3RZM

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.06 Å
  • R-Value Free: 0.289 
  • R-Value Work: 0.253 
  • R-Value Observed: 0.254 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.2 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: https://doi.org/10.1038/nsmb.2320
  • Primary Citation of Related Structures:  
    3RZG, 3RZH, 3RZJ, 3RZK, 3RZL, 3RZM, 3S57, 3S5A

  • 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 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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Alpha-ketoglutarate-dependent dioxygenase alkB homolog 2206Homo sapiensMutation(s): 5 
Gene Names: ALKBH2ABH2
EC: 1.14.11 (PDB Primary Data), 1.14.11.33 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q6NS38 (Homo sapiens)
Explore Q6NS38 
Go to UniProtKB:  Q6NS38
PHAROS:  Q6NS38
GTEx:  ENSG00000189046 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6NS38
Sequence Annotations
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  • Reference Sequence

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Entity ID: 2
MoleculeChains LengthOrganismImage
5'-D(*AP*TP*GP*TP*AP*TP*AP*AP*CP*TP*GP*CP*G)-3'13N/A
Sequence Annotations
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  • Reference Sequence

Find similar nucleic acids by:  Sequence   |   3D Structure  

Entity ID: 3
MoleculeChains LengthOrganismImage
5'-D(*TP*CP*GP*CP*AP*GP*TP*TP*AP*TP*AP*CP*A)-3'13N/A
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
XL3
Query on XL3

Download Ideal Coordinates CCD File 
D [auth B]propane-1-thiol
C3 H8 S
SUVIGLJNEAMWEG-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.06 Å
  • R-Value Free: 0.289 
  • R-Value Work: 0.253 
  • R-Value Observed: 0.254 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 75.05α = 90
b = 75.05β = 90
c = 169.71γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
PHASESphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-06-06
    Type: Initial release
  • Version 1.1: 2013-07-03
    Changes: Database references
  • Version 1.2: 2023-11-01
    Changes: Data collection, Database references, Derived calculations, Refinement description