4HP3

Crystal structure of Tet3 in complex with a CpG dsDNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.215 
  • R-Value Observed: 0.217 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Tet3 CXXC Domain and Dioxygenase Activity Cooperatively Regulate Key Genes for Xenopus Eye and Neural Development.

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) Cell 151: 1200-1213

  • DOI: 10.1016/j.cell.2012.11.014
  • Primary Citation of Related Structures:  
    4HP1, 4HP3

  • PubMed Abstract: 
  • 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 ...

    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.


    Organizational Affiliation

    Division of Endocrinology, Diabetes and Hypertension, Departments of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
LOC100036628 proteinC72Xenopus tropicalisMutation(s): 0 
Gene Names: tet3
EC: 1.14.11
UniProt
Find proteins for A0JP82 (Xenopus tropicalis)
Explore A0JP82 
Go to UniProtKB:  A0JP82
Protein Feature View
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  • Reference Sequence

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Entity ID: 1
MoleculeChainsLengthOrganismImage
DNA (5'-D(*GP*CP*CP*AP*AP*CP*GP*TP*TP*GP*GP*C)-3')A, B12N/A
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 69.892α = 90
b = 39.455β = 99.92
c = 54.134γ = 90
Software Package:
Software NamePurpose
SCALAdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-12-05
    Type: Initial release
  • Version 1.1: 2012-12-19
    Changes: Database references