2IT0

Crystal structure of a two-domain IdeR-DNA complex crystal form II

Summary for 2IT0

• Entry DOI: 10.2210/pdb2it0/pdb
• Related: 1FX7 1U8R 2ISY 2ISZ
• Descriptor: mbtA/mbtB operator strand 1, mbtA/mbtB operator strand 2, Iron-dependent repressor ideR, ... (6 entities in total)
• Functional Keywords: dna-binding protein, transcription-dna complex, transcription/dna
• Biological source: Mycobacterium tuberculosis
• Cellular location: Cytoplasm: P0A672
• Total number of polymer chains: 6
• Total formula weight: 93016.87

Authors

Wisedchaisri, G.,Chou, C.J.,Wu, M.,Roach, C.,Rice, A.E.,Holmes, R.K.,Beeson, C.,Hol, W.G. (deposition date: 2006-10-18, release date: 2007-02-13, Last modification date: 2023-08-30)

Primary citation

Wisedchaisri, G.,Chou, C.J.,Wu, M.,Roach, C.,Rice, A.E.,Holmes, R.K.,Beeson, C.,Hol, W.G.
Crystal structures, metal activation, and DNA-binding properties of two-domain IdeR from Mycobacterium tuberculosis
Biochemistry, 46:436-447, 2007

PubMed Abstract: The iron-dependent regulator IdeR is a key transcriptional regulator of iron uptake in Mycobacterium tuberculosis. In order to increase our insight into the role of the SH3-like third domain of this essential regulator, the metal-binding and DNA-binding properties of two-domain IdeR (2D-IdeR) whose SH3-like domain has been truncated were characterized. The equilibrium dissociation constants for Co2+ and Ni2+ activation of 2D-IdeR for binding to the fxbA operator and the DNA-binding affinities of 2D-IdeR in the presence of excess metal ions were estimated using fluorescence spectroscopy. 2D-IdeR binds to fxbA operator DNA with similar affinity as full-length IdeR in the presence of excess metal ion. However, the Ni2+ concentrations required to activate 2D-IdeR for DNA binding appear to be smaller than that for full-length IdeR while the concentration of Co2+ required for activation remains the same. We have determined the crystal structures of Ni2+-activated 2D-IdeR at 1.96 A resolution and its double dimer complex with the mbtA-mbtB operator DNA in two crystal forms at 2.4 A and 2.6 A, the highest resolutions for DNA complexes for any structures of iron-dependent regulator family members so far. The 2D-IdeR-DNA complex structures confirm the specificity of Ser37 and Pro39 for thymine bases and suggest preferential contacts of Gln43 to cytosine bases of the DNA. In addition, our 2D-IdeR structures reveal a remarkable property of the TEV cleavage sequence remaining after removal of the C-terminal His6. This C-terminal tail promotes crystal contacts by forming a beta-sheet with the corresponding tail of neighboring subunits in two unrelated structures of 2D-IdeR, one with and one without DNA. The contact-promoting properties of this C-terminal TEV cleavage sequence may be beneficial for crystallizing other proteins.

PubMed: 17209554
DOI: 10.1021/bi0609826

Experimental method

X-RAY DIFFRACTION (2.6 Å)