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.





Alpha Fold Predicted Structure:




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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
50100150200250300350SequenceGHITBSN

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:

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