Crystal structure of human ALKBH5 in complex with N-oxalylglycine (NOG) and m6A-containing ssRNA

Experimental Data Snapshot

  • Resolution: 2.50 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.199 

wwPDB Validation   3D Report Full Report

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Mechanisms of substrate recognition and N6-methyladenosine demethylation revealed by crystal structures of ALKBH5-RNA complexes.

Kaur, S.Tam, N.Y.McDonough, M.A.Schofield, C.J.Aik, W.S.

(2022) Nucleic Acids Res 50: 4148-4160

  • DOI: https://doi.org/10.1093/nar/gkac195
  • Primary Citation of Related Structures:  
    7V4G, 7WKV, 7WL0

  • PubMed Abstract: 

    AlkB homologue 5 (ALKBH5) is a ferrous iron and 2-oxoglutarate dependent oxygenase that demethylates RNA N6-methyladenosine (m6A), a post-transcriptional RNA modification with an emerging set of regulatory roles. Along with the fat mass and obesity-associated protein (FTO), ALKBH5 is one of only two identified human m6A RNA oxidizing enzymes and is a potential target for cancer treatment. Unlike FTO, ALKBH5 efficiently catalyzes fragmentation of its proposed nascent hemiaminal intermediate to give formaldehyde and a demethylated nucleoside. A detailed analysis of the molecular mechanisms used by ALKBH5 for substrate recognition and m6A demethylation is lacking. We report three crystal structures of ALKBH5 in complex with an m6A-ssRNA 8-mer substrate and supporting biochemical analyses. Strikingly, the single-stranded RNA substrate binds to the active site of ALKBH5 in a 5'-3' orientation that is opposite to single-stranded or double-stranded DNA substrates observed for other AlkB subfamily members, including single-stranded DNA bound to FTO. The combined structural and biochemical results provide insight into the preference of ALKBH5 for substrates containing a (A/G)m6AC consensus sequence motif. The results support a mechanism involving formation of an m6A hemiaminal intermediate, followed by efficient ALKBH5 catalyzed demethylation, enabled by a proton shuttle network involving Lys132 and Tyr139.

  • Organizational Affiliation

    Department of Chemistry, Hong Kong Baptist University, Kowloon Tong, Hong Kong SAR, China.


Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
RNA demethylase ALKBH5
A, C, E, G, I
220Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for Q6P6C2 (Homo sapiens)
Explore Q6P6C2 
Go to UniProtKB:  Q6P6C2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6P6C2
Sequence Annotations
  • Reference Sequence

Find similar nucleic acids by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains LengthOrganismImage
RNA (5'-R(*UP*GP*GP*(6MZ)P*CP*UP*GP*C)-3')
B, D, F, H, J
8synthetic construct
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
OGA (Subject of Investigation/LOI)
Query on OGA

Download Ideal Coordinates CCD File 
L [auth A],
N [auth C],
Q [auth E],
S [auth G],
U [auth I]
C4 H5 N O5
MN (Subject of Investigation/LOI)
Query on MN

Download Ideal Coordinates CCD File 
K [auth A],
M [auth C],
P [auth E],
R [auth G],
T [auth I]
Query on FMT

Download Ideal Coordinates CCD File 
C H2 O2
Experimental Data & Validation

Experimental Data

  • Resolution: 2.50 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.199 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 59.77α = 90
b = 132.37β = 100.99
c = 77.96γ = 90
Software Package:
Software NamePurpose
xia2data scaling
PDB_EXTRACTdata extraction
xia2data reduction

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
The University Grants Committee, Research Grants Council (RGC)United Kingdom22301719
Wellcome TrustUnited Kingdom106244/Z/14/Z

Revision History  (Full details and data files)

  • Version 1.0: 2022-03-30
    Type: Initial release
  • Version 1.1: 2022-04-06
    Changes: Database references
  • Version 1.2: 2022-05-04
    Changes: Database references
  • Version 1.3: 2023-11-29
    Changes: Data collection, Refinement description