Modomics - A Database of RNA Modifications

ID Card:

Full name: alkB homolog 3, alpha-ketoglutarate dependent dioxygenase
Synonym: DEPC-1
GI: 15929448
UniProt: Q96Q83
Structures: | 2iuw |
Alpha Fold Predicted Structure: AF-Q96Q83-F1


PDB Structures:


2iuw

Structure Description:

Title:
Classification:
Technique:

Abstract of the PDB Structure's related Publication:

Methylating agents are ubiquitous in the environment, and central in cancer therapy. The 1-methyladenine and 3-methylcytosine lesions in DNA/RNA contribute to the cytotoxicity of such agents. These lesions are directly reversed by ABH3 (hABH3) in humans and AlkB in Escherichia coli. Here, we report the structure of the hABH3 catalytic core in complex with iron and 2-oxoglutarate (2OG) at 1.5 A resolution and analyse key site-directed mutants. The hABH3 structure reveals the beta-strand jelly-roll fold that coordinates a catalytically active iron centre by a conserved His1-X-Asp/Glu-X(n)-His2 motif. This experimentally establishes hABH3 as a structural member of the Fe(II)/2OG-dependent dioxygenase superfamily, which couples substrate oxidation to conversion of 2OG into succinate and CO2. A positively charged DNA/RNA binding groove indicates a distinct nucleic acid binding conformation different from that predicted in the AlkB structure with three nucleotides. These results uncover previously unassigned key catalytic residues, identify a flexible hairpin involved in nucleotide flipping and ss/ds-DNA discrimination, and reveal self-hydroxylation of an active site leucine that may protect against uncoupled generation of dangerous oxygen radicals.

Download RCSB-PDB Structures:

Pdb Files   2iuw.pdb  
Pdbx/mmCIF Files   2iuw.cif  


Protein sequence:

MEEKRRRARVQGAWAAPVKSQAIAQPATTAKSHLHQKPGQTWKNKEHHLSDREFVFKEPQQVVRRAPEPRVIDREGVYEISLSPTGVSRVCLYPGFVDVKEADWILEQLCQDVPWKQRTGIREDITYQQPRLTAWYGELPYTYSRITMEPNPHWHPVLRTLKNRIEENTGHTFNSLLCNLYRNEKDSVDWHSDDEPSLGRCPIIASLSFGATRTFEMRKKPPPEENGDYTYVERVKIPLDHGTLLIMEGATQADWQHRVPKEYHSREPRVNLTFRTVYPDPRGAPW

Comments:

Alpha-ketoglutarate Dependent Dioxygenase Homolog 3 is an enzyme belonging to the AlkB enzyme family that utilizes non-heme iron(II), catalyzing biological oxidation (Arne Aas et al. 2003 ). ALKBH3 demethylates both ssDNA and RNA (Ougland et al. 2004 ), being involved in alkylated DNA repair that contains m1A and m3C by oxidative demethylation (Duncan et al. 2002 )

ALKBH3 overexpression is elevated in diverse cancer types (Konishi et al. 2005 ;Tasaki et al. 2011 ;Shimada et al. 2012 ), if compared to normal tissues.

ALKBH3 demethylates m1A in 5'-untranslated regions of mRNA and in close proximity of start codons(Dominissini et al. 2016 ).ALKBH3 is mainly expressed in cytoplasm with a strong binding capability to tRNA, where tRNA demethylation is reported to be an oncogenic marker. Demethylated tRNAs are more sensitive to angiogenin cleavage (ANG) tending to generate tRNA derived smll RNAs that can ultimately strengthen the ribosome assembly and prevent apoptosis in cancer (Chen et al. 2019 ).




