Modomics - A Database of RNA Modifications

ID Card:

Full name: tRNA-dihydrouridine(16/17) synthase [NAD(P)(+)]
GI: 1730621
Orf: YML080W
COG: COG0042
UniProt: P53759
Alpha Fold Predicted Structure: AF-P53759-F1
Enzyme type: dihydrouridine synthase
Position of modification - modification: t:17 - D
t:16 - D



Protein sequence:

MTEPALSSANNALMQKLTGRQLFDKIGRPTRIVAPMVDQSELAWRILSRRYGATLAYTPMLHAKLFATSKKYREDNWSSLDGSSVDRPLVVQFCANDPEYLLAAAKLVEDKCDAVDLNLGCPQGIAKKGHYGSFLMEEWDLIHNLINTLHKNLKVPVTAKIRIFDDCEKSLNYAKMVLDAGAQFLTVHGRVREQKGQKTGLANWETIKYLRDNLPKETVFFANGNILYPEDISRCMEHIGADAVMSAEGNLYNPGVFNVGQTKNKEKIFPRVDKIIREYFQIVKECQESKASKTAMKSHFFKILRPFLPHHTDIRSTLATMNAKATWEEWEEQVVKPVEKVVQEIFEQPDIAIKDEITIGEKQSWGGSYRTVPYWRCQPYFRPVNGITGDKRVMQGLIDESVNKKRKADVPLESADKKKDVKA

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. D is generated post-transcriptionally by Dus enzymes and it is found in different positions of tRNAs. In s.cerevisiae Dus1 catalyzes the hydrogenation of U17 and U16 in multiple tRNA substrates with flavin mononucleotide (FMN) as a cofactor (Nader et al. 2015 ) to catalyze hybride transfer from NAD(P)H to the uridine substrate (Bishop et al. 2002 ).It is not an essential enzyme.




Reaction Substrate SubstrateType Position (Anti)Codon Modified (Anti)Codon Amino Acid Change Transcript Name Transcript Region Cellular Localization References
U:D tRNA   16 IGC IGC tRNAAlaIGC D-loop cytosol
U:D tRNA   16 ACU ACU tRNAArgACU D-loop cytosol
U:D tRNA   16 ICG ICG tRNAArgICG D-loop cytosol
U:D tRNA   16 GUU GUU tRNAAsnGUU D-loop cytosol
U:D tRNA   16 GUC GUC tRNAAspUGUC D-loop cytosol
U:D tRNA   16 GCA GCA tRNACysGCA D-loop cytosol
U:D tRNA   16 GCC GCC tRNAGlyGCC D-loop cytosol
U:D tRNA   16 {CC {CC tRNAGly{CC D-loop cytosol
U:D tRNA   16 GUG GUG tRNAHisGUG D-loop cytosol
U:D tRNA   16 IAU IAU tRNAIleIAU cytosol
U:D tRNA   16 UAU UAU tRNAIleUAU D-loop cytosol
U:D tRNA   16 UAG UAG tRNALeuUAG D-loop cytosol
U:D tRNA   16 UAA UAA tRNALeuUAA D-loop cytosol
U:D tRNA   16 CUU CUU tRNALysCUU D-loop cytosol
U:D tRNA   16 SUU SUU tRNALysSUU D-loop cytosol
U:D tRNA   16 CAU CAU tRNAMetCAU D-loop cytosol
U:D tRNA   16 GAA GAA tRNAPheGAA D-loop cytosol
U:D tRNA   16 UGG UGG tRNAProUGG D-loop cytosol
U:D tRNA   16 CGA CGA tRNASerCGA D-loop cytosol
U:D tRNA   16 UGA UGA tRNASerUGA D-loop cytosol
U:D tRNA   16 IGA IGA tRNASerIGA D-loop cytoplasm
U:D tRNA   16 IGU IGU tRNAThrIGU D-loop cytosol
U:D tRNA   16 CCA CCA tRNATrpCCA D-loop cytoplasm
U:D tRNA   16 GUA GUA tRNATyrGUA D-loop cytoplasm
U:D tRNA   16 IAC IAC tRNAValIAC D-loop cytoplasm
U:D tRNA   17 GUU GUU tRNAAsnGUU D-loop cytosol
U:D tRNA   17 IAU IAU tRNAIleIAU D-loop cytosol
U:D tRNA   17 CUU CUU tRNALysCUU D-loop cytosol
U:D tRNA   17 GAA GAA tRNAPheGAA D-loop cytoplasm
U:D tRNA   17 IGU IGU tRNAThrIGU D-loop cytosol
U:D tRNA   16 UCU UCU tRNAArgUCU D-loop mitochondrion

Alpha Fold Predicted Structure:






Clear Selection and Reset Camera

Protein sequence:

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

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-P53759-F1.pdb  
Alpha Fold Pdbx/mmCIF Files   AF-P53759-F1.cif  
DSSP Secondary Structures   P53759.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 -

Links:

_Wikipedia_
_PubMed_