› 5cg9

X-ray diffraction
2.69Å resolution

NgTET1 in complex with 5mC DNA in space group P3221

Released:
DOI: 10.2210/pdb5cg9/pdb
PDB entry 5cg9 coloured by chain, front view.
PDB entry 5cg9 coloured by chain, side view.
PDB entry 5cg9 coloured by chain, top view.
Source organisms:
Primary publication:
Structure of Naegleria Tet-like dioxygenase (NgTet1) in complexes with a reaction intermediate 5-hydroxymethylcytosine DNA.
Hashimoto H, Pais JE, Dai N, Corrêa IR, Zhang X, Zheng Y, Cheng X
Nucleic Acids Res 43 10713-21 (2015)
PMID: 26323320

Function and Biology Details

Biochemical function:
  • not assigned
Biological process:
  • not assigned
Cellular component:
  • not assigned

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-112423 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
Tet-like dioxygenase 1 Chains: A, D
Molecule details ›
Chains: A, D
Length: 267 amino acids
Theoretical weight: 30.73 KDa
Source organism: Naegleria gruberi
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: D2W6T1 (Residues: 57-321; Coverage: 83%)
Gene names: NAEGRDRAFT_55029, TET1
Structure domains: Double-stranded beta-helix
DNA (5'-D(P*CP*AP*TP*GP*CP*GP*CP*TP*GP*AP*C)-3') Chains: B, E
Molecule details ›
Chains: B, E
Length: 11 nucleotides
Theoretical weight: 3.33 KDa
Source organism: synthetic construct
Expression system: Not provided
DNA (5'-D(*TP*GP*TP*CP*AP*GP*(5CM)P*GP*CP*AP*TP*GP*G)-3') Chains: C, F
Molecule details ›
Chains: C, F
Length: 13 nucleotides
Theoretical weight: 4.02 KDa
Source organism: synthetic construct
Expression system: Not provided

Ligands and Environments

4 bound ligands:
Ligand SO4 3 x SO4
Ligand AKG 2 x AKG
Ligand MN 2 x MN
Ligand EDO 2 x EDO
1 modified residue:
Ligand 5CM 2 x 5CM

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 22-ID
Spacegroup: P3221
Unit cell:
a: 191.216Å b: 191.216Å c: 51.254Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.194 0.193 0.222
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided

Quick links

Citations

10 review citations

Role of TET enzymes in DNA methylation, development, and cancer.
Rasmussen et al. (2016)
9 more

2 mentions without citation

Spectroscopic and in vitro Investigations of Fe2+ /α-Ketoglutarate-Dependent Enzymes Involved in Nucleic Acid Repair and Modification.
Schmidl et al. (2022)
1 more