6L94

The structure of the dioxygenase ABH1 from mouse


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.297 
  • R-Value Work: 0.278 
  • R-Value Observed: 0.279 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

ALKBH1 promotes lung cancer by regulating m6A RNA demethylation.

Li, H.Zhang, Y.Guo, Y.Liu, R.Yu, Q.Gong, L.Liu, Z.Xie, W.Wang, C.

(2021) Biochem Pharmacol 189: 114284-114284

  • DOI: https://doi.org/10.1016/j.bcp.2020.114284
  • Primary Citation of Related Structures:  
    6L94

  • PubMed Abstract: 

    Lung cancer has surpassed breast cancer as the leading cause of cancer death in females in developed countries and the leading cause of cancer death in males. Despite extensive research on lung cancer, the pathogenesis of lung cancer is not fully understood. ALKBH1 is a 2-oxoglutarate and Fe (II)-dependent dioxygenase responsible for the demethylation of 6-methyladenine (m6A) in RNA and is essential to multiple cellular processes in human. Numerous recent studies suggest that ALKBH1 plays a role in tumorigenesis and tumor progression, but the role of ALKBH1 in lung cancer is largely unknown. In this study, we demonstrated that the expression levels of ALKBH1 in lung cancer tissues and cells were up regulated. The invasion and migration abilities of lung cancer cells were significantly suppressed in vitro upon the silencing of ALKBH1 while they were significantly promoted upon its overexpression. We next characterized the enzyme biochemically by analyzing the contribution of essential residues Y184, H231, D233, H287, R338, and R344 to its m6A demethylation activity. Lastly, our 3.1-Å crystal structure of mouse ALKBH1 revealed that the N-terminal domain of the protein forms close contacted with the core catalytic domain and might be responsible for the recognition of nucleic acid substrates. In summary, our combined cellular, biochemical, and structural results provide insight into the potential ALKBH1-based drug design for cancer therapies.


  • Organizational Affiliation

    Guangdong Key Laboratory for Translational Cancer Research of Chinese Medicine, Joint Laboratory for Translational Cancer Research of Chinese Medicine of the Ministry of Education of the People's Republic of China, International Institute for Translational Chinese Medicine, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong 510006, China; Institute of Pharmacy, Pharmaceutical College of Henan University, Jinming District, Kaifeng, Henan Province 475004, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Nucleic acid dioxygenase ALKBH1402Mus musculusMutation(s): 0 
Gene Names: Alkbh1AbhAlkbh
EC: 1.14.11 (PDB Primary Data), 1.14.11.51 (PDB Primary Data), 4.2.99.18 (PDB Primary Data), 1.14.11.33 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for P0CB42 (Mus musculus)
Explore P0CB42 
Go to UniProtKB:  P0CB42
IMPC:  MGI:2384034
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0CB42
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FE2 (Subject of Investigation/LOI)
Query on FE2

Download Ideal Coordinates CCD File 
B [auth A]FE (II) ION
Fe
CWYNVVGOOAEACU-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.297 
  • R-Value Work: 0.278 
  • R-Value Observed: 0.279 
  • Space Group: I 4
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 103.202α = 90
b = 103.202β = 90
c = 86.108γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PHENIXrefinement
CrysalisProdata reduction
CrysalisProdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of ChinaChina31700625

Revision History  (Full details and data files)

  • Version 1.0: 2020-11-11
    Type: Initial release
  • Version 1.1: 2021-05-26
    Changes: Database references
  • Version 1.2: 2021-06-16
    Changes: Database references
  • Version 1.3: 2023-11-22
    Changes: Data collection, Database references, Refinement description