Modomics - A Database of RNA Modifications

ID Card:

Full name: Alkylated DNA repair protein alkB homolog 8
Synonym: ABH8
GI: 189027650
COG: COG3145
UniProt: Q96BT7
Structures: | 3THT | 3THP | 2CQ2 |
Alpha Fold Predicted Structure: AF-Q96BT7-F1
Complex: ALKBH8/TRM112
Enzyme type: methyltransferase, hydroxylase
Position of modification - modification: t:34 - mchm5U
t:34 - mcm5s2U
t:34 - mcm5U
t:34 - mcm5Um


PDB Structures:


3THT

Structure Description:

Title: Solution structure of RNA binding domain in Hypothetical protein LOC91801
Classification: RNA BINDING PROTEIN
Technique: NMR Solution
Resolution:
Conformers calculated: 100
Conformers submitted: 20
Selection criteria: target function, structures with the lowest energy, structures with the least restraint violations

Abstract of the PDB Structure's related Publication:

Yet to be published

Download RCSB-PDB Structures:

Pdb Files   2CQ2.pdb   3THP.pdb   3THT.pdb  
Pdbx/mmCIF Files   2CQ2.cif   3THP.cif   3THT.cif  


Protein sequence:

MDSNHQSNYKLSKTEKKFLRKQIKAKHTLLRHEGIETVSYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPNKPYSFARYRTTEESKRAYVTLNGKEVVDDLGQKITLYLNFVEKVQWKELRPQALPPGLMVVEEIISSEEEKMLLESVDWTEDTDNQNSQKSLKHRRVKHFGYEFHYENNNVDKDKPLSGGLPDICESFLEKWLRKGYIKHKPDQMTINQYEPGQGIPAHIDTHSAFEDEIVSLSLGSEIVMDFKHPDGIAVPVMLPRRSLLVMTGESRYLWTHGITCRKFDTVQASESLKSGIITSDVGDLTLSKRGLRTSFTFRKVRQTPCNCSYPLVCDSQRKETPPSFPESDKEASRLEQEYVHQVYEEIAGHFSSTRHTPWPHIVEFLKALPSGSIVADIGCGNGKYLGINKELYMIGCDRSQNLVDICRERQFQAFVCDALAVPVRSGSCDACISIAVIHHFATAERRVAALQEIVRLLRPGGKALIYVWAMEQEYNKQKSKYLRGNRNSQGKKEEMNSDTSVQRSLVEQMRDMGSRDSASSVPRINDSQEGGCNSRQVSNSKLPVHVNRTSFYSQDVLVPWHLKGNPDKGKPVEPFGPIGSQDPSPVFHRYYHVFREGELEGACRTVSDVRILQSYYDQGNWCVILQKA

Comments:

Alpha-Ketoglutarate-Dependent Dioxygenase AlkB homolog 8 is a member of the superfamily of alpha-ketoglutarate and Fe(II) dependent dioxygenase (Marcinkowski et al. 2020 ).Structurally, and differently from the other family members, ALKBH8 contains DNA/RNA recognition motif (RRM) and SAM-dependent methyltransferase domain, in addition to the conserved AlkB conserved domains (Fu et al. 2010 ).ALKBH8 catalyzes 5-methoxycarbonyl methyluridine (mcm5U) in the final step of its biogenesis . Noteworthy, its methyltransferases domain catalyzes the methylation of 5-carboxymethyl uridine to 5-methyl-carboxymethyl uridine on the the wobble position of the anticodon loop in different tRNAs(Songe-Møller et al. 2010 ;Fu et al. 2010 ;Monies et et al. 2019 ). It moreover shows a preference for tRNA(Arg) and tRNA(Glu), modifying different isoform (Fu et al. 2010 ). Furthermore, it catalyzes 5-methylcarboxyl-methyl-uridine to 5-S-methoxycarbonylhydroxymethyl uridine that depends on the iron and alpha-ketoglutarate dependent hydroxylation(van De Born et al. 2011 ). Exhibits two enzymatic activities: MTase domain provides the mcm5U precursor (ortholog of the yeast Trm9) while AlkB domain is a mchm5U synthesizing oxygenase (hydroxylase activity). AdoMet is the methyl group donor. Interaction with TRM112 is required for MTase activity only. Prior ALKBH8-mediated methylation is a prerequisite for sbsequent thiolation and 2'-O-ribose methylation that form 5-methoxycarbonylmethyl-2-thiouridine (mcm5s2U) and 5-methoxycarbonylmethyl-2'-O-methyluridine (mcm5Um), respectively. ABH8 depleted cells exhibit highly elevated levels of cm5U and lowered levels of mcm5U and shows an increase cellular sensitivity to DNA-damaging agents, attesting for possible regulatory role of ALKBH8 in the DNA damage response pathway. Complementary information in the case of fungi can be obtained under Trm9, Trm112 and Elongation complex Elf 1-6.





Alpha Fold Predicted Structure:




Downloading... [249594/606822]


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Protein sequence:

M D S N H Q S N Y K L S K T E K K F L R K Q I K A K H T L L R H E G I E T V S Y A T Q S L V V A N G G L G N G V S R N Q L L P V L E K C G L V D A L L M P P N K P Y S F A R Y R T T E E S K R A Y V T L N G K E V V D D L G Q K I T L Y L N F V E K V Q W K E L R P Q A L P P G L M V V E E I I S S E E E K M L L E S V D W T E D T D N Q N S Q K S L K H R R V K H F G Y E F H Y E N N N V D K D K P L S G G L P D I C E S F L E K W L R K G Y I K H K P D Q M T I N Q Y E P G Q G I P A H I D T H S A F E D E I V S L S L G S E I V M D F K H P D G I A V P V M L P R R S L L V M T G E S R Y L W T H G I T C R K F D T V Q A S E S L K S G I I T S D V G D L T L S K R G L R T S F T F R K V R Q T P C N C S Y P L V C D S Q R K E T P P S F P E S D K E A S R L E Q E Y V H Q V Y E E I A G H F S S T R H T P W P H I V E F L K A L P S G S I V A D I G C G N G K Y L G I N K E L Y M I G C D R S Q N L V D I C R E R Q F Q A F V C D A L A V P V R S G S C D A C I S I A V I H H F A T A E R R V A A L Q E I V R L L R P G G K A L I Y V W A M E Q E Y N K Q K S K Y L R G N R N S Q G K K E E M N S D T S V Q R S L V E Q M R D M G S R D S A S S V P R I N D S Q E G G C N S R Q V S N S K L P V H V N R T S F Y S Q D V L V P W H L K G N P D K G K P V E P F G P I G S Q D P S P V F H R Y Y H V F R E G E L E G A C R T V S D V R I L Q S Y Y D Q G N W C V I L Q K A
50100150200250300350400450500550600650SequenceGHITBSN

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-Q96BT7-F1.pdb  
Alpha Fold Pdbx/mmCIF Files   AF-Q96BT7-F1.cif  
DSSP Secondary Structures   Q96BT7.dssp  





Publications:

Links:

_PubMed_
_Wikipedia - AlkB_