Modomics - A Database of RNA Modifications

ID Card:

Full name: tRNA 2-thiouridine(34) synthase
Synonym: sirA, yhhP
GI: 16131342
COG: COG0425
UniProt: P0A890
Structures: | 3LVK | 3LVJ | 1DCJ |
Alpha Fold Predicted Structure: AF-P0A890-F1
Enzyme type: sulfurtransferase


PDB Structures:


3LVK

Structure Description:

Title:
Classification:
Technique:

Abstract of the PDB Structure's related Publication:

YhhP, a small protein of 81 amino acid residues encoded by the yhhP gene in the Escherichia coli database, is implicated in cell division although the precise biological function of this protein has not been yet identified. A variety of microorganisms have similar proteins, all of which contain a common CPxP sequence motif in the N-terminal region. We have determined the three-dimensional solution structure of YhhP by NMR spectroscopy in order to obtain insight into its biological function. It folds into a two-layered alpha/beta-sandwich structure with a betaalphabetaalphabetabeta fold, comprising a mixed four-stranded beta-sheet stacked against two alpha-helices, both of which are nearly parallel to the strands of the beta-sheet. The CPxP motif plays a significant structural role in stabilizing the first helix as a part of the new type N-capping box where the Cys-Pro peptide bond adopts a cis configuration. The structure of YhhP displays a striking resemblance to the C-terminal ribosome-binding domain of translation initiation factor IF3 (IF3C). In addition, the surface charge distribution of the RNA-recognition helix of IF3C is nearly the same as that of the corresponding helix of YhhP. These results suggest a structure-based hypothesis in which binding to an RNA target plays an essential role in the function of this ubiquitous protein.

Download RCSB-PDB Structures:

Pdb Files   1DCJ.pdb   3LVJ.pdb   3LVK.pdb  
Pdbx/mmCIF Files   1DCJ.cif   3LVJ.cif   3LVK.cif  


Protein sequence:

MTDLFSSPDHTLDALGLRCPEPVMMVRKTVRNMQPGETLLIIADDPATTRDIPGFCTFMEHELVAKETDGLPYRYLIRKGG

Comments:

TusA is a part of sulfur-relay system required for sulfur transfer from IscS cysteine desulfurase to MnmA protein which participates in mnm5s2U synthesis at tRNA wobble positions. TusA accepts a sulfur from IscS and transfers it to TusD.





Alpha Fold Predicted Structure:






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Protein sequence:

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

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-P0A890-F1.pdb  
Alpha Fold Pdbx/mmCIF Files   AF-P0A890-F1.cif  
DSSP Secondary Structures   P0A890.dssp  





Publications:

Title Authors Journal Details PubMed Id DOI
Structural basis for Fe-S cluster assembly and tRNA thiolation mediated by IscS protein-protein interactions. Shi R, Proteau A, Villarroya M, Moukadiri I, Zhang L, Trempe JF, Matte A, Armengod ME, Cygler M PLoS Biol [details] 20404999 -
Mechanistic insights into sulfur relay by multiple sulfur mediators involved in thiouridine biosynthesis at tRNA wobble positions. Ikeuchi Y, Shigi N, Kato J, Nishimura A, Suzuki T Mol Cell [details] 16387657 -
High precision NMR structure of YhhP, a novel Escherichia coli protein implicated in cell division. Katoh E, Hatta T, Shindo H, Ishii Y, Yamada H, Mizuno T, Yamazaki T J Mol Biol [details] 11080457 -

Links:

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