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PDBsum entry 3rzj

Go to PDB code: 
protein dna_rna ligands metals links
Oxidoreductase/DNA PDB id
3rzj
Jmol
Contents
Protein chain
203 a.a.
DNA/RNA
Ligands
AKG
XL3
Metals
_MN
Waters ×44
PDB id:
3rzj
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 56-261. Synonym: alkylated DNA repair protein alkb homolog 2, oxy d engineered: yes. Mutation: yes. 5'-d( Cp Tp Gp Tp Cp Tp (Me6)p Ap Cp Tp Gp Cp G)- 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
Resolution:
2.50Å     R-factor:   0.229     R-free:   0.259
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
Date:
11-May-11     Release date:   06-Jun-12    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
Q6NS38  (ALKB2_HUMAN) -  Alpha-ketoglutarate-dependent dioxygenase alkB homolog 2
Seq:
Struc:
261 a.a.
203 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 7 residue positions (black crosses)

 Enzyme reactions 
   Enzyme class: E.C.1.14.11.33  - Dna oxidative demethylase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: DNA-base-CH3 + 2-oxoglutarate + O2 = DNA-base + formaldehyde + succinate + CO2
DNA-base-CH(3)
+
2-oxoglutarate
Bound ligand (Het Group name = AKG)
corresponds exactly
+ O(2)
= DNA-base
+ formaldehyde
+ succinate
+ CO(2)
      Cofactor: Iron
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  

 

 
    reference    
 
 
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.
 
  ABSTRACT  
 
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.