PDBsum entry 4z3c

DNA binding protein/DNA

PDB id: 4z3c

Contents

Protein chain

45 a.a.

DNA/RNA

Ligands

UNX ×4

Metals

_ZN ×2

Waters ×85

PDB id:

4z3c

Name:

DNA binding protein/DNA

Title:

Zinc finger region of human tet3 in complex with cpg DNA

Structure:

DNA (5'-d( Gp Cp Cp Ap Ap Cp Gp Tp Tp Gp Gp C)-3'). Chain: a, b. Engineered: yes. Methylcytosine dioxygenase. Chain: c. Engineered: yes

Source:

Synthetic: yes. Synthetic construct. Organism_taxid: 32630. Other_details: synthetic. Homo sapiens. Human. Organism_taxid: 9606. Gene: tet3. Expressed in: escherichia coli.

Resolution:

1.57Å R-factor: 0.216 R-free: 0.253

Authors:

K.Liu,C.Xu,W.Tempel,A.Dong,C.H.Arrowsmith,C.Bountra,A.M.Edwards, J.Min,Structural Genomics Consortium (Sgc)

Key ref:

C.Xu et al. (2018). DNA Sequence Recognition of Human CXXC Domains and Their Structural Determinants. Structure, 26, 85. PubMed id: 29276034 DOI: 10.1016/j.str.2017.11.022

Date:

31-Mar-15 Release date: 29-Apr-15

Protein chain

O43151  (TET3_HUMAN) -  Methylcytosine dioxygenase TET3 from Homo sapiens

Seq: 1795 a.a.

Struc: 45 a.a.

DNA/RNA chains

G-C-C-A-A-C-G-T-T-G-G-C 12 bases

G-C-C-A-A-C-G-T-T-G-G-C 12 bases

Enzyme reactions

• Enzyme class: E.C.1.14.11.80 - methylcytosine dioxygenase.
• Reaction:
  1. a 5-methyl-2'-deoxycytidine in DNA + 2-oxoglutarate + O2 = a 5-hydroxymethyl-2'-deoxycytidine in DNA + succinate + CO2
  2. a 5-hydroxymethyl-2'-deoxycytidine in DNA + 2-oxoglutarate + O2 = a 5-formyl-2'-deoxycytidine in DNA + succinate + CO2 + H2O
  3. a 5-formyl-2'-deoxycytidine in DNA + 2-oxoglutarate + O2 = a 5-carboxyl-2'-deoxycytidine in DNA + succinate + CO2 + H⁺

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

reference

DOI no: 10.1016/j.str.2017.11.022

Structure 26:85 (2018)

PubMed id: 29276034

DNA Sequence Recognition of Human CXXC Domains and Their Structural Determinants.

C.Xu, K.Liu, M.Lei, A.Yang, Y.Li, T.R.Hughes, J.Min.

ABSTRACT

The CXXC domain, first identified as the reader of unmodified CpG dinucleotide, plays important roles in epigenetic regulation by targeting various activities to CpG islands. Here we systematically measured and compared the DNA-binding selectivities of all known human CXXC domains by different binding assays, and complemented the existing function-based classification of human CXXC domains with a classification based on their DNA selectivities. Through a series of crystal structures of CXXC domains with DNA ligands, we unravel the molecular mechanisms of how these CXXC domains, including single CXXC domains and tandem CXXC-PHD domains, recognize distinct DNA ligands, which further supports our classification of human CXXC domains and also provides insights into selective recruitment of chromatin modifiers to their respective targets via CXXC domains recognizing different genomic DNA sequences. Our study facilitates the understanding of the relationship between the DNA-binding specificities of the CXXC proteins and their biological functions.