6XP8 | pdb_00006xp8

The crystal structure of TfuA involved in peptide backbone thioamidation from Methanosarcina acetivorans


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 
    0.234 (Depositor), 0.234 (DCC) 
  • R-Value Work: 
    0.196 (Depositor), 0.196 (DCC) 
  • R-Value Observed: 
    0.198 (Depositor) 

wwPDB Validation 3D Report Full Report

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This is version 1.3 of the entry. See complete history

Literature

Functional elucidation of TfuA in peptide backbone thioamidation.

Liu, A.Si, Y.Dong, S.H.Mahanta, N.Penkala, H.N.Nair, S.K.Mitchell, D.A.

(2021) Nat Chem Biol 17: 585-592

  • DOI: https://doi.org/10.1038/s41589-021-00771-0
  • Primary Citation Related Structures: 
    6XP8

  • PubMed Abstract: 

    YcaO enzymes catalyze several post-translational modifications on peptide substrates, including thioamidation, which substitutes an amide oxygen with sulfur. Most predicted thioamide-forming YcaO enzymes are encoded adjacent to TfuA, which when present, is required for thioamidation. While activation of the peptide amide backbone is well established for YcaO enzymes, the function of TfuA has remained enigmatic. Here we characterize the TfuA protein involved in methyl-coenzyme M reductase thioamidation and demonstrate that TfuA catalyzes the hydrolysis of thiocarboxylated ThiS (ThiS-COSH), a proteinaceous sulfur donor, and enhances the affinity of YcaO toward the thioamidation substrate. We also report a crystal structure of a TfuA, which displays a new protein fold. Our structural and mutational analyses of TfuA have uncovered conserved binding interfaces with YcaO and ThiS in addition to revealing a hydrolase-like active site featuring a Ser-Lys catalytic pair.


  • Organizational Affiliation
    • Department of Microbiology, University of Illinois, Urbana, IL, USA.

Macromolecule Content 

  • Total Structure Weight: 23.89 kDa 
  • Atom Count: 1,919 
  • Modeled Residue Count: 217 
  • Deposited Residue Count: 217 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
TfuA domain-containing protein217Methanosarcina acetivoransMutation(s): 0 
UniProt
Find proteins for Q8TUA9 (Methanosarcina acetivorans (strain ATCC 35395 / DSM 2834 / JCM 12185 / C2A))
Explore Q8TUA9 
Go to UniProtKB:  Q8TUA9
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8TUA9
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free:  0.234 (Depositor), 0.234 (DCC) 
  • R-Value Work:  0.196 (Depositor), 0.196 (DCC) 
  • R-Value Observed: 0.198 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 103.475α = 90
b = 36.837β = 121.77
c = 59.959γ = 90
Software Package:
Software NamePurpose
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
AutoSolphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2021-03-17
    Type: Initial release
  • Version 1.1: 2021-03-24
    Changes: Database references
  • Version 1.2: 2021-05-05
    Changes: Database references
  • Version 1.3: 2024-03-06
    Changes: Data collection, Database references