PDBsum entry: 1mkm

Transcription

PDB id: 1mkm

Contents

Protein chains

246 a.a. *

Ligands

FMT

Metals

_ZN ×2

Waters ×111

* Residue conservation analysis

PDB id:

1mkm

Name:

Transcription

Title:

Crystal structure of the thermotoga maritima iclr

Structure:

Iclr transcriptional regulator. Chain: a, b. Engineered: yes

Source:

Thermotoga maritima. Organism_taxid: 2336. Expressed in: escherichia coli. Expression_system_taxid: 562

Biol. unit:

Tetramer (from PDB file)

Resolution:

2.20Å R-factor: 0.232 R-free: 0.300

Authors:

Y.Kim,R.G.Zhang,A.Joachimiak,T.Skarina,A.Edwards, A.Savchenko,Midwest Center For Structural Genomics (Mcsg)

Key ref:

R.G.Zhang et al. (2002). Crystal structure of Thermotoga maritima 0065, a member of the IclR transcriptional factor family. J Biol Chem, 277, 19183-19190. PubMed id: 11877432 DOI: 10.1074/jbc.M112171200

Date:

29-Aug-02 Release date: 11-Sep-02

Supersedes:

1jmr

Protein chains

Q9WXS0  (Q9WXS0_THEMA) -  Transcriptional regulator, IclR family

Seq: 246 a.a.

Struc: 246 a.a.

 Gene Ontology (GO) functional annotation 

• Biological process: regulation of transcription (3 terms)
• Biochemical function: DNA binding (1 term)

DOI no: 10.1074/jbc.M112171200

J Biol Chem 277:19183-19190 (2002)

PubMed id: 11877432

Crystal structure of Thermotoga maritima 0065, a member of the IclR transcriptional factor family.

R.G.Zhang, Y.Kim, T.Skarina, S.Beasley, R.Laskowski, C.Arrowsmith, A.Edwards, A.Joachimiak, A.Savchenko.

ABSTRACT

Members of the IclR family of transcription regulators modulate signal-dependent expression of genes involved in carbon metabolism in bacteria and archaea. The Thermotoga maritima TM0065 gene codes for a protein (TM-IclR) that is homologous to the IclR family. We have determined the crystal structure of TM-IclR at 2.2 A resolution using MAD phasing and synchrotron radiation. The protein is composed of two domains: the N-terminal DNA-binding domain contains the winged helix-turn-helix motif, and the C-terminal presumed regulatory domain is involved in binding signal molecule. In a proposed signal-binding site, a bound Zn(2+) ion was found. In the crystal, TM-IclR forms a dimer through interactions between DNA-binding domains. In the dimer, the DNA-binding domains are 2-fold related, but the dimer is asymmetric with respect to the orientation of signal-binding domains. Crystal packing analysis showed that TM-IclR dimers form a tetramer through interactions exclusively by signal-binding domains. A model is proposed for binding of IclR-like factors to DNA, and it suggests that signal-dependent transcription regulation is accomplished by affecting an oligomerization state of IclR and therefore its affinity for DNA target.

Selected figure(s)

Figure 3.
Fig. 3. IclR topology and its dimer and tetramer arrangement. A, IclR topology. The DNA-binding domain consists of three -helices (H1-H3) and a -hairpin forming a wing. The signal-binding domain forms a half TIM barrel with three small -helices in the concave side and two longer -helices in the convex side of the barrel. The two domains are linked by an -helix (H4). B, the asymmetric dimer. The dimer interface is formed exclusively between the two HTH DNA-binding domains. Each monomer is color-coded red and green. C, the tetramer viewed from the top (DBD) is composed of two asymmetric dimers represented as four different colors, red and green for one asymmetric unit and yellow and magenta for the other. The tetramer interface is formed exclusively between signal-binding domains, which also include a metal ion in a putative ligand-binding pocket in each domain. D, IclR tetramer represented as a charge potential surface drawing in top and side views.

Figure 5.
Fig. 5. DNA binding model. A, B-DNA is modeled to bind a IclR tetramer as shown in the space-filling model on top of the IclR tetramer represented in the charge potential surface drawing. The known IclR DNA target and the consensus sequences are included. B, proposed DNA binding model A: a tetramer IclR binds to two consecutive palindromic DNA targets. C, proposed DNA binding model B: a tetrameric IclR binds to two palindromic DNA targets that are far apart (>100 bp), looped, and come back and lined either in parallel (left) or in anti-parallel (right).

The above figures are reprinted by permission from the ASBMB: J Biol Chem (2002, 277, 19183-19190) copyright 2002.

Figures were selected by an automated process.