5BOX

Structure of TrmBL2, an archaeal chromatin protein, shows a novel mode of DNA binding.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.224 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural Insights into Nonspecific Binding of DNA by TrmBL2, an Archaeal Chromatin Protein.

Ahmad, M.U.Waege, I.Hausner, W.Thomm, M.Boos, W.Diederichs, K.Welte, W.

(2015) J.Mol.Biol. 427: 3216-3229

  • DOI: 10.1016/j.jmb.2015.08.012
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The crystal structure of TrmBL2 from the archaeon Pyrococcus furiosus shows an association of two pseudosymmetric dimers. The dimers follow the prototypical design of known bacterial repressors with two helix-turn-helix (HTH) domains binding to succe ...

    The crystal structure of TrmBL2 from the archaeon Pyrococcus furiosus shows an association of two pseudosymmetric dimers. The dimers follow the prototypical design of known bacterial repressors with two helix-turn-helix (HTH) domains binding to successive major grooves of the DNA. However, in TrmBL2, the two dimers are arranged at a mutual displacement of approximately 2bp so that they associate with the DNA along the double-helical axis at an angle of approximately 80°. While the deoxyribose phosphate groups of the double-stranded DNA (dsDNA) used for co-crystallization are clearly seen in the electron density map, most of the nucleobases are averaged out. Refinement required to assume a superposition of at least three mutually displaced dsDNAs. The HTH domains interact primarily with the deoxyribose phosphate groups and polar interactions with the nucleobases are almost absent. This hitherto unseen mode of DNA binding by TrmBL2 seems to arise from nonoptimal protein-DNA contacts made by its four HTH domains resulting in a low-affinity, nonspecific binding to DNA.


    Organizational Affiliation

    University of Konstanz Department of Biology, Universitätsstrasse 10, 78456 Konstanz, Germany. Electronic address: wolfram.welte@uni-konstanz.de.,University of Konstanz Department of Biology, Universitätsstrasse 10, 78456 Konstanz, Germany.,University Regensburg Lehrstuhl für Mikrobiologie, Universitätsstrasse 31, 93053 Regensburg, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Putative HTH-type transcriptional regulator TrmBL2
A, B, C, D
263Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1)Mutation(s): 0 
Gene Names: trmBL2
Find proteins for Q8U3H1 (Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1))
Go to UniProtKB:  Q8U3H1
Entity ID: 2
MoleculeChainsLengthOrganism
DNA TGM (25-MER)E25Pyrococcus furiosus
Entity ID: 3
MoleculeChainsLengthOrganism
DNA (25-MER)F25Pyrococcus furiosus
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download SDF File 
Download CCD File 
A, B, C, D
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
MPD
Query on MPD

Download SDF File 
Download CCD File 
A, B
(4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.224 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 83.619α = 90.00
b = 105.790β = 96.75
c = 93.235γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
Cootmodel building
PHENIXphasing
PDB_EXTRACTdata extraction
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-09-02
    Type: Initial release
  • Version 1.1: 2015-10-07
    Type: Database references
  • Version 1.2: 2016-09-21
    Type: Data collection