PDBsum entry 4zhn

Oxidoreductase/DNA

PDB id: 4zhn

Contents

Protein chain

201 a.a.

DNA/RNA

Ligands

AKG

Metals

_CO

Waters ×250

PDB id:

4zhn

Name:

Oxidoreductase/DNA

Title:

Crystal structure of alkb t208a mutant protein in complex with co(ii), 2-oxoglutarate, and methylated trinucleotide t-mea-t

Structure:

Methylated trinucleotide DNA t-mea-t. Chain: b. Engineered: yes. Alpha-ketoglutarate-dependent dioxygenase alkb. Chain: a. Fragment: residues 12-216. Synonym: alkylated DNA repair protein alkb,DNA oxidative demethylase alkb. Engineered: yes.

Source:

Synthetic: yes. Synthetic construct. Organism_taxid: 32630. Escherichia coli (strain k12). Organism_taxid: 83333. Strain: k12. Gene: alkb, aidd, b2212, jw2200. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.

Resolution:

1.33Å R-factor: 0.119 R-free: 0.147

Authors:

B.Ergel,B.Yu,S.M.Vorobiev,F.Forouhar,J.F.Hunt,Northeast Structural Genomics Consortium (Nesg)

Key ref:

M.L.Hall et al. Dft studies of the rate-Limiting step in the reaction of the fe/2og dioxygenase alkb and related experiment studies. To be published, .

Date:

25-Apr-15 Release date: 23-Dec-15

Protein chain

P05050  (ALKB_ECOLI) -  Alpha-ketoglutarate-dependent dioxygenase AlkB from Escherichia coli (strain K12)

Seq: 216 a.a.

Struc: 201 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

DNA/RNA chain

T-MA7-T 3 bases

Enzyme reactions

• Enzyme class: E.C.1.14.11.33 - Dna oxidative demethylase.
• Reaction: a methylated nucleobase within DNA + 2-oxoglutarate + O2 = a nucleobase within DNA + formaldehyde + succinate + CO2

methylated nucleobase within DNA (Bound ligand (Het Group name = AKG) corresponds exactly) + 2-oxoglutarate + O2 = nucleobase within DNA + formaldehyde + succinate + CO2

• Cofactor: Fe cation

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