Modomics - A Database of RNA Modifications

ID Card:

Full name: Ribosomal large subunit pseudouridine synthase C
Synonym: YceC
GI: 76363884
Orf: yceC, b1086
COG: COG0564
UniProt: P0AA39
Structures: | 1V9K | 1XPI |
Alpha Fold Predicted Structure: AF-P0AA39-F1
Enzyme type: pseudouridine synthase
Position of modification - modification: l:955(955) - Y
l:2504(2504) - Y
l:2580(2580) - Y


PDB Structures:


1V9K

Structure Description:

Title: The crystal structure of the catalytic domain of pseudouridine synthase RluC from Escherichia coli
Classification: LYASE
Technique: X-Ray Diffraction
Resolution: 2.0
R value free: 0.276
R value observed: 0.213
R value work: 0.209

Abstract of the PDB Structure's related Publication:

The most frequent modification of RNA, the conversion of uridine bases to pseudouridines, is found in all living organisms and often in highly conserved locations in ribosomal and transfer RNA. RluC and RluD are homologous enzymes which each convert three specific uridine bases in Escherichia coli ribosomal 23S RNA to pseudouridine: bases 955, 2504, and 2580 in the case of RluC and 1911, 1915, and 1917 in the case of RluD. Both have an N-terminal S4 RNA binding domain. While the loss of RluC has little phenotypic effect, loss of RluD results in a much reduced growth rate. We have determined the crystal structures of the catalytic domain of RluC, and full-length RluD. The S4 domain of RluD appears to be highly flexible or unfolded and is completely invisible in the electron density map. Despite the conserved topology shared by the two proteins, the surface shape and charge distribution are very different. The models suggest significant differences in substrate binding by different pseudouridine synthases.

Download RCSB-PDB Structures:

Pdb Files   1V9K.pdb   1XPI.pdb  
Pdbx/mmCIF Files   1V9K.cif   1XPI.cif  


Protein sequence:

MKTETPSVKIVAITADEAGQRIDNFLRTQLKGVPKSMIYRILRKGEVRVNKKRIKPEYKLEAGDEVRIPPVRVAEREEEAVSPHLQKVAALADVILYEDDHILVLNKPSGTAVHGGSGLSFGVIEGLRALRPEARFLELVHRLDRDTSGVLLVAKKRSALRSLHEQLREKGMQKDYLALVRGQWQSHVKSVQAPLLKNILQSGERIVRVSQEGKPSETRFKVEERYAFATLVRCSPVTGRTHQIRVHTQYAGHPIAFDDRYGDREFDRQLTEAGTGLNRLFLHAAALKFTHPGTGEVMRIEAPMDEGLKRCLQKLRNAR

Comments:

The multi-site specific RluC catalyzes isomerization of uridines to pseudouridines at positions 955 (in hairpin 39 of Domain II), 2504 (in single stranded region between hairpins 89-90 of Domain V in Peptidyl Transferase Center) and 2580 (in stem of helix 90 of the same Domain V) in 23S rRNA. In vitro transcript of 23S ribosomal RNA was used as substrate. RluC possess a N-terminal S4 RNA binding domain. Proteolytically derived fragment of the enzyme consisting of residues 89-319 has been crystallized and shown to retain catalytic activity. RluC belongs to the same subgroup of RNA pseudourodine synthases as RluA, RluD, TruC, Pus5, Pus6, Pus8 and Pus9.





Alpha Fold Predicted Structure:






Clear Selection and Reset Camera

Protein sequence:

M K T E T P S V K I V A I T A D E A G Q R I D N F L R T Q L K G V P K S M I Y R I L R K G E V R V N K K R I K P E Y K L E A G D E V R I P P V R V A E R E E E A V S P H L Q K V A A L A D V I L Y E D D H I L V L N K P S G T A V H G G S G L S F G V I E G L R A L R P E A R F L E L V H R L D R D T S G V L L V A K K R S A L R S L H E Q L R E K G M Q K D Y L A L V R G Q W Q S H V K S V Q A P L L K N I L Q S G E R I V R V S Q E G K P S E T R F K V E E R Y A F A T L V R C S P V T G R T H Q I R V H T Q Y A G H P I A F D D R Y G D R E F D R Q L T E A G T G L N R L F L H A A A L K F T H P G T G E V M R I E A P M D E G L K R C L Q K L R N A R
50100150200250300SequenceHTBSN

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-P0AA39-F1.pdb  
Alpha Fold Pdbx/mmCIF Files   AF-P0AA39-F1.cif  
DSSP Secondary Structures   P0AA39.dssp  





Publications: