5EHK

Crystal structure of tRNA dependent lantibiotic dehydratase MibB from Microbispora sp. 107891


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.708 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.204 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structure and tRNA Specificity of MibB, a Lantibiotic Dehydratase from Actinobacteria Involved in NAI-107 Biosynthesis.

Ortega, M.A.Hao, Y.Walker, M.C.Donadio, S.Sosio, M.Nair, S.K.van der Donk, W.A.

(2016) Cell Chem Biol 23: 370-380

  • DOI: 10.1016/j.chembiol.2015.11.017

  • PubMed Abstract: 
  • Class I lantibiotic dehydratases dehydrate selected Ser/Thr residues of a precursor peptide. Recent studies demonstrated the requirement of glutamyl-tRNA(Glu) for Ser/Thr activation by one of these enzymes (NisB) from the Firmicute Lactococcus lactis ...

    Class I lantibiotic dehydratases dehydrate selected Ser/Thr residues of a precursor peptide. Recent studies demonstrated the requirement of glutamyl-tRNA(Glu) for Ser/Thr activation by one of these enzymes (NisB) from the Firmicute Lactococcus lactis. However, the generality of glutamyl-tRNA(Glu) usage and the tRNA specificity of lantibiotic dehydratases have not been established. Here we report the 2.7-Å resolution crystal structure, along with the glutamyl-tRNA(Glu) utilization of MibB, a lantibiotic dehydratase from the Actinobacterium Microbispora sp. 107891 involved in the biosynthesis of the clinical candidate NAI-107. Biochemical assays revealed nucleotides A73 and U72 within the tRNA(Glu) acceptor stem to be important for MibB glutamyl-tRNA(Glu) usage. Using this knowledge, an expression system for the production of NAI-107 analogs in Escherichia coli was developed, overcoming the inability of MibB to utilize E. coli tRNA(Glu). Our work provides evidence for a common tRNA(Glu)-dependent dehydration mechanism, paving the way for the characterization of lantibiotics from various phyla.


    Organizational Affiliation

    Department of Biochemistry; University of Illinois at Urbana-Champaign, Roger Adams Laboratory, 600 S. Mathews Ave., Urbana IL, 61801, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Lantibiotic dehydratase
A, B
1115Microbispora corallinaMutation(s): 0 
Gene Names: mibB
Find proteins for E2IHB7 (Microbispora corallina)
Go to UniProtKB:  E2IHB7
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.708 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.204 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 85.137α = 90.00
b = 151.112β = 90.00
c = 205.744γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
Cootmodel building
HKL-2000data collection
HKL-2000data reduction
SHARPphasing
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2015-10-28 
  • Released Date: 2016-03-02 
  • Deposition Author(s): Hao, Y., Nair, S.K.

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical SciencesUnited StatesR01 GM 079038

Revision History 

  • Version 1.0: 2016-03-02
    Type: Initial release
  • Version 1.1: 2016-03-30
    Type: Database references
  • Version 1.2: 2017-09-20
    Type: Author supporting evidence, Database references, Derived calculations