Glutamylation domain, TbtB, from thiomuracin biosynthesis bound to 5'-phosphodesmethylglutamycin

Experimental Data Snapshot

  • Resolution: 2.15 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.213 
  • R-Value Observed: 0.216 

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This is version 1.2 of the entry. See complete history


Characterization of glutamyl-tRNA-dependent dehydratases using nonreactive substrate mimics.

Bothwell, I.R.Cogan, D.P.Kim, T.Reinhardt, C.J.van der Donk, W.A.Nair, S.K.

(2019) Proc Natl Acad Sci U S A 116: 17245-17250

  • DOI: https://doi.org/10.1073/pnas.1905240116
  • Primary Citation of Related Structures:  
    6EC7, 6EC8, 6M7Y

  • PubMed Abstract: 

    The peptide natural product nisin has been used as a food preservative for 6 decades with minimal development of resistance. Nisin contains the unusual amino acids dehydroalanine and dehydrobutyrine, which are posttranslationally installed by class I lanthipeptide dehydratases (LanBs) on a linear peptide substrate through an unusual glutamyl-tRNA-dependent dehydration of Ser and Thr. To date, little is known about how LanBs catalyze the transfer of glutamate from charged tRNA Glu to the peptide substrate, or how they carry out the subsequent elimination of the peptide-glutamyl adducts to afford dehydro amino acids. Here, we describe the synthesis of inert analogs that mimic substrate glutamyl-tRNA Glu and the glutamylated peptide intermediate, and determine the crystal structures of 2 LanBs in complex with each of these compounds. Mutational studies were used to characterize the function of the glutamylation and glutamate elimination active-site residues identified through the structural analysis. These combined studies provide insights into the mechanisms of substrate recognition, glutamylation, and glutamate elimination by LanBs to effect a net dehydration reaction of Ser and Thr.

  • Organizational Affiliation

    Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Lantibiotic dehydratase domain protein861Thermobispora bispora DSM 43833Mutation(s): 0 
Gene Names: Tbis_0550
Find proteins for D6Y502 (Thermobispora bispora (strain ATCC 19993 / DSM 43833 / CBS 139.67 / JCM 10125 / KCTC 9307 / NBRC 14880 / R51))
Explore D6Y502 
Go to UniProtKB:  D6Y502
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupD6Y502
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on J4G

Download Ideal Coordinates CCD File 
B [auth A]3'-deoxy-3'-[(L-alpha-glutamyl)amino]adenosine 5'-(dihydrogen phosphate)
C15 H22 N7 O9 P
Experimental Data & Validation

Experimental Data

  • Resolution: 2.15 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.213 
  • R-Value Observed: 0.216 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 44.503α = 90
b = 96.098β = 98.84
c = 107.128γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
autoPROCdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-06-19
    Type: Initial release
  • Version 1.1: 2019-09-25
    Changes: Data collection, Database references
  • Version 1.2: 2023-10-11
    Changes: Data collection, Database references, Refinement description