PDBsum entry 3rzm

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protein dna_rna ligands links
Oxidoreductase/DNA PDB id
Protein chain
200 a.a.
PDB id:
Name: Oxidoreductase/DNA
Title: Duplex interrogation by a direct DNA repair protein in the s damage
Structure: Alpha-ketoglutarate-dependent dioxygenase alkb ho chain: a. Fragment: unp residues 56-260. Synonym: alkylated DNA repair protein alkb homolog 2, oxy d engineered: yes. Mutation: yes. 5'-d( Ap Tp Gp Tp Ap Tp Ap Ap Cp Tp Gp Cp G)-3'. Chain: b. Engineered: yes.
Source: Homo sapiens. Human. Organism_taxid: 9606. Gene: alkbh2, abh2. Expressed in: escherichia coli. Expression_system_taxid: 562. Synthetic: yes. Synthetic: yes
3.06Å     R-factor:   0.254     R-free:   0.289
Authors: C.Yi,B.Chen,B.Qi,W.Zhang,G.Jia,L.Zhang,C.Li,A.Dinner,C.Yang,
Key ref: C.Yi et al. (2012). Duplex interrogation by a direct DNA repair protein in search of base damage. Nat Struct Mol Biol, 19, 671-676. PubMed id: 22659876
11-May-11     Release date:   06-Jun-12    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
Q6NS38  (ALKB2_HUMAN) -  Alpha-ketoglutarate-dependent dioxygenase alkB homolog 2
261 a.a.
200 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 6 residue positions (black crosses)

 Enzyme reactions 
   Enzyme class: E.C.  - Dna oxidative demethylase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: DNA-base-CH3 + 2-oxoglutarate + O2 = DNA-base + formaldehyde + succinate + CO2
+ 2-oxoglutarate
+ O(2)
= DNA-base
+ formaldehyde
+ succinate
+ CO(2)
      Cofactor: Fe cation
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     oxidation-reduction process   1 term 
  Biochemical function     oxidoreductase activity     2 terms  


Nat Struct Mol Biol 19:671-676 (2012)
PubMed id: 22659876  
Duplex interrogation by a direct DNA repair protein in search of base damage.
C.Yi, B.Chen, B.Qi, W.Zhang, G.Jia, L.Zhang, C.J.Li, A.R.Dinner, C.G.Yang, C.He.
ALKBH2 is a direct DNA repair dioxygenase guarding the mammalian genome against N(1)-methyladenine, N(3)-methylcytosine and 1,N(6)-ethenoadenine damage. A prerequisite for repair is to identify these lesions in the genome. Here we present crystal structures of human ALKBH2 bound to different duplex DNAs. Together with computational and biochemical analyses, our results suggest that DNA interrogation by ALKBH2 has two previously unknown features: (i) ALKBH2 probes base-pair stability and detects base pairs with reduced stability, and (ii) ALKBH2 does not have nor need a damage-checking site, which is critical for preventing spurious base cleavage for several glycosylases. The demethylation mechanism of ALKBH2 insures that only cognate lesions are oxidized and reversed to normal bases, and that a flipped, non-substrate base remains intact in the active site. Overall, the combination of duplex interrogation and oxidation chemistry allows ALKBH2 to detect and process diverse lesions efficiently and correctly.