PDBsum entry 3h4c

Transcription

PDB id: 3h4c

Contents

Protein chain

207 a.a.

Ligands

EDO

Waters ×56

PDB id:

3h4c

Name:

Transcription

Title:

Structure of thE C-terminal domain of transcription factor iib from trypanosoma brucei

Structure:

Transcription factor tfiib-like. Chain: a. Fragment: c-terminal domain. Engineered: yes

Source:

Trypanosoma brucei brucei. Organism_taxid: 5702. Strain: 427. Gene: tfiib-like. Expressed in: escherichia coli. Expression_system_taxid: 562

Resolution:

2.30Å R-factor: 0.208 R-free: 0.249

Authors:

B.Syed Ibrahim,N.Kanneganti,G.E.Rieckhof,A.Das,D.V.Laurents, J.B.Palenchar,V.Bellofatto,D.A.Wah

Key ref:

B.S.Ibrahim et al. (2009). Structure of the C-terminal domain of transcription factor IIB from Trypanosoma brucei. Proc Natl Acad Sci U S A, 106, 13242-13247. PubMed id: 19666603 DOI: 10.1073/pnas.0904309106

Date:

18-Apr-09 Release date: 11-Aug-09

Protein chain

Q257B3  (TF2B_TRYBB) -  Transcription initiation factor IIB from Trypanosoma brucei brucei

Seq: 345 a.a.

Struc: 207 a.a.

Enzyme reactions

• Enzyme class: E.C.?

DOI no: 10.1073/pnas.0904309106

Proc Natl Acad Sci U S A 106:13242-13247 (2009)

PubMed id: 19666603

Structure of the C-terminal domain of transcription factor IIB from Trypanosoma brucei.

B.S.Ibrahim, N.Kanneganti, G.E.Rieckhof, A.Das, D.V.Laurents, J.B.Palenchar, V.Bellofatto, D.A.Wah.

ABSTRACT

In trypanosomes, the production of mRNA relies on the synthesis of the spliced leader (SL) RNA. Expression of the SL RNA is initiated at the only known RNA polymerase II promoter in these parasites. In the pathogenic trypanosome, Trypanosoma brucei, transcription factor IIB (tTFIIB) is essential for SL RNA gene transcription and cell viability, but has a highly divergent primary sequence in comparison to TFIIB in well-studied eukaryotes. Here we describe the 2.3 A resolution structure of the C-terminal domain of tTFIIB (tTFIIB(C)). The tTFIIB(C) structure consists of 2 closely packed helical modules followed by a C-terminal extension of 32 aa. Using the structure as a guide, alanine substitutions of basic residues in regions analogous to functionally important regions of the well-studied eukaryotic TFIIB support conservation of a general mechanism of TFIIB function in eukaryotes. Strikingly, tTFIIB(C) contains additional loops and helices, and, in contrast to the highly basic DNA binding surface of human TFIIB, contains a neutral surface in the corresponding region. These attributes probably mediate trypanosome-specific interactions and have implications for the apparent bidirectional transcription by RNA polymerase II in protein-encoding gene expression in these organisms.

Selected figure(s)

Figure 2.
Structure of the C-terminal domain of T. brucei TFIIB (tTFIIB[C]) and comparison to human TFIIB[C]. (A) Structure of tTFIIB[C] (this work). Each helix of the 5-helix cyclin fold is colored identically in each of the 2 modules. Additional motifs distinct in tTFIIB (H6, H2′A, H3′A, and H6′) are blue. H2′A is behind H2 in this view. Dashed lines denote amino acids not visible in the crystal, and the number of residues is in parentheses. Arrows denote regions for comparison between tTFIIB[C] and human TFIIB[C] in panel B and their position in the sequence in panel C as discussed in the text: Helix H6 (blue arrow) and the linker between H3′A and H4′ (black arrow). (B) Structure of human TFIIB[C] (PDB ID 1c9b) (29). (C) The amino acid sequence of tTFIIB[C] (Tb; accession no. EAN76636) is aligned with that of T. cruzi (Tc; XP 806216), S. cerevisiae (Sc; P29055), and the sequences of known TFIIB[C] structures from P. woesei (Pw; 1d3u), and Homo sapiens (Hs; 1c9b). Sequence gaps are denoted by dashes in panel C. tTFIIB[C] amino acid numbers and secondary structure elements are indicated above the alignment, and human TFIIB[C] secondary structure elements are indicated below the alignment. Helices are depicted as boxes, intervening segments as lines, gaps in the structural alignment are blank, and residues not visible in the electron density are denoted by dashes. Amino acids that were changed to alanine in tTFIIB variants are indicated by asterisks (see Figs. 3 and 4). Structurally equivalent residues in human TFIIB that affected function when mutated are denoted by equal signs (19). Residues Asp-229 to Thr-237 are omitted from the S. cerevisiae sequence for clarity.

Figure 3.
Putative DNA binding surface and electrostatic potential surface properties of tTFIIB[C] compared to human TFIIB[C]. (A) The putative DNA binding face of tTFIIB[C] (Left) reveals a more neutral surface than the highly basic DNA binding surface of human tTFIIB[C] (Right). Areas colored in blue, white, and red denote positive, neutral, and negative potential contoured at +3, 0, −3 kT/e, respectively. Black arrows in panels A and C indicate the basic patches in tTFIIB[C] and the corresponding regions (recognition loop and HTH motif) in human TFIIB[C]. (B) In the human TFIIB[C]/TBP/DNA complex, TFIIB[C] contacts the DNA at BRE^D and BRE^U through its basic surface (29). TBP, which binds the minor groove, is omitted for clarity. (C) Ribbon diagram of putative DNA binding surface. The green arrow indicates the additional turn on H2 unique to the trypanosome protein. View in this figure is rotated 180° around the horizontal axis relative to Fig. 2.

Figures were selected by an automated process.