Modomics - A Database of RNA Modifications

ID Card:

Full name: tRNA pseudouridine(32) synthase / Ribosomal large subunit pseudouridine synthase A
Synonym: YabO
GI: 76363883
Orf: yabO, b0058
COG: COG0564
UniProt: P0AA37
Structures: | 2I82 |
Alpha Fold Predicted Structure: AF-P0AA37-F1
Enzyme type: pseudouridine synthase
Position of modification - modification: l:746(746) - Y
t:32 - Y


PDB Structures:


2I82

Structure Description:

Title:
Classification:
Technique:

Abstract of the PDB Structure's related Publication:

RluA is a dual-specificity enzyme responsible for pseudouridylating 23S rRNA and several tRNAs. The 2.05 A resolution structure of RluA bound to a substrate RNA comprising the anticodon stem loop of tRNA(Phe) reveals that enzyme binding induces a dramatic reorganization of the RNA. Instead of adopting its canonical U turn conformation, the anticodon loop folds into a new structure with a reverse-Hoogsteen base pair and three flipped-out nucleotides. Sequence conservation, the cocrystal structure, and the results of structure-guided mutagenesis suggest that RluA recognizes its substrates indirectly by probing RNA loops for their ability to adopt the reorganized fold. The planar, cationic side chain of an arginine intercalates between the reverse-Hoogsteen base pair and the bottom pair of the anticodon stem, flipping the nucleotide to be modified into the active site of RluA. Sequence and structural comparisons suggest that pseudouridine synthases of the RluA, RsuA, and TruA families employ an equivalent arginine for base flipping.

Download RCSB-PDB Structures:

Pdb Files   2I82.pdb  
Pdbx/mmCIF Files   2I82.cif  


Protein sequence:

MGMENYNPPQEPWLVILYQDDHIMVVNKPSGLLSVPGRLEEHKDSVMTRIQRDYPQAESVHRLDMATSGVIVVALTKAAERELKRQFREREPKKQYVARVWGHPSPAEGLVDLPLICDWPNRPKQKVCYETGKPAQTEYEVVEYAADNTARVVLKPITGRSHQLRVHMLALGHPILGDRFYASPEARAMAPRLLLHAEMLTITHPAYGNSMTFKAPADF

Comments:

RluA forms pseudouridines at positions 746 in the loop of hairpin 35 of 23S ribosomal RNA (Domain II) and 32 in the loop of anticodon branch of a few E. coli tRNA. It reacts efficiently with full-length 23S RNA, a rRNA fragment encompassing the hairpin 35 (residues 1-847) and the mini tRNA comprising the anticodon stem-loop. RluA induces a dramatic reorganization of the RNA substrate allowing the target U to flip into the active site of the enzyme. Pseudouridylation occurs in single-stranded segments closed by a stem. The enzyme has no dependence on Mg2+, the rate of U-isomerisation is even faster in EDTA than in the presence of Mg2+. E. coli RluA belongs to the same subgroup of RNA pseudouridine synthases as E. coli, RluC, RluD and TruC as well as S. cerevisiae Pus5, Pus6, Pus8 and Pus9.




Reaction Substrate SubstrateType Position (Anti)Codon Modified (Anti)Codon Amino Acid Change Transcript Name Transcript Region Cellular Localization References
U:Y RNA tRNA 32 GCA GCA tRNACysGCA anticodon-stem loop Prokaryotic Cytosol 7493321   
U:Y RNA tRNA 32 UAA UAA tRNALeuUAA anticodon-stem loop Prokaryotic Cytosol 7493321   
U:Y RNA tRNA 32 GAA GAA tRNAPheGAA anticodon-stem loop Prokaryotic Cytosol 7493321   
U:Y RNA rRNA 746 LSU-23S Prokaryotic Cytosol 7493321   

Alpha Fold Predicted Structure:






Clear Selection and Reset Camera

Protein sequence:

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

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-P0AA37-F1.pdb  
Alpha Fold Pdbx/mmCIF Files   AF-P0AA37-F1.cif  
DSSP Secondary Structures   P0AA37.dssp  





Publications:

Title Authors Journal Details PubMed Id DOI
Mechanistic investigations of the pseudouridine synthase RluA using RNA containing 5-fluorouridine. Hamilton CS, Greco TM, Vizthum CA, Ginter JM, Johnston MV, Mueller EG Biochemistry [details] 17002302 -
A dual-specificity pseudouridine synthase: an Escherichia coli synthase purified and cloned on the basis of its specificity for psi 746 in 23S RNA is also specific for psi 32 in tRNA(phe). Wrzesinski J, Nurse K, Bakin A, Lane BG, Ofengand J RNA [details] 7493321 -
Crystal structure of pseudouridine synthase RluA: indirect sequence readout through protein-induced RNA structure. Hoang C, Chen J, Vizthum CA, Kandel JM, Hamilton CS, Mueller EG, Ferre-D'Amare AR Mol Cell [details] 17188032 -
Functional effect of deletion and mutation of the Escherichia coli ribosomal RNA and tRNA pseudouridine synthase RluA. Raychaudhuri S, Niu L, Conrad J, Lane BG, Ofengand J J Biol Chem [details] 10383384 -
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 -
The Handling of the Mechanistic Probe 5-Fluorouridine by the Pseudouridine Synthase TruA and Its Consistency with the Handling of the Same Probe by the Pseudouridine Synthases TruB and RluA. McDonald MK, Miracco EJ, Chen J, Xie Y, Mueller EG Biochemistry [details] 21142053 -

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