6KSF

Crystal Structure of ALKBH1 bound to 21-mer DNA bulge


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.228 
  • R-Value Observed: 0.230 

wwPDB Validation 3D Report Full Report



Literature

Mammalian ALKBH1 serves as an N6-mA demethylase of unpairing DNA.

Zhang, M.Yang, S.Nelakanti, R.Zhao, W.Liu, G.Li, Z.Liu, X.Wu, T.Xiao, A.Li, H.

(2020) Cell Res 30: 197-210

  • DOI: 10.1038/s41422-019-0237-5
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • N 6 -methyladenine (N 6 -mA) of DNA is an emerging epigenetic mark in mammalian genome. Levels of N 6 -mA undergo drastic fluctuation during early embryogenesis, indicative of active regulation. Here we show that the ...

    N 6 -methyladenine (N 6 -mA) of DNA is an emerging epigenetic mark in mammalian genome. Levels of N 6 -mA undergo drastic fluctuation during early embryogenesis, indicative of active regulation. Here we show that the 2-oxoglutarate-dependent oxygenase ALKBH1 functions as a nuclear eraser of N 6 -mA in unpairing regions (e.g., SIDD, Stress-Induced DNA Double Helix Destabilization regions) of mammalian genomes. Enzymatic profiling studies revealed that ALKBH1 prefers bubbled or bulged DNAs as substrate, instead of single-stranded (ss-) or double-stranded (ds-) DNAs. Structural studies of ALKBH1 revealed an unexpected "stretch-out" conformation of its "Flip1" motif, a conserved element that usually bends over catalytic center to facilitate substrate base flipping in other DNA demethylases. Thus, lack of a bending "Flip1" explains the observed preference of ALKBH1 for unpairing substrates, in which the flipped N 6 -mA is primed for catalysis. Co-crystal structural studies of ALKBH1 bound to a 21-mer bulged DNA explained the need of both flanking duplexes and a flipped base for recognition and catalysis. Key elements (e.g., an ALKBH1-specific α1 helix) as well as residues contributing to structural integrity and catalytic activity were validated by structure-based mutagenesis studies. Furthermore, ssDNA-seq and DIP-seq analyses revealed significant co-occurrence of base unpairing regions with N 6 -mA in mouse genome. Collectively, our biochemical, structural and genomic studies suggest that ALKBH1 is an important DNA demethylase that regulates genome N 6 -mA turnover of unpairing regions associated with dynamic chromosome regulation.


    Organizational Affiliation

    MOE Key Laboratory of Protein Sciences, Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, Tsinghua-Peking Joint Center for Life Sciences, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, 100084, Beijing, China. lht@tsinghua.edu.cn.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Alpha-ketoglutarate-dependent dioxygenase alkB homolog 1
A
336Homo sapiensMutation(s): 0 
Gene Names: ALKBH1
Protein Feature View is not available: No corresponding UniProt sequence found.

Find similar nucleic acids by: Sequence  |  Structure

Entity ID: 2
MoleculeChainsLengthOrganism
DNA (5'-D(*DGP*DCP*DTP*DGP*DAP*DGP*DTP*DGP*DCP*DCP*DCP*DGP*DCP*DGP*DTP*DGP*DCP*DTP*DGP*DGP*DAP*DTP*DCP*DC)-3')B24Homo sapiens

Find similar nucleic acids by: Sequence  |  Structure

Entity ID: 3
MoleculeChainsLengthOrganism
DNA (5'-D(*DGP*DGP*DAP*DTP*DCP*DCP*DAP*DGP*DCP*DAP*DCP*DGP*DCP*DCP*DAP*DCP*DTP*DCP*DAP*DGP*DC)-3')C21Homo sapiens
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SIN
Query on SIN

Download CCD File 
A
SUCCINIC ACID
C4 H6 O4
KDYFGRWQOYBRFD-UHFFFAOYSA-N
 Ligand Interaction
XL3
Query on XL3

Download CCD File 
B
propane-1-thiol
C3 H8 S
SUVIGLJNEAMWEG-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.228 
  • R-Value Observed: 0.230 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 67.482α = 90
b = 67.482β = 90
c = 263.641γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
MOLREPphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2019-08-23 
  • Released Date: 2020-04-08 
  • Deposition Author(s): Li, H., Zhang, M.

Funding OrganizationLocationGrant Number
National Natural Science Foundation of ChinaChina31725014

Revision History 

  • Version 1.0: 2020-04-08
    Type: Initial release