Modomics - A Database of RNA Modifications

ID Card:

Full name: tRNA pseudouridine(38,39,40) synthase
Synonym: HisT, AsuC, HisT, LeuK
GI: 123176
Orf: b2318
COG: COG0101
UniProt: P07649
Structures: | 1DJ0 | 2NQP | 2NR0 | 2NRE |
Alpha Fold Predicted Structure: AF-P07649-F1
Enzyme type: pseudouridine synthase
Position of modification - modification: t:38 - Y
t:39 - Y
t:40 - Y


PDB Structures:


1DJ0

Structure Description:

Title:
Classification:
Technique:

Abstract of the PDB Structure's related Publication:

Pseudouridine synthases catalyze the isomerization of specific uridines to pseudouridine in a variety of RNAs, yet the basis for recognition of the RNA sites or how they catalyze this reaction is unknown. The crystal structure of pseudouridine synthase I from Escherichia coli, which, for example, modifies positions 38, 39 and/or 40 in tRNA, reveals a dimeric protein that contains two positively charged, RNA-binding clefts along the surface of the protein. Each cleft contains a highly conserved aspartic acid located at its center. The structural domains have a topological similarity to those of other RNA-binding proteins, though the mode of interaction with tRNA appears to be unique. The structure suggests that a dimeric enzyme is required for binding transfer RNA and subsequent pseudouridine formation.

Download RCSB-PDB Structures:

Pdb Files   1DJ0.pdb   2NQP.pdb   2NR0.pdb   2NRE.pdb  
Pdbx/mmCIF Files   1DJ0.cif   2NQP.cif   2NR0.cif   2NRE.cif  


Protein sequence:

MSDQQQPPVYKIALGIEYDGSKYYGWQRQNEVRSVQEKLEKALSQVANEPITVFCAGRTDAGVHGTGQVVHFETTALRKDAAWTLGVNANLPGDIAVRWVKTVPDDFHARFSATARRYRYIIYNHRLRPAVLSKGVTHFYEPLDAERMHRAAQCLLGENDFTSFRAVQCQSRTPWRNVMHINVTRHGPYVVVDIKANAFVHHMVRNIVGSLMEVGAHNQPESWIAELLAAKDRTLAAATAKAEGLYLVAVDYPDRYDLPKPPMGPLFLAD

Comments:

Five pseudo (Y)-uridine synthases are conserved across all three life domains, including eukarya, bacteria, and archaea. In E.coli, these are named RluA, RsuA, TruA, TruB, and TruD. These families share poor sequence similarity. Nonetheless, these families share a core with a common fold and a conserved active cleft. This fold consists of an eight-stranded mixed beta-sheet with several helices and loops flanking the catalytic a cleft that bisects the sheet. Each of these families carries an essential aspartate residue that is catalytically active. This is the only residue that is absolutely conserved in all the Y-synthases. Depending on the enzyme, each core is additionally decorated with several secondary structural elements ( Hamma et al. 2006). TruA is responsible for the pseudouridylation in positions 38, 39, and 40 in many E.coli tRNAs. The catalytically conserved aspartate is in position 60 (Asp60) ( Hur et al. 2007).




Reaction Substrate SubstrateType Position (Anti)Codon Modified (Anti)Codon Amino Acid Change Transcript Name Transcript Region Cellular Localization References
U:Y RNA tRNA 38 UUG UUG tRNAGlnUUG anticodon-stem loop Prokaryotic Cytosol 3276686   
U:Y RNA tRNA 38 CUG CUG tRNAGlnCUG anticodon-stem loop Prokaryotic Cytosol 3276686   
U:Y RNA tRNA 38 GUG GUG tRNAHisGUG anticodon-stem loop Prokaryotic Cytosol 3276686   
U:Y RNA tRNA 38 CAG CAG tRNALeuCAG anticodon-stem loop Prokaryotic Cytosol 3276686   
U:Y RNA tRNA 38 GAG GAG tRNALeuGAG anticodon-stem loop Prokaryotic Cytosol 3276686   
U:Y RNA tRNA 39 GUU GUU tRNAAsnGUU anticodon-stem loop Prokaryotic Cytosol 3276686   
U:Y RNA tRNA 39 GCA GCA tRNACysGCA anticodon-stem loop Prokaryotic Cytosol 3276686   
U:Y RNA tRNA 39 CUG CUG tRNAGlnCUG anticodon-stem loop Prokaryotic Cytosol 3276686   
U:Y RNA tRNA 39 GUG GUG tRNAHisGUG anticodon-stem loop Prokaryotic Cytosol 3276686   
U:Y RNA tRNA 39 CAU CAU tRNAIleCAU anticodon-stem loop Prokaryotic Cytosol 3276686   
U:Y RNA tRNA 39 UAA UAA tRNALeuUAA anticodon-stem loop Prokaryotic Cytosol 3276686   
U:Y RNA tRNA 39 SUU SUU tRNALysSUU anticodon-stem loop Prokaryotic Cytosol 3276686   
U:Y RNA tRNA 39 CAU CAU tRNAMetCAU anticodon-stem loop Prokaryotic Cytosol 3276686   
U:Y RNA tRNA 39 GAA GAA tRNAPheGAA anticodon-stem loop Prokaryotic Cytosol 3276686   
U:Y RNA tRNA 39 GUA GUA tRNATyrGUA anticodon-stem loop Prokaryotic Cytosol 3276686   
U:Y RNA tRNA 40 UCU UCU tRNAArgUCU anticodon-stem loop Prokaryotic Cytosol 3276686   
U:Y RNA tRNA 40 CAG CAG tRNALeuCAG anticodon-stem loop Prokaryotic Cytosol 3276686   
U:Y RNA tRNA 40 GGA GGA tRNASerGGA anticodon-stem loop Prokaryotic Cytosol 3276686   

Alpha Fold Predicted Structure:






Clear Selection and Reset Camera

Protein sequence:

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

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-P07649-F1.pdb  
Alpha Fold Pdbx/mmCIF Files   AF-P07649-F1.cif  
DSSP Secondary Structures   P07649.dssp  





Publications:

Title Authors Journal Details PubMed Id DOI
Purification, structure, and properties of Escherichia coli tRNA pseudouridine synthase I. Kammen HO, Marvel CC, Hardy L, Penhoet EE J Biol Chem [details] 3276686 -
Pre-steady-state kinetic analysis of the three Escherichia coli pseudouridine synthases TruB, TruA, and RluA reveals uniformly slow catalysis. Wright JR, Keffer-Wilkes LC, Dobing SR, Kothe U RNA [details] 21998096 -