3RZJ

Duplex Interrogation by a Direct DNA Repair Protein in the Search of Damage


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.227 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Duplex interrogation by a direct DNA repair protein in search of base damage

Yi, C.Chen, B.Qi, B.Zhang, W.Jia, G.Zhang, L.Li, C.J.Dinner, A.R.Yang, C.G.He, C.

(2012) Nat.Struct.Mol.Biol. 19: 671-676

  • DOI: 10.1038/nsmb.2320
  • Primary Citation of Related Structures:  

  • PubMed 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 str ...

    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.


    Organizational Affiliation

    State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, China.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Alpha-ketoglutarate-dependent dioxygenase alkB homolog 2
A
209Homo sapiensMutation(s): 4 
Gene Names: ALKBH2 (ABH2)
EC: 1.14.11.33
Find proteins for Q6NS38 (Homo sapiens)
Go to Gene View: ALKBH2
Go to UniProtKB:  Q6NS38
Entity ID: 2
MoleculeChainsLengthOrganism
5'-D(*CP*TP*GP*TP*CP*TP*(ME6)P*AP*CP*TP*GP*CP*G)-3'B13N/A
Entity ID: 3
MoleculeChainsLengthOrganism
5'-D(*TP*CP*GP*CP*AP*GP*TP*GP*AP*GP*AP*CP*A)-3'C13N/A
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MN
Query on MN

Download SDF File 
Download CCD File 
A
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
XL3
Query on XL3

Download SDF File 
Download CCD File 
A
propane-1-thiol
C3 H8 S
SUVIGLJNEAMWEG-UHFFFAOYSA-N
 Ligand Interaction
AKG
Query on AKG

Download SDF File 
Download CCD File 
A
2-OXOGLUTARIC ACID
C5 H6 O5
KPGXRSRHYNQIFN-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
ME6
Query on ME6
B
DNA linkingC10 H17 N3 O7 PDC
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.227 
  • Space Group: P 65 2 2
Unit Cell:
Length (Å)Angle (°)
a = 77.779α = 90.00
b = 77.779β = 90.00
c = 229.016γ = 120.00
Software Package:
Software NamePurpose
HKL-2000data collection
PHASESphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-06-06
    Type: Initial release
  • Version 1.1: 2013-07-03
    Type: Database references