Biomaterial Database

Structural characterization of the interaction between TFIIIB components Bdp1 and Brf1. 2008

Fakhri Saïda

Center for Molecular Genetics, University of California at San Diego, 9500 Gilman Drive, La Jolla, California 92093, USA. fsaida@biomail.ucsd.edu

Transcription factor TFIIIB plays key roles in transcription by RNA polymerase III. Its three components (TBP, Brf1, and Bdp1) participate in crucial molecular events that include RNA polymerase recruitment, formation of the open initiation complex, and recycling of transcription. Although the details of the interaction among DNA, TBP, and Brf1 have been, in part, revealed through the crystal structure of their ternary complex, structural details of the Brf1-Bdp1 interaction are lacking. In this paper, nuclear magnetic resonance (NMR) is used to map the interaction interface between Bdp1 and Brf1 at single-amino acid resolution, using minimal functional segments of the two proteins. An NMR-derived structural model shows that the principal anchorage site of Brf1 is located on a convex surface of Bdp1 that encompasses helix 1 and helix 3 of its conserved SANT domain. The main Bdp1 anchorage site is provided by a small set of residues belonging to a Brf1 segment of residues 470-495.

UI	MeSH Term	Description	Entries
D008969	Molecular Sequence Data	Descriptions of specific amino acid, carbohydrate, or nucleotide sequences which have appeared in the published literature and/or are deposited in and maintained by databanks such as GENBANK, European Molecular Biology Laboratory (EMBL), National Biomedical Research Foundation (NBRF), or other sequence repositories.	Sequence Data, Molecular,Molecular Sequencing Data,Data, Molecular Sequence,Data, Molecular Sequencing,Sequencing Data, Molecular
D010446	Peptide Fragments	Partial proteins formed by partial hydrolysis of complete proteins or generated through PROTEIN ENGINEERING techniques.	Peptide Fragment,Fragment, Peptide,Fragments, Peptide
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
D000595	Amino Acid Sequence	The order of amino acids as they occur in a polypeptide chain. This is referred to as the primary structure of proteins. It is of fundamental importance in determining PROTEIN CONFORMATION.	Protein Structure, Primary,Amino Acid Sequences,Sequence, Amino Acid,Sequences, Amino Acid,Primary Protein Structure,Primary Protein Structures,Protein Structures, Primary,Structure, Primary Protein,Structures, Primary Protein
D013816	Thermodynamics	A rigorously mathematical analysis of energy relationships (heat, work, temperature, and equilibrium). It describes systems whose states are determined by thermal parameters, such as temperature, in addition to mechanical and electromagnetic parameters. (From Hawley's Condensed Chemical Dictionary, 12th ed)	Thermodynamic
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
D018360	Crystallography, X-Ray	The study of crystal structure using X-RAY DIFFRACTION techniques. (McGraw-Hill Dictionary of Scientific and Technical Terms, 4th ed)	X-Ray Crystallography,Crystallography, X Ray,Crystallography, Xray,X Ray Crystallography,Xray Crystallography,Crystallographies, X Ray,X Ray Crystallographies
D029701	Saccharomyces cerevisiae Proteins	Proteins obtained from the species SACCHAROMYCES CEREVISIAE. The function of specific proteins from this organism are the subject of intense scientific interest and have been used to derive basic understanding of the functioning similar proteins in higher eukaryotes.	Baker's Yeast Proteins,S cerevisiae Proteins
D035361	Transcription Factor TFIIIB	One of several general transcription factors that are specific for RNA POLYMERASE III. TFIIIB recruits and positions pol III over the initiation site and remains stably bound to the DNA through multiple rounds of re-initiation by RNA POLYMERASE III.	TFIIIB,TFIIIB-alpha,TFIIIB-beta,Transcription Factor IIIB,Factor IIIB, Transcription,Factor TFIIIB, Transcription,TFIIIB alpha,TFIIIB, Transcription Factor