Modomics - A Database of RNA Modifications

ID Card:

Full name: Ribosomal small subunit pseudouridine synthase A
Synonym: YejD
GI: 76364197
Orf: yejD, b2183, c2720, z3442, ECs3075, SF2270, S2399
COG: COG1187
UniProt: P0AA43
Structures: | 1KSV | 1KSL | 1KSK |
Alpha Fold Predicted Structure: AF-P0AA43-F1
Enzyme type: pseudouridine synthase
Position of modification - modification: s:516(516) - Y


PDB Structures:


1KSV

Structure Description:

Title:
Classification:
Technique:

Abstract of the PDB Structure's related Publication:

In Escherichia coli, the pseudouridine synthase RsuA catalyzes formation of pseudouridine (psi) at position 516 in 16S rRNA during assembly of the 30S ribosomal subunit. We have determined the crystal structure of RsuA bound to uracil at 2.0 A resolution and to uridine 5'-monophosphate (UMP) at 2.65 A resolution. RsuA consists of an N-terminal domain connected by an extended linker to the central and C-terminal domains. Uracil and UMP bind in a cleft between the central and C-terminal domains near the catalytic residue Asp 102. The N-terminal domain shows structural similarity to the ribosomal protein S4. Despite only 15% amino acid identity, the other two domains are structurally similar to those of the tRNA-specific psi-synthase TruA, including the position of the catalytic Asp. Our results suggest that all four families of pseudouridine synthases share the same fold of their catalytic domain(s) and uracil-binding site.

Download RCSB-PDB Structures:

Pdb Files   1KSK.pdb   1KSL.pdb   1KSV.pdb  
Pdbx/mmCIF Files   1KSK.cif   1KSL.cif   1KSV.cif  


Protein sequence:

MRLDKFIAQQLGVSRAIAGREIRGNRVTVDGEIVRNAAFKLLPEHDVAYDGNPLAQQHGPRYFMLNKPQGYVCSTDDPDHPTVLYFLDEPVAWKLHAAGRLDIDTTGLVLMTDDGQWSHRITSPRHHCEKTYLVTLESPVADDTAEQFAKGVQLHNEKDLTKPAVLEVITPTQVRLTISEGRYHQVKRMFAAVGNHVVELHRERIGGITLDADLAPGEYRPLTEEEIASVV

Comments:

RsuA catalyzes formation of pseudouridine at position 516 in hairpin 18 of 16S rRNA during assembly of the 30S ribosomal subunit. RsuA does not react with free unmodified 16S RNA, and only poorly with 30S particles containing unmodified RNA. The preferred substrate is an RNA fragment from residues 1 to 678 which has been complexed with 30S ribosomal proteins, suggesting that Y516 formation in vivo occurs at an intermediate stage of 30S assembly. RsuA consists of an N-terminal domain connected by an extended linker to the central and C-terminal domains. The N-terminal domain shows structural similarity to the ribosomal protein S4. RsuA is very similar in both catalytic domain structure and active site arrangement to the pseudouridine synthases RluD, TruB, and TruA, including the position of a catalytic Asp.




Reaction Substrate SubstrateType Position (Anti)Codon Modified (Anti)Codon Amino Acid Change Transcript Name Transcript Region Cellular Localization References
U:Y RNA rRNA 516 SSU-16S 5' domain Prokaryotic Cytosol 10376875   

Alpha Fold Predicted Structure:






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Protein sequence:

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

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-P0AA43-F1.pdb  
Alpha Fold Pdbx/mmCIF Files   AF-P0AA43-F1.cif  
DSSP Secondary Structures   P0AA43.dssp  





Publications:

Title Authors Journal Details PubMed Id DOI
Purification, cloning, and properties of the 16S RNA pseudouridine 516 synthase from Escherichia coli. Wrzesinski J, Bakin A, Nurse K, Lane BG, Ofengand J Biochemistry [details] 7612632 -
16S ribosomal RNA pseudouridine synthase RsuA of Escherichia coli: deletion, mutation of the conserved Asp102 residue, and sequence comparison among all other pseudouridine synthases. Conrad J, Niu L, Rudd K, Lane BG, Ofengand J RNA [details] 10376875 -
Structure of the 16S rRNA pseudouridine synthase RsuA bound to uracil and UMP. Sivaraman J, Sauve V, Larocque R, Stura EA, Schrag JD, Cygler M, Matte A Nat Struct Biol [details] 11953756 -