4X9J

EGR-1 with Doubly Methylated DNA

Summary for 4X9J

• Entry DOI: 10.2210/pdb4x9j/pdb
• Related: 4R2A
• Descriptor: Early growth response protein 1, DNA (5'-D(*AP*GP*(5CM)P*GP*TP*GP*GP*GP*(5CM)P*GP*T)-3'), DNA (5'-D(*TP*AP*(5CM)P*GP*CP*CP*CP*AP*(5CM)P*GP*C)-3'), ... (5 entities in total)
• Functional Keywords: dna binding, methylated dna, zinc finger, transcription, transcription regulator-dna complex, transcription regulator/dna
• Biological source: Homo sapiens (Human); More
• Cellular location: Nucleus : P18146
• Total number of polymer chains: 3
• Total formula weight: 17684.02

Authors

White, M.A.,Zandarashvili, L.,Iwahara, J. (deposition date: 2014-12-11, release date: 2015-05-13, Last modification date: 2023-09-27)

Primary citation

Zandarashvili, L.,White, M.A.,Esadze, A.,Iwahara, J.
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, 2015

PubMed Abstract: 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.

PubMed: 25999311
DOI: 10.1016/j.febslet.2015.05.022

Experimental method

X-RAY DIFFRACTION (1.412 Å)