Modomics - A Database of RNA Modifications

ID Card:

Full name: tRNA-dihydrouridine(47) synthase [NAD(P)(+)]
GI: 547573
Orf: YLR401C
UniProt: Q06053
Alpha Fold Predicted Structure: AF-Q06053-F1
Enzyme type: dihydrouridine synthase
Position of modification - modification: t:47 - D



Protein sequence:

MEQNAEKRSIVGDDNSTVKRQDTSPSKGIAHIKPEYIVPLKQNENQKVAIYDEEMSSDRMTNEFAGGTNKKNKNGRGKKRGQNKNRDNRQVKEQNVLCPRLIHGDISKCSFGDNCRFVHDINLYLSTKKPEVESNIFPSCPVFNSLGFCPMGFKCRFLSSHLNKEDNILISKKEIDPDAQTIWSVKGEVNHISPERKLDLIKRRFPFTKSNEILEIIDSFQQECRDSMKPEEEVESTPQLKKQDPDVEQPVAPQVEQRNKELSEHRMKQREVYLKYKDTRYFAQEKKPLDLYHKKIVSPLTTVGNLPYRRLMRKLGADVTYSEMALAVPLIQGTNSEWALPKAHTSEFPGFGVQVACSKAWQAAKAAEALANSVSEISEINLNSGCPIDLLYRQGSGSALLDNPARMIRCLNAMNYVSKDIPITVKIRTGTKEGHPIAEGLVKRLVNETDVAAITLHGRSRQQRYTKSADWDYVSQVADTLRSAEADFIETEQGKEGRDSKNRIQFVGNGDVNNFEDWYRYLNGNENIDSVMVARGALIKPWIFEEVESQQYLDKTSTERLDILRDYAQFSMEHWGTDEYGISQCRRFFCEFMSFFHRYVPWVFVKDTL

Comments:

Dihydrouridine synthases are a conserved enzyme family that is encoded by the orthologous COG0042 gene family (Kasprzak et al. 2012 ). Dihydrouridine (D) is a post-trascriptionally modified pyrimidine nucleoside. D results from the reduction of C5,6-double bondof a uridine residue in RNA transcripts (Kasprzak et al. 2012 ) that brings to the addition of two hydrogen atoms C6 and C5. With the absence of the double bond, dihydrouridine is believed to decrease region stability, promoting dynamic motion and accommodating loop structure.Indeed, Dihydrouridine (D) appears as important in the maintenance of tRNA stability (Alexandrov et al. 2006 ). It appears acting as a quality control marker, with its absence provoking rapid tRNA decays. D is generated post-transcriptionally by Dus enzymes and it is found in different positions of tRNAs. Dus3 modifies U47 in different tRNA substrates. Dus3 catalyzes the D formation of tRNA through reduction of uracil base with flavin mononucleotide (FMN) as a cofactor. Not essential enzyme. Dus3 modifies all tRNAs with U at position 47, with the exception of tRNAPhe1, Phe2, and Lys1.




Reaction Substrate SubstrateType Position (Anti)Codon Modified (Anti)Codon Amino Acid Change Transcript Name Transcript Region Cellular Localization References
U:D tRNA   47 IGC IGC tRNAAlaIGC V-loop cytosol
U:D tRNA   47 ICG ICG tRNAArgICG V-loop cytosol
U:D tRNA   47 ICU ICU tRNAArgICU V-loop cytosol
U:D tRNA   47 GUU GUU tRNAAsnGUU V-loop cytosol
U:D tRNA   47 GCA GCA tRNACysGCA V-loop cytosol
U:D tRNA   47 IAU IAU tRNAIleIAU V-loop cytosol
U:D tRNA   47 UAU UAU tRNAIleUAU V-loop cytosol
U:D tRNA   47 CUU CUU tRNALysCUU V-loop cytosol
U:D tRNA   47 CAU CAU tRNAMetCAU V-loop cytosol
U:D tRNA   47 IGU IGU tRNAThrIGU V-loop cytosol
U:D tRNA   47 CCA CCA tRNATrpCCA V-loop cytosol
U:D tRNA   47 GUA GUA tRNATyrGUA V-loop cytosol
U:D tRNA   47 UAC UAC tRNAThrAGT V-loop cytosol
U:D tRNA   47 CAC CAC tRNAValCAC V-loop cytosol
U:D tRNA   47 IAC IAC tRNAValIAC V-loop cytosol

Alpha Fold Predicted Structure:






Clear Selection and Reset Camera

Protein sequence:

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

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-Q06053-F1.pdb  
Alpha Fold Pdbx/mmCIF Files   AF-Q06053-F1.cif  
DSSP Secondary Structures   Q06053.dssp  





Publications:

Title Authors Journal Details PubMed Id DOI
The specificities of four yeast dihydrouridine synthases for cytoplasmic tRNAs. Xing F, Hiley SL, Hughes TR, Phizicky EM J Biol Chem [details] 14970222 -
A conserved family of Saccharomyces cerevisiae synthases effects dihydrouridine modification of tRNA. Xing F, Martzen MR, Phizicky EM RNA [details] 12003496 -
Molecular evolution of dihydrouridine synthases. Kasprzak JM, Czerwoniec A, Bujnicki JM... BMC Bioinformatics [details] 22741570 -

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