5mC interactions in PDB entry 4HP1 auto-curated with SNAP

Last updated on 2019-09-30 by Xiang-Jun Lu <xiangjun@x3dna.org>. The block schematics were created with DSSR and rendered using PyMOL.

Summary information and primary citation [schematics · contacts · top · homepage · tutorial]

DNA binding protein-DNA
X-ray (2.25 Å)
Crystal structure of tet3 in complex with a non-cpg dsDNA
List of 2 5mC-amino acid contacts:
  1. A.5CM6: other-contacts is-WC-paired is-in-duplex [+]:CcG/cGG
  2. B.5CM6: other-contacts is-WC-paired is-in-duplex [-]:cGG/CcG
direct SNAP output · DNAproDB 2.0
Xu, Y., Xu, C., Kato, A., Tempel, W., Abreu, J.G., Bian, C., Hu, Y., Hu, D., Zhao, B., Cerovina, T., Diao, J., Wu, F., He, H.H., Cui, Q., Clark, E., Ma, C., Barbara, A., Veenstra, G.J., Xu, G., Kaiser, U.B., Liu, X.S., Sugrue, S.P., He, X., Min, J., Kato, Y., Shi, Y.G.: (2012) "Tet3 CXXC Domain and Dioxygenase Activity Cooperatively Regulate Key Genes for Xenopus Eye and Neural Development." Cell, 151, 1200-1213.
Ten-Eleven Translocation (Tet) family of dioxygenases dynamically regulates DNA methylation and has been implicated in cell lineage differentiation and oncogenesis. Yet their functions and mechanisms of action in gene regulation and embryonic development are largely unknown. Here, we report that Xenopus Tet3 plays an essential role in early eye and neural development by directly regulating a set of key developmental genes. Tet3 is an active 5mC hydroxylase regulating the 5mC/5hmC status at target gene promoters. Biochemical and structural studies further demonstrate that the Tet3 CXXC domain is critical for specific Tet3 targeting. Finally, we show that the enzymatic activity and CXXC domain are both crucial for Tet3's biological function. Together, these findings define Tet3 as a transcription regulator and reveal a molecular mechanism by which the 5mC hydroxylase and DNA binding activities of Tet3 cooperate to control target gene expression and embryonic development.

Base-block schematics in six views [summary · contacts · top · homepage · tutorial]

List of 2 5mC-amino acid contacts [summary · schematics · top · homepage · tutorial]

No. 1 A.5CM6: download PDB file for the 5mC entry
other-contacts is-WC-paired is-in-duplex [+]:CcG/cGG
No. 2 B.5CM6: download PDB file for the 5mC entry
other-contacts is-WC-paired is-in-duplex [-]:cGG/CcG