Summary information and primary citation
- PDB-id
- 4i2o; SNAP-derived features in text and JSON formats;
DNAproDB
- Class
- transcription regulator-DNA
- Method
- X-ray (1.77 Å)
- Summary
- The structure of fixk2 from bradyrhizobium japonicum
- Reference
- Bonnet M, Kurz M, Mesa S, Briand C, Hennecke H, Grutter MG (2013): "The Structure of Bradyrhizobium japonicum Transcription Factor FixK2 Unveils Sites of DNA Binding and Oxidation." J.Biol.Chem., 288, 14238-14246. doi: 10.1074/jbc.M113.465484.
- Abstract
- FixK2 is an important regulatory protein that helps activating a large number of genes for the anoxic and microoxic, endosymbiotic and nitrogen-fixing life styles of the α-proteobacterium Bradyrhizobium japonicum. FixK2 belongs to the cyclic AMP receptor protein (CRP) superfamily. While most CRP-family members are co-regulated by effector molecules, the activity of FixK2 is negatively controlled by oxidation of its single cysteine (C183) located next to the DNA binding domain, and possibly also by proteolysis. Here we report the three-dimensional X-ray structure of FixK2, a representative of the FixK subgroup of the CRP superfamily. Crystallization succeeded only (i) when an oxidation- and protease-insensitive protein variant (C183S-FixK2His6) was used, in which C183 was replaced by serine and the C-terminus fused with a hexa-histidine tag, and (ii) when this protein was allowed to form a complex with a 30mer double-strand target DNA. The structure of the FixK2-DNA complex was solved at a resolution of 1.77 Å in which the protein formed a homodimer. The precise protein-DNA contacts were identified which led to an affirmation of the canonical target sequence, the so-called FixK2 box. The C-terminus is surface-exposed which might explain its sensitivity to specific cleavage and degradation. The oxidation-sensitive C183 is also surface-exposed and in close proximity to DNA. Therefore, we propose a mechanism whereby the oxo-acids generated after oxidation of the cysteine thiol cause an electrostatic repulsion, thus preventing specific DNA binding.
