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.





Alpha Fold Predicted Structure:




Downloading... [114426/616242]


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
50100150200250300350400450500550600SequenceGHTBSN

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:

Links:

_Wikipedia_
_PubMed_