Modomics - A Database of RNA Modifications

ID Card:

Full name: tRNA-dihydrouridine(20) synthase [NAD(P)+]
Synonym: Smm1p
GI: 1730664
Orf: YNR015W
COG: COG0042
UniProt: P53720
Alpha Fold Predicted Structure: AF-P53720-F1
Enzyme type: dihydrouridine synthase
Position of modification - modification: t:20 - D



Protein sequence:

MVTYAGKLVLAPMVRAGELPTRLMALAHGADLVWSPEIIDKKLIQCVRKENTALQTVDYVVPSKVQTRPETLVFRTYPKLESSKLIFQIGSASPALATQAALKVINDVSGIDINAGCPKHFSIHSGMGSALLRTPDTLCLILKELVKNVGNPHSKPISVKIRLLDTKQDTLQLVKRLCATGITNLTVHCRKTEMRNREQPITDYIAEIYEICQANNVSLIVNGAIRDRSHFHDLQANHWKNTNIGGMIAECAERDPTVFDHTSKPSEDGPSWVVACREFIQWATKFDNHIGNTKYMLSRIVPGKSVFFQYFARCKSPEEVSFVLKQLNDDGSAQTDPSEYLENCRAQEKALKNANAIAKQKRKQTDHIGSDTKKQKVVPLPTDI

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. 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. Dus genes have been identified in E.coli and S.cerevisiae. Homologous to COG0042 gene family, they use flavin mononucleotide (FMN) (Nader et al. 2015 ) to catalyze hybrid transfer from NAD(P)H to uridine substrate (Bishop et al. 2002 ). In s.cerevisiae every sequenced tRNA has at least one such modification. All but one have two or more Ds. Dus1 and Dus2 are active as a single subunit protein (Xing et al. 2002 ). Dus2 catalyzes the reduction of uridine in the 20th position of many tRNA D-loops. Similarly to Dus1, flavin mononucleotide is used as a cofactor.




Reaction Substrate SubstrateType Position (Anti)Codon Modified (Anti)Codon Amino Acid Change Transcript Name Transcript Region Cellular Localization References
U:D tRNA   20 IGC IGC tRNAAlaIGC D-loop cytosol
U:D tRNA   20 ICG ICG tRNAArgICG D-loop cytosol
U:D tRNA   20 GUU GUU tRNAAsnGUU D-loop cytosol
U:D tRNA   20 GUC GUC tRNAAspGUC D-loop cytosol
U:D tRNA   20 GCA GCA tRNACysGCA D-loop cytosol
U:D tRNA   20 GCC GCC tRNAGlyGCC D-loop cytosol
U:D tRNA   20 {CC {CC tRNAGly{CC D-loop cytosol
U:D tRNA   20 GUG GUG tRNAHisGUG D-loop cytosol
U:D tRNA   20 IAU IAU tRNAIleIAU D-loop cytosol
U:D tRNA   20 UAU UAU tRNAIleUAU D-loop cytosol
U:D tRNA   20 UAG UAG tRNALeuUAG D-loop cytosol
U:D tRNA   20 CAA CAA tRNALeuCAA D-loop cytosol
U:D tRNA   20 UAA UAA tRNALeuUAA D-loop cytosol
U:D tRNA   20 UGG UGG tRNAProUGG D-loop cytosol
U:D tRNA   20 CGA CGA tRNASerCGA D-loop cytosol
U:D tRNA   20 UGA UGA tRNASerUGA D-loop cytosol
U:D tRNA   20 IGA IGA tRNASerIGA D-loop cytosol
U:D tRNA   20 IGU IGU tRNAThrIGU D-loop cytosol
U:D tRNA   20 CCA CCA tRNATrpCCA D-loop cytosol
U:D tRNA   20 GUA GUA tRNAThrGUA D-loop cytosol
U:D tRNA   20 UAC UAC tRNAValUAC D-loop cytosol
U:D tRNA   20 IAC IAC tRNAValIAC D-loop cytosol

Alpha Fold Predicted Structure:






Clear Selection and Reset Camera

Protein sequence:

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

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-P53720-F1.pdb  
Alpha Fold Pdbx/mmCIF Files   AF-P53720-F1.cif  
DSSP Secondary Structures   P53720.dssp  





Publications:

Title Authors Journal Details PubMed Id DOI
A novel human tRNA-dihydrouridine synthase involved in pulmonary carcinogenesis. Kato T, Daigo Y, Hayama S, Ishikawa N, Yamabuki T, Ito T, Miyamoto M, Kondo S, Nakamura Y Cancer Res [details] 15994936 -
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 -
Mechanism of dihydrouridine synthase 2 from yeast and the importance of modifications for efficient tRNA reduction. Rider LW, Ottosen MB, Gattis SG, Palfey BA... J Biol Chem [details] 19139092 -

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