Modomics - A Database of RNA Modifications

ID Card:

Full name: Nucleic acid dioxygenase ALKBH1
Synonym: ABH1
GI: 87298839
UniProt: Q13686
Structures: | 6IE2 | 6IE3 |
Alpha Fold Predicted Structure: AF-Q13686-F1
Enzyme type: dioxygenase


PDB Structures:


6IE2

Structure Description:

Title:
Classification:
Technique:

Abstract of the PDB Structure's related Publication:

We determined two crystal structures of binary and ternary complex of hALKBH1, hALKBH1-Mn2+ and hALKBH1-Mn2+-α-KG at resolutions of 1.97 and 2.8 Å, respectively. hALKBH1 (referred to as hALKBH1 hereafter) contained the enzymatically active center and retained full demethylation activity toward 6mA ssDNA, but not toward 6mA on dsDNA or m1A on ssDNA, the same as hALKBH1 WT. The overall structures of hALKBH1-Mn2+-α-KG and hALKBH1-Mn2+ are similar, with root mean square deviation of 1.4 Å. The hALKBH1 contains a unique N-terminal Flip0, the nucleotide recognition lid (NRL, containing Flip1 and Flip2), and the central catalytic core. A highly conservative double-stranded β-helix (DSBH) fold in the catalytic core is a characteristic of the α-KG-dependent dioxygenase superfamily. Four antiparallel β-strands β7, β9, β12, and β14 form the major sheet, whereas β8, β10, β11 and β13 form the minor sheet. hALKBH1 has a conservative HxD…H metal ion-binding sequence and an R…R α-KG-binding sequence. Apart from Mn2+, α-KG is further stabilized by three hydrogen bonds formed by the side chains of Asn220, Asn340 and Tyr222 as well as three salt bridges formed by Arg338 and Arg344. Isothermal titration calorimetry analysis of the hALKBH1-α-KG interaction revealed a dissociation constant (Kd) of 4.5 μM and a 1:1 stoichiometry. The total surface area of hALKBH1 decreased obviously from 14,445 to 13,893 Å2 during the addition of α-KG, indicating that hALKBH1 whole structure shrank with the association of α-KG, which caused many conformational changes including those of active sites, β5, β8, Flip1 and Flip2. Moreover, of the eight catalytic residues, Arg344 and Tyr222 showed significant conformational changes, interacting with α-KG through moving 2.5 Å and 2.3 Å toward the active center, respectively. Besides, Tyr184 and Glu236 of Flip2 exhibited the most obvious conformational changes and moved to Arg344, forming a stabilization triangle by hydrogen bonds. The stability triangle of Tyr184-Arg344-Glu236 near the α-KG-binding site is essential for 6mA ssDNA demethylation activity. Any single mutation of the triangle abolished the demethylation activity, but did not reduce the DNA-binding affinity. Interestingly, these large conformational changes induced by α-KG were not observed in other AlkB members, revealing a novel function of the essential triangle as a scaffold for the catalytic activity of hALKBH1.

Download RCSB-PDB Structures:

Pdb Files   6IE2.pdb   6IE3.pdb  
Pdbx/mmCIF Files   6IE2.cif   6IE3.cif  


Protein sequence:

MGKMAAAVGSVATLATEPGEDAFRKLFRFYRQSRPGTADLEGVIDFSAAHAARGKGPGAQKVIKSQLNVSSVSEQNAYRAGLQPVSKWQAYGLKGYPGFIFIPNPFLPGYQWHWVKQCLKLYSQKPNVCNLDKHMSKEETQDLWEQSKEFLRYKEATKRRPRSLLEKLRWVTVGYHYNWDSKKYSADHYTPFPSDLGFLSEQVAAACGFEDFRAEAGILNYYRLDSTLGIHVDRSELDHSKPLLSFSFGQSAIFLLGGLQRDEAPTAMFMHSGDIMIMSGFSRLLNHAVPRVLPNPEGEGLPHCLEAPLPAVLPRDSMVEPCSMEDWQVCASYLKTARVNMTVRQVLATDQNFPLEPIEDEKRDISTEGFCHLDDQNSEVKRARINPDS

Comments:

ALKBH1 is a 2-oxoglutarate and Fe2+ dependent dioxygenase. The biosynthetic pathways of hm5Cm34 and f5Cm34 in ct-tRNALeu (CAA) initially involve NSUN2 to methylate C34 to form m5C34 in the presence of AdoMet. ALKBH1 hydroxylates m5C34 to form hm5C34, then oxidizes hm5C34 to produce f5C34. These reactions require O2 and 2-OG as substrates. The biosynthetic pathway of f5C34 in mt-tRNAMet implies NSUN3 to methylate C34 to form m5C34 in the presence of AdoMet. ALKBH1 hydroxylates m5C34 to form hm5C34, and then oxidizes hm5C34 to yield f5C34. These reactions require O2 and 2-OG as substrates.




Reaction Substrate SubstrateType Position (Anti)Codon Modified (Anti)Codon Amino Acid Change Transcript Name Transcript Region Cellular Localization References
m5C:hm5C tRNA (t)   34 ?AA ∅AA tRNALeuCAA anticodon-loop cytoplasm 28472312   
hm5C:f5Cm tRNA (t)   34 ∅AA °AA tRNALeuCAA anticodon-loop cytoplasm 28472312   
hm5C:f5C tRNA (t)   34 ∅AU >AU mt-tRNAMetCAU anticodon-loop mitochondrion 28472312   

Alpha Fold Predicted Structure:






Clear Selection and Reset Camera

Protein sequence:

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

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-Q13686-F1.pdb  
Alpha Fold Pdbx/mmCIF Files   AF-Q13686-F1.cif  
DSSP Secondary Structures   Q13686.dssp  





Publications:

Title Authors Journal Details PubMed Id DOI
NSUN3 and ABH1 modify the wobble position of mt-tRNAMet to expand codon recognition in mitochondrial translation. Haag S, Sloan KE, Ranjan N, Warda AS, Kretschmer J, Blessing C, Hübner B, Seikowski J, Dennerlein S, Rehling P, Rodnina MV, Höbartner C, Bohnsack MT ENBO J. [details] 27497299 10.15252/embj.201694885