2CZR

Crystal structure of TBP-interacting protein (Tk-TIP26) and implications for its inhibition mechanism of the interaction between TBP and TATA-DNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.191 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal structure of TBP-interacting protein (Tk-TIP26) and implications for its inhibition mechanism of the interaction between TBP and TATA-DNA

Yamamoto, T.Matsuda, T.Inoue, T.Matsumura, H.Morikawa, M.Kanaya, S.Kai, Y.

(2006) Protein Sci. 15: 152-161

  • DOI: 10.1110/ps.051788906

  • PubMed Abstract: 
  • TATA-binding protein (TBP)-interacting protein from the hyperthermophilic archaeon Thermococcus kodakaraensis strain KOD1 (Tk-TIP26) is a possible transcription regulatory protein in Thermococcales. Here, we report the crystal structure of Tk-TIP26 d ...

    TATA-binding protein (TBP)-interacting protein from the hyperthermophilic archaeon Thermococcus kodakaraensis strain KOD1 (Tk-TIP26) is a possible transcription regulatory protein in Thermococcales. Here, we report the crystal structure of Tk-TIP26 determined at 2.3 A resolution with multiple-wavelength anomalous dispersion (MAD) method. The overall structure of Tk-TIP26 consists of two domains. The N-terminal domain forms an alpha/beta structure, in which three alpha-helices enclose the central beta-sheet. The topology of this domain is similar to that of holliday junction resolvase Hjc from Pyrococcus furiosus. The C-terminal domain comprises three alpha-helices, six beta-strands, and two 3(10)-helices. In the dimer structure of Tk-TIP26, two molecules are related with the crystallographic twofold axis, and these molecules rigidly interact with each other via hydrogen bonds. The complex of Tk-TIP26/Tk-TBP is isolated and analyzed by SDS-PAGE and gel filtration column chromatography, resulting in a stoichiometric ratio of the interaction between Tk-TIP26 and Tk-TBP of 4:2, i.e., two dimer molecules of Tk-TIP26 formed a complex with one dimeric TBP. The electrostatic surfaces of Tk-TIP26 and TBP from Pyrocuccus woesei (PwTBP) allowed us to build a model of the Tk-TIP26/TBP complex, and to propose the inhibition mechanism where two dimer molecules of Tk-TIP26 bind to a dimeric TBP, preventing its binding to TATA-DNA.


    Organizational Affiliation

    Department of Applied Chemistry, Graduate School of Engineering, Osaka University, 2-1 Yamada-oka, Suita, Osaka 565-0871, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
TBP-interacting protein
A
226Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1)Mutation(s): 0 
Find proteins for Q9V2W6 (Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1))
Go to UniProtKB:  Q9V2W6
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.191 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 73.834α = 90.00
b = 73.834β = 90.00
c = 86.414γ = 90.00
Software Package:
Software NamePurpose
CCP4data scaling
CNSphasing
CNSrefinement
MOSFLMdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-02-14
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Derived calculations, Source and taxonomy, Version format compliance