Modomics - A Database of RNA Modifications

ID Card:

Full name: tRNA 2-thiouridine(34) synthase
Synonym: yheL
GI: 16131222
COG: COG2168
UniProt: P45530
Structures: | 2D1P |
Alpha Fold Predicted Structure: AF-P45530-F1
Complex: TusBCD


PDB Structures:


2D1P

Structure Description:

Title: crystal structure of heterohexameric TusBCD proteins, which are crucial for the tRNA modification
Classification: TRANSLATION
Technique: X-Ray Diffraction
Resolution: 2.15
R value free: 0.242
R value observed: 0.209
R value work: 0.209

Abstract of the PDB Structure's related Publication:

Uridine at wobble position 34 of tRNA(Lys), tRNA(Glu), and tRNA(Gln) is exclusively modified into 2-thiouridine (s2U), which is crucial for both precise codon recognition and recognition by the cognate aminoacyl-tRNA synthetases. Recent Escherichia coli genetic studies revealed that the products of five novel genes, tusABCDE, function in the s2U modification. Here, we solved the 2.15 angstroms crystal structure of the E. coli TusBCD complex, a sulfur transfer mediator, forming a heterohexamer composed of a dimer of the heterotrimer. Structure-based sequence alignment suggested two putative active site Cys residues, Cys79 (in TusC) and Cys78 (in TusD), which are exposed on the hexameric complex. In vivo mutant analyses revealed that only Cys78, in the TusD subunit, participates in sulfur transfer during the s2U modification process. Since the single Cys acts as a catalytic residue, we proposed that TusBCD mediates sulfur relay via a putative persulfide state of the TusD subunit.

Download RCSB-PDB Structures:

Pdb Files   2D1P.pdb  
Pdbx/mmCIF Files   2D1P.cif  


Protein sequence:

MLHTLHRSPWLTDFAALLRLLSEGDELLLLQDGVTAAVDGNRYLESLRNAPIKVYALNEDLIARGLTGQISNDIILIDYTDFVRLTVKHPSQMAW

Comments:

Part of a TusBCD complex which functions as a heterohexamer (a dimer of the heterotrimer). TusBCD complex participates in sulfur transfer from IscS cystein desulfurase to MnmA protein which participates in mnm5s2U synthesis at tRNA wobble positions. It mediates sulfur relay via a putative persulfide state of the TusD subunit. It transfers sulfur from TusA to TusE.





Alpha Fold Predicted Structure:






Clear Selection and Reset Camera

Protein sequence:

M L H T L H R S P W L T D F A A L L R L L S E G D E L L L L Q D G V T A A V D G N R Y L E S L R N A P I K V Y A L N E D L I A R G L T G Q I S N D I I L I D Y T D F V R L T V K H P S Q M A W
102030405060708090MLHTLHRSPWLTDFAALLRLLSEGDELLLLQDGVTAAVDGNRYLESLRNAPIKVYALNEDLIARGLTGQISNDIILIDYTDFVRLTVKHPSQMAWSequenceGHTBSN

Enter the variants

Position

Original

Variant

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-P45530-F1.pdb  
Alpha Fold Pdbx/mmCIF Files   AF-P45530-F1.cif  
DSSP Secondary Structures   P45530.dssp  





Publications:

Links:

_PubMed_
_EcoCyc_