Modomics - A Database of RNA Modifications

ID Card:

Full name: tRNA-dihydrouridine(20a/20b) synthase [NAD(P)+]
GI: 2833204
Orf: YLR405W, L8084.2
COG: COG0042
UniProt: Q06063
Alpha Fold Predicted Structure: AF-Q06063-F1
Enzyme type: dihydrouridine synthase
Position of modification - modification: t:20a - D
t:20b - D



Protein sequence:

MHTMHIPSGDVLIPKPKLITEETDPLHIIKTRQKTHGRPVTIAGPMVRYSKLPFRQLCREYNVDIVYSPMILAREYVRNEHARISDLSTNNEDTPLIVQVGVNNVADLLKFVEMVAPYCDGIGINCGCPIKEQIREGIGCALIYNSDLLCSMVHAVKDKYGDKLRIETKIRIHEALDETVELCRKLCDAGVDWITIHGRTRRTRSSQPANLDAIKYIIENISDKNVPVIANGDCFKLSDLERITKYTGAHGVMAVRGLLSNPALFAGYTTCPWGCIEKFCYWALEFGGLPFQLAQHHLYCMLENMELKKSLLKKMMNLKNYISLIDWFNKTFEFKRYGEDGFGMGVEIPYKANSCVQRSASVVERQE

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. Dus4 specifically modifies position 20a, 20b, and 20 in the D-loop of many tRNA substrates.




Reaction Substrate SubstrateType Position (Anti)Codon Modified (Anti)Codon Amino Acid Change Transcript Name Transcript Region Cellular Localization References
U:D tRNA   20a GUU GUU tRNAAsnGUU D-loop cytosol
U:D tRNA   20a CUC CUC tRNAGluCUC D-loop cytosol
U:D tRNA   20a {CC {CC tRNAGly{CC D-loop cytosol
U:D tRNA   20a GUG GUG tRNAHisGUG D-loop cytosol
U:D tRNA   20a IAU IAU tRNAIleIAU D-loop cytosol
U:D tRNA   20a UAU UAU tRNAIleUAU D-loop cytosol
U:D tRNA   20a UAG UAG tRNALeuUAG D-loop cytosol
U:D tRNA   20a CGA CGA tRNASerCGA D-loop cytosol
U:D tRNA   20a UGA UGA tRNASerUGA D-loop cytosol
U:D tRNA   20a IGA IGA tRNASerIGA D-loop cytosol
U:D tRNA   20a GUA GUA tRNATyrGUA D-loop cytosol
U:D tRNA   20a UAC UAC tRNAValUAC D-loop cytosol
U:D tRNA   20a CAC CAC tRNAValCAC D-loop cytosol
U:D tRNA   20a IAC IAC tRNAValIAC D-loop cytosol
U:D tRNA   20b UAG UAG tRNALeuUAG D-loop cytosol
U:D tRNA   20b CAA CAA tRNALeuCAA D-loop cytosol
U:D tRNA   20b UAA UAA tRNALeuUAA D-loop cytosol
U:D tRNA   20b GUA GUA tRNATyrGUA D-loop cytosol

Alpha Fold Predicted Structure:






Clear Selection and Reset Camera

Protein sequence:

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

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-Q06063-F1.pdb  
Alpha Fold Pdbx/mmCIF Files   AF-Q06063-F1.cif  
DSSP Secondary Structures   Q06063.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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