATAAAA. Hogness Box,Box, Hogness,Box, TATA
D017434 Protein Structure, Tertiary The level of protein structure in which combinations of secondary protein structures (ALPHA HELICES; BETA SHEETS; loop regions, and AMINO ACID MOTIFS) pack together to form folded shapes. Disulfide bridges between cysteines in two different parts of the polypeptide chain along with other interactions between the chains play a role in the formation and stabilization of tertiary structure. Tertiary Protein Structure,Protein Structures, Tertiary,Tertiary Protein Structures

Related Publications

Roberto F Delgadillo, and Jodell E Whittington, and Laura K Parkhurst, and Lawrence J Parkhurst
May 2001, The Journal of biological chemistry,
Roberto F Delgadillo, and Jodell E Whittington, and Laura K Parkhurst, and Lawrence J Parkhurst
December 1999, Molecular and cellular biology,
Roberto F Delgadillo, and Jodell E Whittington, and Laura K Parkhurst, and Lawrence J Parkhurst
August 2003, The Journal of biological chemistry,
Roberto F Delgadillo, and Jodell E Whittington, and Laura K Parkhurst, and Lawrence J Parkhurst
September 1995, Cell,
Roberto F Delgadillo, and Jodell E Whittington, and Laura K Parkhurst, and Lawrence J Parkhurst
December 1999, The EMBO journal,
Roberto F Delgadillo, and Jodell E Whittington, and Laura K Parkhurst, and Lawrence J Parkhurst
March 2001, The Journal of biological chemistry,
Roberto F Delgadillo, and Jodell E Whittington, and Laura K Parkhurst, and Lawrence J Parkhurst
April 1993, Molecular and cellular biology,
Roberto F Delgadillo, and Jodell E Whittington, and Laura K Parkhurst, and Lawrence J Parkhurst
May 2000, Molecular and cellular biology,
Roberto F Delgadillo, and Jodell E Whittington, and Laura K Parkhurst, and Lawrence J Parkhurst
February 1993, Genes & development,
Roberto F Delgadillo, and Jodell E Whittington, and Laura K Parkhurst, and Lawrence J Parkhurst
December 1992, Cell,
Copied contents to your clipboard!