6OD5

Human TCF4 C-terminal bHLH domain in Complex with 12-bp Oligonucleotide Containing E-box Sequence with 5-carboxylcytosines

Summary for 6OD5

• Entry DOI: 10.2210/pdb6od5/pdb
• Descriptor: Transcription factor 4, DNA (5'-D(*AP*(1CC)P*GP*CP*AP*CP*GP*TP*GP*(1CC)P*G)-3'), 1,2-ETHANEDIOL, ... (6 entities in total)
• Functional Keywords: protein-dna complex, transcription factor, bhth, e-box, transcription-dna complex, transcription/dna
• Biological source: Homo sapiens (Human); More
• Total number of polymer chains: 8
• Total formula weight: 45050.48

Authors

Horton, J.R.,Cheng, X.,Yang, J. (deposition date: 2019-03-25, release date: 2019-05-29, Last modification date: 2023-10-11)

Primary citation

Yang, J.,Horton, J.R.,Li, J.,Huang, Y.,Zhang, X.,Blumenthal, R.M.,Cheng, X.
Structural basis for preferential binding of human TCF4 to DNA containing 5-carboxylcytosine.
Nucleic Acids Res., 47:8375-8387, 2019

PubMed Abstract: The psychiatric risk-associated transcription factor 4 (TCF4) is linked to schizophrenia. Rare TCF4 coding variants are found in individuals with Pitt-Hopkins syndrome-an intellectual disability and autism spectrum disorder. TCF4 contains a C-terminal basic-helix-loop-helix (bHLH) DNA binding domain which recognizes the enhancer-box (E-box) element 5'-CANNTG-3' (where N = any nucleotide). A subset of the TCF4-occupancy sites have the expanded consensus binding specificity 5'-C(A/G)-CANNTG-3', with an added outer Cp(A/G) dinucleotide; for example in the promoter for CNIH3, a gene involved in opioid dependence. In mammalian genomes, particularly brain, the CpG and CpA dinucleotides can be methylated at the 5-position of cytosine (5mC), and then may undergo successive oxidations to the 5-hydroxymethyl (5hmC), 5-formyl (5fC), and 5-carboxyl (5caC) forms. We find that, in the context of 5'-0CG-1CA-2CG-3TG-3'(where the numbers indicate successive dinucleotides), modification of the central E-box 2CG has very little effect on TCF4 binding, E-box 1CA modification has a negative influence on binding, while modification of the flanking 0CG, particularly carboxylation, has a strong positive impact on TCF4 binding to DNA. Crystallization of TCF4 in complex with unmodified or 5caC-modified oligonucleotides revealed that the basic region of bHLH domain adopts multiple conformations, including an extended loop going through the DNA minor groove, or the N-terminal portion of a long helix binding in the DNA major groove. The different protein conformations enable arginine 576 (R576) to interact, respectively, with a thymine in the minor groove, a phosphate group of DNA backbone, or 5caC in the major groove. The Pitt-Hopkins syndrome mutations affect five arginine residues in the basic region, two of them (R569 and R576) involved in 5caC recognition. Our analyses indicate, and suggest a structural basis for, the preferential recognition of 5caC by a transcription factor centrally important in brain development.

PubMed: 31081034
DOI: 10.1093/nar/gkz381

Experimental method

X-RAY DIFFRACTION (2.05 Å)