PDBsum entry 3h8x

Oxidoreductase/DNA

PDB id: 3h8x

Contents

Protein chain

204 a.a. *

DNA/RNA

Waters ×177

* Residue conservation analysis

PDB id:

3h8x

Name:

Oxidoreductase/DNA

Title:

Structure determination of DNA methylation lesions n1-mea and n3-mec in duplex DNA using a cross-linked host-guest system

Structure:

Alpha-ketoglutarate-dependent dioxygenase alkb homolog 2. Chain: a. Fragment: residues 56-261. Synonym: alkylated DNA repair protein alkb homolog 2, oxy dc1. Engineered: yes. Mutation: yes. 5'-d( Cp Tp Gp Tp (Me6)p Tp (2Yr)p Ap Tp Tp Gp Cp G)-3'. Chain: b. Engineered: yes.

Source:

Homo sapiens. Human. Organism_taxid: 9606. Gene: abh2, alkbh2. Expressed in: escherichia coli. Expression_system_taxid: 469008. Synthetic: yes. Synthetic construct. Organism_taxid: 32630.

Resolution:

1.95Å R-factor: 0.207 R-free: 0.236

Authors:

L.Lu,C.Yi,X.Jian,G.Zheng,C.He

Key ref:

L.Lu et al. (2010). Structure determination of DNA methylation lesions N1-meA and N3-meC in duplex DNA using a cross-linked protein-DNA system. Nucleic Acids Res, 38, 4415-4425. PubMed id: 20223766

Date:

29-Apr-09 Release date: 31-Mar-10

Protein chain

Q6NS38  (ALKB2_HUMAN) -  DNA oxidative demethylase ALKBH2 from Homo sapiens

Seq: 261 a.a.

Struc: 204 a.a.*

* PDB and UniProt seqs differ at 5 residue positions (black crosses)

DNA/RNA chains

C-T-G-T-ME6-T-2YR-A-T-T-G-C-G 13 bases

T-C-G-C-A-A-T-A-A-G-A-C-A 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
• Cofactor: Fe cation

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

reference

Nucleic Acids Res 38:4415-4425 (2010)

PubMed id: 20223766

Structure determination of DNA methylation lesions N1-meA and N3-meC in duplex DNA using a cross-linked protein-DNA system.

L.Lu, C.Yi, X.Jian, G.Zheng, C.He.

ABSTRACT

N(1)-meA and N(3)-meC are cytotoxic DNA base methylation lesions that can accumulate in the genomes of various organisms in the presence of S(N)2 type methylating agents. We report here the structural characterization of these base lesions in duplex DNA using a cross-linked protein-DNA crystallization system. The crystal structure of N(1)-meA:T pair shows an unambiguous Hoogsteen base pair with a syn conformation adopted by N(1)-meA, which exhibits significant changes in the opening, roll and twist angles as compared to the normal A:T base pair. Unlike N(1)-meA, N(3)-meC does not establish any interaction with the opposite G, but remains partially intrahelical. Also, structurally characterized is the N(6)-meA base modification that forms a normal base pair with the opposite T in duplex DNA. Structural characterization of these base methylation modifications provides molecular level information on how they affect the overall structure of duplex DNA. In addition, the base pairs containing N(1)-meA or N(3)-meC do not share any specific characteristic properties except that both lesions create thermodynamically unstable regions in a duplex DNA, a property that may be explored by the repair proteins to locate these lesions.