Modomics - A Database of RNA Modifications

ID Card:

Full name: tRNA dihydrouridine synthase A
Synonym: YjbN
GI: 3183570
Orf: yjbN, b4049
COG: COG0042
UniProt: P32695
Alpha Fold Predicted Structure: AF-P32695-F1
Enzyme type: dihydrouridine synthase
Position of modification - modification: t:20 - D



Protein sequence:

MPEKTDVHWSGRFSVAPMLDWTDRHCRYFLRLLSRNTLLYTEMVTTGAIIHGKGDYLAYSEEEHPVALQLGGSDPAALAQCAKLAEARGYDEINLNVGCPSDRVQNGMFGACLMGNAQLVADCVKAMRDVVSIPVTVKTRIGIDDQDSYEFLCDFINTVSGKGECEMFIIHARKAWLSGLSPKENREIPPLDYPRVYQLKRDFPHLTMSINGGIKSLEEAKAHLQHMDGVMVGREAYQNPGILAAVDREIFGSSDTDADPVAVVRAMYPYIERELSQGTYLGHITRHMLGLFQGIPGARQWRRYLSENAHKAGADINVLEHALKLVADKR

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-transcriptionally modified pyrimidine nucleoside. D results from the reduction of C5,6-double bond of 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 E.coli, tRNA-dihydro uridine (20/20a) synthase catalyzes the synthesis of 5,6-dihydro uridine (D) via the reduction of C5,6. It is responsible for half of the wild-cellular tRNA modifications (Bishop et al. 2002 )




Reaction Substrate SubstrateType Position (Anti)Codon Modified (Anti)Codon Amino Acid Change Transcript Name Transcript Region Cellular Localization References
U:D RNA tRNA 20 CAU CAD tRNAIniCAU anticodon-loop 11983710   

Alpha Fold Predicted Structure:






Clear Selection and Reset Camera

Protein sequence:

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

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-P32695-F1.pdb  
Alpha Fold Pdbx/mmCIF Files   AF-P32695-F1.cif  
DSSP Secondary Structures   P32695.dssp  





Publications:

Title Authors Journal Details PubMed Id DOI
Identification of the tRNA-dihydrouridine synthase family. Bishop AC, Xu J, Johnson RC, Schimmel P, de Crecy-Lagard V J Biol Chem [details] 11983710 -
Molecular determinants of dihydrouridine synthase activity. Savage DF, de Crecy-Lagard V, Bishop AC FEBS Lett [details] 16962594 -
Molecular evolution of dihydrouridine synthases. Kasprzak JM, Czerwoniec A, Bujnicki JM... BMC Bioinformatics [details] 22741570 -

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