Reaction Substrate SubstrateType Position (Anti)Codon Modified (Anti)Codon Amino Acid Change Transcript Name Transcript Region Cellular Localization References
m1A:A tRNA (t)   58 tRNAGluCTC TΨC-loop cytoplasm 30541109   
m1A:A tRNA (t)   58 tRNASecTCA TΨC-loop cytoplasm 30541109   
m1A:A tRNA (t)   58 tRNAGlyCCC TΨC-loop cytoplasm 30541109   
m1A:A tRNA (t)   58 tRNAHisGTG TΨC-loop cytoplasm 30541109   
m1A:A tRNA (t)   58 tRNASerGCT TΨC-loop cytoplasm 30541109   
m1A:A tRNA (t)   58 tRNAGluCTC TΨC-loop cytoplasm 30541109   
m1A:A tRNA (t)   58 tRNAValCAC TΨC-loop cytoplasm 30541109   
m1A:A tRNA (t)   58 tRNAArgCCT TΨC-loop cytoplasm 30541109   
m1A:A tRNA (t)   58 tRNALeuCAA TΨC-loop cytoplasm 30541109   
m1A:A tRNA (t)   58 tRNAGlyCCC TΨC-loop cytoplasm 30541109   
m1A:A tRNA (t)   58 tRNAAlaCGC TΨC-loop cytoplasm 30541109   
m1A:A tRNA (t)   58 tRNA e-MetCAT TΨC-loop cytoplasm 30541109   
m3C:C tRNA (t)   32 tRNASerGCT anticodon-loop cytoplasm 30541109   
m3C:C tRNA (t)   32 tRNAArgCCT anticodon-loop cytoplasm 30541109   
m3C:C tRNA (t)   32 tRNALeuCAA anticodon-loop cytoplasm 30541109   
m3C:C tRNA (t)   32 tRNA e-MetCAT anticodon-loop cytoplasm 30541109   
m3C:C tRNA (t)   47 tRNASerGCT V-loop cytoplasm 30541109   
m3C:C tRNA (t)   47 tRNAArgCTT V-loop cytoplasm 30541109   
m3C:C tRNA (t)   47 tRNALeuCAA V-loop cytoplasm 30541109   
m3C:C tRNA (t)   47 tRNA e-MetCAT V-loop cytoplasm 30541109   

Alpha Fold Predicted Structure:






Clear Selection and Reset Camera

Protein sequence:

M E E K R R R A R V Q G A W A A P V K S Q A I A Q P A T T A K S H L H Q K P G Q T W K N K E H H L S D R E F V F K E P Q Q V V R R A P E P R V I D R E G V Y E I S L S P T G V S R V C L Y P G F V D V K E A D W I L E Q L C Q D V P W K Q R T G I R E D I T Y Q Q P R L T A W Y G E L P Y T Y S R I T M E P N P H W H P V L R T L K N R I E E N T G H T F N S L L C N L Y R N E K D S V D W H S D D E P S L G R C P I I A S L S F G A T R T F E M R K K P P P E E N G D Y T Y V E R V K I P L D H G T L L I M E G A T Q A D W Q H R V P K E Y H S R E P R V N L T F R T V Y P D P R G A P W

Secondary Structure Alphabet

  • G: 3-turn helix (310helix)
  • H: α-helix
  • I: 𝝅-helix (5 - turn helix)
  • T: Hydrogen Bonded Turn
  • B: β-sheet
  • S: Bend
  • C: Coil (residues not present in any of the above conformations)
  • N: Not assigned

Download PDB Structures & DSSP Secondary Structures:

Alpha Fold Pdb Files   AF-Q96Q83-F1.pdb  
Alpha Fold Pdbx/mmCIF Files   AF-Q96Q83-F1.cif  
DSSP Secondary Structures   Q96Q83.dssp  





Diseases connected to this enzyme:

Description Reaction Disease Name
The genes related to migration and cytoskeleton are the target of m1A modification. This epigenetic chaneg cause poor overall survival. A:m1A
Hodgkin lymphoma
CSF-1 expression is increased by the overexpression of ALKBH3. This results in cancer cell invasiveness without affecting cell proliferation and migration A:m1A
Ovarian and breast cancer
In tumor samples, dysregulation and genetic alteartions of putative m1A-related enzymes are observed. Also, m1A-related enzymes regulate the ErbB and mTOR pathways. A:m1A
Gastrointestinal cancer

Publications:

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