Summary information and primary citation

4x9j; SNAP-derived features in text and JSON formats; DNAproDB
transcription regulator-DNA
X-ray (1.412 Å)
Egr-1 with doubly methylated DNA
Zandarashvili L, White MA, Esadze A, Iwahara J (2015): "Structural impact of complete CpG methylation within target DNA on specific complex formation of the inducible transcription factor Egr-1." Febs Lett., 589, 1748-1753. doi: 10.1016/j.febslet.2015.05.022.
The inducible transcription factor Egr-1 binds specifically to 9-bp target sequences containing two CpG sites that can potentially be methylated at four cytosine bases. Although it appears that complete CpG methylation would make an unfavorable steric clash in the previous crystal structures of the complexes with unmethylated or partially methylated DNA, our affinity data suggest that DNA recognition by Egr-1 is insensitive to CpG methylation. We have determined, at a 1.4-Å resolution, the crystal structure of the Egr-1 zinc-finger complex with completely methylated target DNA. Structural comparison of the three different methylation states reveals why Egr-1 can recognize the target sequences regardless of CpG methylation.

Cartoon-block schematics in six views (download the tarball)

PyMOL session file Download PDB file View in 3Dmol.js

List of 4 5mC-amino acid contacts

No. 1 B.5CM3: stacking-with-A.ARG174 is-WC-paired is-in-duplex [+]:GcG/cGC
No. 2 B.5CM9: stacking-with-A.ARG118 is-WC-paired is-in-duplex [+]:GcG/cGC
No. 3 C.5CM53: other-contacts is-WC-paired is-in-duplex [-]:cGT/AcG
No. 4 C.5CM59: other-contacts is-WC-paired is-in-duplex [-]:cGT/AcG