7NE3

Human TET2 in complex with favourable DNA substrate.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.26 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.175 
  • R-Value Observed: 0.177 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Pronounced sequence specificity of the TET enzyme catalytic domain guides its cellular function.

Ravichandran, M.Rafalski, D.Davies, C.I.Ortega-Recalde, O.Nan, X.Glanfield, C.R.Kotter, A.Misztal, K.Wang, A.H.Wojciechowski, M.Razew, M.Mayyas, I.M.Kardailsky, O.Schwartz, U.Zembrzycki, K.Morison, I.M.Helm, M.Weichenhan, D.Jurkowska, R.Z.Krueger, F.Plass, C.Zacharias, M.Bochtler, M.Hore, T.A.Jurkowski, T.P.

(2022) Sci Adv 8: eabm2427-eabm2427

  • DOI: 10.1126/sciadv.abm2427
  • Primary Citation of Related Structures:  
    7NE3, 7NE6

  • PubMed Abstract: 
  • TET (ten-eleven translocation) enzymes catalyze the oxidation of 5-methylcytosine bases in DNA, thus driving active and passive DNA demethylation. Here, we report that the catalytic domain of mammalian TET enzymes favor CGs embedded within basic helix-loop-helix and basic leucine zipper domain transcription factor-binding sites, with up to 250-fold preference in vitro ...

    TET (ten-eleven translocation) enzymes catalyze the oxidation of 5-methylcytosine bases in DNA, thus driving active and passive DNA demethylation. Here, we report that the catalytic domain of mammalian TET enzymes favor CGs embedded within basic helix-loop-helix and basic leucine zipper domain transcription factor-binding sites, with up to 250-fold preference in vitro. Crystal structures and molecular dynamics calculations show that sequence preference is caused by intrasubstrate interactions and CG flanking sequence indirectly affecting enzyme conformation. TET sequence preferences are physiologically relevant as they explain the rates of DNA demethylation in TET-rescue experiments in culture and in vivo within the zygote and germ line. Most and least favorable TET motifs represent DNA sites that are bound by methylation-sensitive immediate-early transcription factors and octamer-binding transcription factor 4 (OCT4), respectively, illuminating TET function in transcriptional responses and pluripotency support.


    Organizational Affiliation

    Cardiff University, School of Biosciences, Museum Avenue, CF10 3AX Cardiff, Wales, UK.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Methylcytosine dioxygenase TET2A463Homo sapiensMutation(s): 0 
Gene Names: TET2KIAA1546Nbla00191
EC: 1.14.11
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Protein Feature View
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  • Reference Sequence

Find similar nucleic acids by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChainsLengthOrganismImage
DNA (5'-D(*AP*CP*AP*GP*GP*(5CM)P*GP*CP*CP*TP*G)-3')B, C12synthetic construct
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MES
Query on MES

Download Ideal Coordinates CCD File 
K [auth A]2-(N-MORPHOLINO)-ETHANESULFONIC ACID
C6 H13 N O4 S
SXGZJKUKBWWHRA-UHFFFAOYSA-N
 Ligand Interaction
OGA
Query on OGA

Download Ideal Coordinates CCD File 
H [auth A]N-OXALYLGLYCINE
C4 H5 N O5
BIMZLRFONYSTPT-UHFFFAOYSA-N
 Ligand Interaction
ZN
Query on ZN

Download Ideal Coordinates CCD File 
D [auth A],
E [auth A],
F [auth A]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO

Download Ideal Coordinates CCD File 
I [auth A],
J [auth A]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
FE2
Query on FE2

Download Ideal Coordinates CCD File 
G [auth A]FE (II) ION
Fe
CWYNVVGOOAEACU-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 47.994α = 90
b = 87.711β = 90
c = 260.531γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PHENIXdata processing
XDSdata reduction
XDSdata scaling
MxCuBEdata collection

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Foundation for Polish SciencePolandPOIR.04.04.00-00-5D81/17-00

Revision History  (Full details and data files)

  • Version 1.0: 2022-03-02
    Type: Initial release
  • Version 1.1: 2022-08-24
    Changes: Database references, Source and taxonomy, Structure summary
  • Version 1.2: 2022-09-21
    Changes: Database references