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 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 26440.06 
• Atom Count: 1640 
• Residue Count: 230 
• Unique protein chains: 1

4O7X

Crystal structure of human ALKBH5 in complex with Mn2+

• DOI: 10.2210/pdb4O7X/pdb

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


• Deposited: 2013-12-26 Released: 2014-03-19 
• Deposition Author(s): Feng, C., Chen, Z., Liu, Y.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.78 Å
• R-Value Free: 0.238 
• R-Value Work: 0.214 

Literature

Crystal structures of the human RNA demethylase Alkbh5 reveal basis for substrate recognition

Feng, C., Liu, Y., Wang, G., Deng, Z., Zhang, Q., Wu, W., Tong, Y., Cheng, C., Chen, Z.

(2014) J.Biol.Chem. 289: 11571-11583

• PubMed: 24616105 
• DOI: 10.1074/jbc.M113.546168
• Primary Citation of Related Structures:  
  4NRQ, 4NRP, 4NRO, 4NRM


• PubMed Abstract: 
  

N(6)-Methylation of adenosine is the most ubiquitous and abundant modification of nucleoside in eukaryotic mRNA and long non-coding RNA. This modification plays an essential role in the regulation of mRNA translation and RNA metabolism. Recently, human AlkB homolog 5 (Alkbh5) and fat mass- and obesity-associated protein (FTO) were shown to erase this methyl modification on mRNA. Here, we report five high resolution crystal structures of the catalytic core of Alkbh5 in complex with different ligands. Compared with other AlkB proteins, Alkbh5 displays several unique structural features on top of the conserved double-stranded β-helix fold typical of this protein family. Among the unique features, a distinct "lid" region of Alkbh5 plays a vital role in substrate recognition and catalysis. An unexpected disulfide bond between Cys-230 and Cys-267 is crucial for the selective binding of Alkbh5 to single-stranded RNA/DNA by bringing a "flipping" motif toward the central β-helix fold. We generated a substrate binding model of Alkbh5 based on a demethylation activity assay of several structure-guided site-directed mutants. Crystallographic and biochemical studies using various analogs of α-ketoglutarate revealed that the active site cavity of Alkbh5 is much smaller than that of FTO and preferentially binds small molecule inhibitors. Taken together, our findings provide a structural basis for understanding the substrate recognition specificity of Alkbh5 and offer a foundation for selective drug design against AlkB members.

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Organizational Affiliation: 

From the State Key Laboratory of Agrobiotechnology, China Agricultural University, Beijing 100193, China.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
RNA demethylase ALKBH5	A	230	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 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
MN	A	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.78 Å
• R-Value Free: 0.238 
• R-Value Work: 0.214 
• Space Group: P 4₃ 2₁ 2

Unit Cell:

Length (Å)	Angle (°)
a = 57.093	α = 90.00
b = 57.093	β = 90.00
c = 145.729	γ = 90.00

Software Package:

Software Name	Purpose
BALBES	phasing
HKL-2000	data scaling
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data collection

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2013-12-26 
• Released Date: 2014-03-19 
• Deposition Author(s): Feng, C., Chen, Z., Liu, Y.

Revision History 

• Version 1.0: 2014-03-19
  Type: Initial release
• Version 1.1: 2015-10-21
  Type: Database references