PDBsum entry 4nii

Oxidoreductase/DNA

PDB id: 4nii

Contents

Protein chain

200 a.a.

DNA/RNA

Ligands

AKG

Metals

_MN

Waters ×328

PDB id:

4nii

Name:

Oxidoreductase/DNA

Title:

Crystal structure of alkb d135i mutant protein with cofactors bound to dsdna containing m6a/a

Structure:

Alpha-ketoglutarate-dependent dioxygenase alkb. Chain: a. Fragment: unp residues 12-215. Synonym: alkylated DNA repair protein alkb, DNA oxidative demethylase alkb. Engineered: yes. Mutation: yes. 5'-d( Tp Ap Gp Gp Tp Ap Ap (6Ma)p Ap Cp Cp Gp T)-3'. Chain: b.

Source:

Escherichia coli. Organism_taxid: 562. Gene: alkb, aidd, b2212, jw2200. Expressed in: escherichia coli. Expression_system_taxid: 562. Synthetic: yes. Synthetic: yes

Resolution:

1.62Å R-factor: 0.176 R-free: 0.209

Authors:

C.Q.Yi,C.X.Zhu

Key ref:

C.Zhu and C.Yi (2014). Switching demethylation activities between AlkB family RNA/DNA demethylases through exchange of active-site residues. Angew Chem Int Ed Engl, 53, 3659-3662. PubMed id: 24596302 DOI: 10.1002/anie.201310050

Date:

06-Nov-13 Release date: 16-Apr-14

Protein chain

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

Seq: 216 a.a.

Struc: 200 a.a.*

* PDB and UniProt seqs differ at 2 residue positions (black crosses)

DNA/RNA chains

A-G-G-T-A-A-6MA-A-2YR-C-G-T 12 bases

A-A-C-G-G-T-A-T-T-A-C-C-T 13 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

reference

DOI no: 10.1002/anie.201310050

Angew Chem Int Ed Engl 53:3659-3662 (2014)

PubMed id: 24596302

Switching demethylation activities between AlkB family RNA/DNA demethylases through exchange of active-site residues.

C.Zhu, C.Yi.

ABSTRACT

The AlkB family demethylases AlkB, FTO, and ALKBH5 recognize differentially methylated RNA/DNA substrates, which results in their distinct biological roles. Here we identify key active-site residues that contribute to their substrate specificity. Swapping such active-site residues between the demethylases leads to partially switched demethylation activities. Combined evidence from X-ray structures and enzyme kinetics suggests a role of the active-site residues in substrate recognition. Such a divergent active-site sequence may aid the design of selective inhibitors that can discriminate these homologue RNA/DNA demethylases.