title: Solution structure of the first HMG box domain in human upstream binding factor.
abstract: Human upstream binding factor is a nucleolar transcription factor involved in transcription by RNA polymerase I. It contains six HMG box domains; the HMG box is a minor groove DNA-binding domain that has been found in hundreds of proteins with different functions. Among the six HMG box domains in hUBF, the first one can bind to the ribosomal promoter specifically by itself and is essential for the whole protein's DNA binding specificity. Here we report the three-dimensional structure of this first HMG box free in solution determined by multidimensional NMR using (13)C,(15)N-labeled protein. Like the previously determined HMG box structures, hUBF HMG box 1 adopts a twisted L-shape consisting of three alpha-helices: helix 1 (17-30) and helix 2 (38-51) pack onto each other to form the short arm, while helix 3 (57-76) is associated with an extended strand N-terminal to helix 1 and forms the long arm. A cluster of conserved residues, in particular the aromatic residues F21, Y49, and Y60, is important to maintain the fold. The short arm is rigid due to extensive hydrophobic interaction between helix 1 and helix 2, while the long arm is less rigid.
authors.affiliation: Laboratory of Structural Biology, School of Life Science, University of Science and Technology of China, Hefei, Anhui 230026, Peoples Republic of China.
authors.forename: Yingqi
authors.initials: Y
authors.lastname: Xu
authors.forename: Wulin
authors.initials: W
authors.lastname: Yang
authors.forename: Jihui
authors.initials: J
authors.lastname: Wu
authors.forename: Yunyu
authors.initials: Y
authors.lastname: Shi
mesh_terms: D000595:Amino Acid Sequence; D018360:Crystallography, X-Ray; D004247:DNA / Q000737:chemistry / Q000378:metabolism; D004268:DNA-Binding Proteins / Q000737:chemistry* / Q000378:metabolism; D024742:HMG-Box Domains; D024002:HMGB Proteins / Q000737:chemistry*; D006801:Humans; D008969:Molecular Sequence Data; D019906:Nuclear Magnetic Resonance, Biomolecular / Q000379:methods; D035463:Pol1 Transcription Initiation Complex Proteins; D011487:Protein Conformation; D017433:Protein Structure, Secondary; D012996:Solutions; D013816:Thermodynamics; D014157:Transcription Factors / Q000737:chemistry* / Q000378:metabolism
chemical_list: D004268:DNA-Binding Proteins; D024002:HMGB Proteins; D035463:Pol1 Transcription Initiation Complex Proteins; D012996:Solutions; D014157:Transcription Factors; C063844:transcription factor UBF; D004247:DNA