Modomics - A Database of RNA Modifications

ID Card:

Full name: Ribosomal large subunit pseudouridine synthase D
Synonym: YfiI, SfhB
GI: 2507541
Orf: yfiI, b2594
COG: COG0564
UniProt: P33643
Structures: | 1PRZ | 1QYU | 1V9F | 2IST |
Alpha Fold Predicted Structure: AF-P33643-F1
Enzyme type: pseudouridine synthase
Position of modification - modification: l:1911(1911) - Y
l:1917(1917) - Y
l:1915(1915) - Y


PDB Structures:


1PRZ

Structure Description:

Title:
Classification:
Technique:

Abstract of the PDB Structure's related Publication:

Pseudouridine (5-beta-D-ribofuranosyluracil, Psi) is the most commonly found modified base in RNA. Conversion of uridine to Psi is performed enzymatically in both prokaryotes and eukaryotes by pseudouridine synthases (EC 4.2.1.70). The Escherichia coli Psi-synthase RluD modifies uridine to Psi at positions 1911, 1915 and 1917 within 23S rRNA. RluD also possesses a second function related to proper assembly of the 50S ribosomal subunit that is independent of Psi-synthesis. Here, we report the crystal structure of the catalytic module of RluD (residues 68-326; DeltaRluD) refined at 1.8A to a final R-factor of 21.8% (R(free)=24.3%). DeltaRluD is a monomeric enzyme having an overall mixed alpha/beta fold. The DeltaRluD molecule consists of two subdomains, a catalytic subdomain and C-terminal subdomain with the RNA-binding cleft formed by loops extending from the catalytic sub-domain. The catalytic sub-domain of DeltaRluD has a similar fold as in TruA, TruB and RsuA, with the location of the RNA-binding cleft, active-site and conserved, catalytic Asp residue superposing in all four structures. Superposition of the crystal structure of TruB bound to a T-stem loop with RluD reveals that similar RNA-protein interactions for the flipped-out uridine base would exist in both structures, implying that base-flipping is necessary for catalysis. This observation also implies that the specificity determinants for site-specific RNA-binding and recognition likely reside in parts of RluD beyond the active site.

Download RCSB-PDB Structures:

Pdb Files   1PRZ.pdb   1QYU.pdb   1V9F.pdb   2IST.pdb  
Pdbx/mmCIF Files   1PRZ.cif   1QYU.cif   1V9F.cif   2IST.cif  


Protein sequence:

MAQRVQLTATVSENQLGQRLDQALAEMFPDYSRSRIKEWILDQRVLVNGKVCDKPKEKVLGGEQVAINAEIEEEARFEPQDIPLDIVYEDEDIIIINKPRDLVVHPGAGNPDGTVLNALLHYYPPIADVPRAGIVHRLDKDTTGLMVVAKTVPAQTRLVESLQRREITREYEAVAIGHMTAGGTVDEPISRHPTKRTHMAVHPMGKPAVTHYRIMEHFRVHTRLRLRLETGRTHQIRVHMAHITHPLVGDPVYGGRPRPPKGASEAFISTLRKFDRQALHATMLRLYHPISGIEMEWHAPIPQDMVELIEVMRADFEEHKDEVDWL

Comments:

RluD makes pseudouridines at positions 1911, 1915, and 1917 in the loop of hairpin 69 in 23S RNA (Domain IV). These are the most conserved (and probably best studied) ribosomal pseudouridines known in Bacteria. RluD lacking cells exhibit growth defects and abnormal ribosome biogenesis. Moreover, the interactions around the Y1917 was shown to be critical for a proper interaction of helix 69 with release factors. When tested in vitro, recombinant RluD works best at low Mg concentrations. While in vivo, naturally occurring RluD modifies all three sites, U1911 has never been modified in vitro, even after conditions optimisation. RluD molecule consists of two subdomains, a catalytic subdomain and C-terminal subdomain with the RNA-binding cleft formed by loops extending from the catalytic subdomain. The catalytic subdomain of RluD has a similar fold as TruA, TruB and RsuA, with the location of the RNA-binding cleft, active-site and conserved, catalytic Asp residue 169 superposing in all four structures. The RluD N-terminal S4 domain is connected to the rest of the protein by a flexible linker. RluD is among the best studied RNA pseudouridine synthases.




Reaction Substrate SubstrateType Position (Anti)Codon Modified (Anti)Codon Amino Acid Change Transcript Name Transcript Region Cellular Localization References
U:Y RNA rRNA 1911 LSU-23S DOMAIN-IV Prokaryotic Cytosol 17937767   
U:Y RNA rRNA 1915 LSU-23S DOMAIN-IV Prokaryotic Cytosol 17937767   
U:Y RNA rRNA 1917 LSU-23S DOMAIN-IV Prokaryotic Cytosol 17937767   

Alpha Fold Predicted Structure:






Clear Selection and Reset Camera

Protein sequence:

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

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-P33643-F1.pdb  
Alpha Fold Pdbx/mmCIF Files   AF-P33643-F1.cif  
DSSP Secondary Structures   P33643.dssp  





Publications:

Title Authors Journal Details PubMed Id DOI
A second function for pseudouridine synthases: A point mutant of RluD unable to form pseudouridines 1911, 1915, and 1917 in Escherichia coli 23S ribosomal RNA restores normal growth to an RluD-minus strain. Gutgsell NS, Del Campo M, Raychaudhuri S, Ofengand J RNA [details] 11453071 -
The pseudouridine synthase RluD is required for normal ribosome assembly and function in Escherichia coli. Gutgsell NS, Deutscher MP, Ofengand J RNA [details] 15928344 -
RluD, a highly conserved pseudouridine synthase, modifies 50S subunits more specifically and efficiently than free 23S rRNA. Vaidyanathan PP, Deutscher MP, Malhotra A RNA [details] 17872507 -
Specificity and kinetics of 23S rRNA modification enzymes RlmH and RluD. Ero R, Leppik M, Liiv A, Remme J RNA [details] 20817755 -
Crystal structures of the catalytic domains of pseudouridine synthases RluC and RluD from Escherichia coli. Mizutani K, Machida Y, Unzai S, Park SY, Tame JR Biochemistry [details] 15078091 -
Crystal structure of the catalytic domain of RluD, the only rRNA pseudouridine synthase required for normal growth of Escherichia coli. Del Campo M, Ofengand J, Malhotra A RNA [details] 14730022 -
Substrate specificity of the pseudouridine synthase RluD in Escherichia coli. Leppik M, Peil L, Kipper K, Liiv A, Remme J FEBS J [details] 17937767 -
Crystal structure of the RluD pseudouridine synthase catalytic module, an enzyme that modifies 23S rRNA and is essential for normal cell growth of Escherichia coli. Sivaraman J, Iannuzzi P, Cygler M, Matte A J Mol Biol [details] 14659742 -