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. 1999 Nov 23;96(24):13668–13673. doi: 10.1073/pnas.96.24.13668

Figure 1.

Figure 1

Oligonucleotides and sequence alignment. (A) Oligonucleotides used in previous crystal structures (14, 15, 20). The abbreviations used are as follows: h, human; at, Arabidopsis thaliana; pw, Pyrococcus woesei; TF(II)Bc, C-terminal core of TF(II)B; and ad MLPromoter, adenovirus major late promoter. (B) Comparison of the archaeal BRE consensus (18) with the oligonucleotide used in the current TBP/TFB/DNA structure. (C) clustalw (21) alignment of the C-terminal cores of TFB and TFIIB. The TFBs listed (and their database accession numbers) are from Pyrococcus woesei (P29095), Archaeoglobus fulgidus (AE001014), Methanococcus jannaschii (AAB98771), Methanobacterium thermoautotrophicum (AE000864), and Sulfolobus shibatae (AAA81380). The metazoan TFIIBs listed are from Drosophila melanogaster (AAA79093), Homo sapiens (AAA61149), Rattus norvegicus (CAA46766), and Xenopus laevis (CAA44668). The plant TFIIBs listed are from Arabidopsis thaliana (AAC35529) and Glycine max (AAB09756). The fungal TFIIBs listed are from Saccharomyces cerevisiae (AAB68135) and Kluyveromyces lactis (AAA35258). Conservation is indicated as follows: white text on a black background, completely conserved; white text on a dark gray background, conserved; black text on a light gray background, similar; black text on a white background, unconserved; black text on a light green background, conserved in all metazoan and archaeal proteins and contacts BRE; black text on a light yellow background, similar and contacts BRE; black text on a light blue background, unconserved and contacts BRE; and black text on a magenta background, contacts the DNA downstream of the TATA box. Helices are indicated as green boxes above the sequence alignment, labeled using the nomenclature of Nikolov et al. (9). The two helices of the helix–turn–helix (HTH) motif are colored pink. Residues explicitly mentioned in the text are indicated by numbers underneath the alignment. C was made with boxshade [maintained by K. Hofmann (khofmann@isrec-sun1.unil.ch) and M. D. Baron (michael.baron@bbsrc.ac.uk)].