PDBsum entry: 1d3u

Gene regulation/DNA

PDB id: 1d3u

Contents

Protein chains

181 a.a. *

201 a.a. *

DNA/RNA

Waters ×180

* Residue conservation analysis

PDB id:

1d3u

Name:

Gene regulation/DNA

Title:

Tata-binding protein/transcription factor (ii)b/bre+tata- box complex from pyrococcus woesei

Structure:

DNA 24-mer: bre+tata-box. Chain: c. Engineered: yes. DNA 23-mer: bre+tata-box. Chain: d. Engineered: yes. Tata-binding protein. Chain: a. Fragment: residues 1-180.

Source:

Synthetic: yes. Pyrococcus woesei. Organism_taxid: 2262. Expressed in: escherichia coli. Expression_system_taxid: 562.

Biol. unit:

Octamer (from PQS)

Resolution:

2.40Å R-factor: 0.206 R-free: 0.245

Authors:

O.Littlefield,Y.Korkhin,P.B.Sigler

Key ref:

O.Littlefield et al. (1999). The structural basis for the oriented assembly of a TBP/TFB/promoter complex. Proc Natl Acad Sci U S A, 96, 13668-13673. PubMed id: 10570130 DOI: 10.1073/pnas.96.24.13668

Date:

01-Oct-99 Release date: 15-Nov-99

Protein chain

P62001  (TBP_PYRWO) -  TATA-box-binding protein

Seq: 191 a.a.

Struc: 181 a.a.

Protein chain

P61999  (TF2B_PYRWO) -  Transcription initiation factor IIB

Seq: 300 a.a.

Struc: 201 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

 Gene Ontology (GO) functional annotation 

• Biological process: regulation of transcription (6 terms)
• Biochemical function: binding (7 terms)

DOI no: 10.1073/pnas.96.24.13668

Proc Natl Acad Sci U S A 96:13668-13673 (1999)

PubMed id: 10570130

The structural basis for the oriented assembly of a TBP/TFB/promoter complex.

O.Littlefield, Y.Korkhin, P.B.Sigler.

ABSTRACT

Recently the definition of the metazoan RNA polymerase II and archaeal core promoters has been expanded to include a region immediately upstream of the TATA box called the B recognition element (BRE), so named because eukaryal transcription factor TFIIB and its archaeal orthologue TFB interact with the element in a sequence-specific manner. Here we present the 2.4-A crystal structure of archaeal TBP and the C-terminal core of TFB (TFB(c)) in a complex with an extended TATA-box-containing promoter that provides a detailed picture of the stereospecific interactions between the BRE and a helix-turn-helix motif in the C-terminal cyclin repeat of TFB(c). This interaction is important in determining the level of basal transcription and explicitly defines the direction of transcription.

Selected figure(s)

Figure 1.
Fig. 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)B[c], 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{at}isrec-sun1.unil.ch) and M. D. Baron (michael.baron{at}bbsrc.ac.uk)].

Figure 2.
Fig. 2. Overall view of the TBP/TFB[c]/DNA complex. TBP is shown as a ribbon diagram with the N-terminal repeat colored red and the C-terminal repeat colored pink. TFB[c] is shown as a ribbon diagram with the N-terminal cyclin repeat colored dark green and the C-terminal cyclin repeat colored green with the HTH highlighted in magenta. The DNA is shown as a stick drawing with the sense strand in cyan and the antisense strand in yellow. The TATA box is colored blue and orange. (A) View of the complex looking down the distorted double-helical axis of the TATA-box DNA. The upstream DNA is nearest the viewer. (B) View of the complex rotated from the orientation in A by 90° about the vertical axis. The arrow points in the direction of the start site of initiation. (C) View of the complex, highlighting the TFB[c]/BRE interaction. (D) Stereo diagram of a (2F[o] F[c]) electron-density map contoured at 1 rms deviation, showing contacts between TFB[c] and the phosphate backbone of the BRE upstream of the TATA box. Red dots represent water molecules. (E) Same view as D with hydrogen bonds shown as dashed black lines. The phosphates are numbered with respect to the TATA-box sequence. Figures were created with BOBSCRIPT (28) and RASTER-3D (29).

Figures were selected by the author.