Modomics - A Database of RNA Modifications

ID Card:

Full name: Ribosomal large subunit pseudouridine synthase F
Synonym: YjbC
GI: 418534
Orf: yjbC, b4022
COG: COG1187
UniProt: P32684
Structures: | 2GML | 3DH3 |
Alpha Fold Predicted Structure: AF-P32684-F1
Enzyme type: pseudouridine synthase
Position of modification - modification: l:2604(2604) - Y


PDB Structures:


2GML

Structure Description:

Title:
Classification:
Technique:

Abstract of the PDB Structure's related Publication:

Pseudouridine synthases catalyze the isomerization of uridine to pseudouridine (Psi) in rRNA and tRNA. The pseudouridine synthase RluF from Escherichia coli (E.C. 4.2.1.70) modifies U2604 in 23S rRNA, and belongs to a large family of pseudouridine synthases present in all kingdoms of life. Here we report the domain architecture and crystal structure of the catalytic domain of E.coli RluF at 2.6A resolution. Limited proteolysis, mass spectrometry and N-terminal sequencing indicate that RluF has a distinct domain architecture, with the catalytic domain flanked at the N and C termini by additional domains connected to it by flexible linkers. The structure of the catalytic domain of RluF is similar to those of RsuA and TruB. RluF is a member of the RsuA sequence family of Psi-synthases, along with RluB and RluE. Structural comparison of RluF with its closest structural homologues, RsuA and TruB, suggests possible functional roles for the N-terminal and C-terminal domains of RluF.

Download RCSB-PDB Structures:

Pdb Files   2GML.pdb   3DH3.pdb  
Pdbx/mmCIF Files   2GML.cif   3DH3.cif  


Protein sequence:

MLPDSSVRLNKYISESGICSRREADRYIEQGNVFLNGKRATIGDQVKPGDVVKVNGQLIEPREAEDLVLIALNKPVGIVSTTEDGERDNIVDFVNHSKRVFPIGRLDKDSQGLIFLTNHGDLVNKILRAGNDHEKEYLVTVDKPITEEFIRGMSAGVPILGTVTKKCKVKKEAPFVFRITLVQGLNRQIRRMCEHFGYEVKKLERTRIMNVSLSGIPLGEWRDLTDDELIDLFKLIENSSSEVKPKAKAKPKTAGIKRPVVKMEKTAEKGGRPASNGKRFTSPGRKKKGR

Comments:

RluF modifies U2604 in a stem-loop (helix 93 of the Peptidyl transferase Center on Domain V) of 23S RNA, while its homologue, RluB, modifies the adjacent base, U2605. Both uridines are in the same RNA stem, separated by only 4 A. The RNA stem-loop is bound to a conserved binding groove in the catalytic domain. A base from a bulge in the stem, A2602, folds into the stem, forcing one strand of the RNA stem to translate by one position and thus positioning U2604 to flip into the active site. The structure of the catalytic domain of RluF is similar to those of RsuA and TruB. RluF is a member of the RsuA family of pseudouridine synthases, along with RluB and RluE (but not TruB), present in all kingdoms of life.




Reaction Substrate SubstrateType Position (Anti)Codon Modified (Anti)Codon Amino Acid Change Transcript Name Transcript Region Cellular Localization References
U:Y RNA rRNA 2604 LSU-23S DOMAIN-V Prokaryotic Cytosol 11720289   

Alpha Fold Predicted Structure:






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Protein sequence:

M L P D S S V R L N K Y I S E S G I C S R R E A D R Y I E Q G N V F L N G K R A T I G D Q V K P G D V V K V N G Q L I E P R E A E D L V L I A L N K P V G I V S T T E D G E R D N I V D F V N H S K R V F P I G R L D K D S Q G L I F L T N H G D L V N K I L R A G N D H E K E Y L V T V D K P I T E E F I R G M S A G V P I L G T V T K K C K V K K E A P F V F R I T L V Q G L N R Q I R R M C E H F G Y E V K K L E R T R I M N V S L S G I P L G E W R D L T D D E L I D L F K L I E N S S S E V K P K A K A K P K T A G I K R P V V K M E K T A E K G G R P A S N G K R F T S P G R K K K G 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-P32684-F1.pdb  
Alpha Fold Pdbx/mmCIF Files   AF-P32684-F1.cif  
DSSP Secondary Structures   P32684.dssp  





Publications:

Title Authors Journal Details PubMed Id DOI
Identification and site of action of the remaining four putative pseudouridine synthases in Escherichia coli. Del Campo M, Kaya Y, Ofengand J RNA [details] 11720289 -
Domain organization and crystal structure of the catalytic domain of E.coli RluF, a pseudouridine synthase that acts on 23S rRNA. Sunita S, Zhenxing H, Swaathi J, Cygler M, Matte A, Sivaraman J J Mol Biol [details] 16712869 -
Crystal structure of an RluF-RNA complex: a base-pair rearrangement is the key to selectivity of RluF for U2604 of the ribosome. Alian A, DeGiovanni A, Griner SL, Finer-Moore JS, Stroud RM J Mol Biol [details] 19298824 -