Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A 

Biological assembly 1 generated by PISA (software)

Biological Assembly 2  

 3D View: Structure | Electron Density | Ligand Interaction

Standalone Viewers  
Protein Workshop | Ligand Explorer

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A 

Biological assembly 2 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 51246.46 
• Atom Count: 3431 
• Residue Count: 444 
• Unique protein chains: 1

4O61

Structure of human ALKBH5 crystallized in the presence of citrate

• DOI: 10.2210/pdb4O61/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21


• Deposited: 2013-12-20 Released: 2014-02-26 
• Deposition Author(s): Tempel, W., Chao, X., Liu, K., Dong, A., Cerovina, T., He, H., Bountra, C., Arrowsmith, C.H., Edwards, A.M., Min, J., Structural Genomics Consortium (SGC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.9 Å
• R-Value Free: 0.230 
• R-Value Work: 0.174 

Literature

Structures of human ALKBH5 demethylase reveal a unique binding mode for specific single-stranded N6-methyladenosine RNA demethylation.

Xu, C., Liu, K., Tempel, W., Demetriades, M., Aik, W., Schofield, C.J., Min, J.

(2014) J.Biol.Chem. 289: 17299-17311

• PubMed: 24778178 
• DOI: 10.1074/jbc.M114.550350
• Primary Citation of Related Structures:  
  4OCT


• PubMed Abstract: 
  

N(6)-Methyladenosine (m(6)A) is the most prevalent internal RNA modification in eukaryotes. ALKBH5 belongs to the AlkB family of dioxygenases and has been shown to specifically demethylate m(6)A in single-stranded RNA. Here we report crystal structures of ALKBH5 in the presence of either its cofactors or the ALKBH5 inhibitor citrate. Catalytic assays demonstrate that the ALKBH5 catalytic domain can demethylate both single-stranded RNA and single-stranded DNA. We identify the TCA cycle intermediate citrate as a modest inhibitor of ALKHB5 (IC50, ∼488 μm). The structural analysis reveals that a loop region of ALKBH5 is immobilized by a disulfide bond that apparently excludes the binding of dsDNA to ALKBH5. We identify the m(6)A binding pocket of ALKBH5 and the key residues involved in m(6)A recognition using mutagenesis and ITC binding experiments.

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Organizational Affiliation: 

the Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7, Canada.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
RNA demethylase ALKBH5	A, B	222	Homo sapiens	Mutation(s): 0  Gene Names: ALKBH5 (ABH5, OFOXD1) EC: 1.14.11.53
Find proteins for Q6P6C2 (Homo sapiens) Go to Gene View: ALKBH5 Go to UniProtKB:  Q6P6C2

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
CIT	A, B	CITRIC ACID C6 H8 O7 KRKNYBCHXYNGOX-UHFFFAOYSA-N
GOL	A, B	GLYCEROL GLYCERIN; PROPANE-1,2,3-TRIOL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
UNX	A, B	UNKNOWN ATOM OR ION X *

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
CIT	IC50: 488000 nM BINDINGMOAD

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.9 Å
• R-Value Free: 0.230 
• R-Value Work: 0.174 
• Space Group: P 1 2₁ 1

Unit Cell:

Length (Å)	Angle (°)
a = 50.471	α = 90.00
b = 57.172	β = 102.23
c = 78.644	γ = 90.00

Software Package:

Software Name	Purpose
BALBES	phasing
PDB_EXTRACT	data extraction
REFMAC	refinement
Aimless	data scaling
XDS	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2013-12-20 
• Released Date: 2014-02-26 
• Deposition Author(s): Tempel, W., Chao, X., Liu, K., Dong, A., Cerovina, T., He, H., Bountra, C., Arrowsmith, C.H., Edwards, A.M., Min, J., Structural Genomics Consortium (SGC)

Revision History 

• Version 1.0: 2014-02-26
  Type: Initial release
• Version 1.1: 2014-05-07
  Type: Database references
• Version 1.2: 2014-06-04
  Type: Database references
• Version 1.3: 2015-07-01
  Type: Database references