6SRN

Structural basis for control of antibiotic production by bacterial hormones

  • Classification: ANTIBIOTIC
  • Organism(s): Streptomyces coelicolor
  • Expression System: Escherichia coli
  • Mutation(s): No 

  • Deposited: 2019-09-05 Released: 2020-09-30 
  • Deposition Author(s): Fulop, V.
  • Funding Organization(s): Royal Society, Biotechnology and Biological Sciences Research Council

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.174 
  • R-Value Observed: 0.175 

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Molecular basis for control of antibiotic production by a bacterial hormone.

Zhou, S.Bhukya, H.Malet, N.Harrison, P.J.Rea, D.Belousoff, M.J.Venugopal, H.Sydor, P.K.Styles, K.M.Song, L.Cryle, M.J.Alkhalaf, L.M.Fulop, V.Challis, G.L.Corre, C.

(2021) Nature 590: 463-467

  • DOI: https://doi.org/10.1038/s41586-021-03195-x
  • Primary Citation of Related Structures:  
    6SRN, 7KY1

  • PubMed Abstract: 

    Actinobacteria produce numerous antibiotics and other specialized metabolites that have important applications in medicine and agriculture 1 . Diffusible hormones frequently control the production of such metabolites by binding TetR family transcriptional repressors (TFTRs), but the molecular basis for this remains unclear 2 . The production of methylenomycin antibiotics in Streptomyces coelicolor A3(2) is initiated by the binding of 2-alkyl-4-hydroxymethylfuran-3-carboxylic acid (AHFCA) hormones to the TFTR MmfR 3 . Here we report the X-ray crystal structure of an MmfR-AHFCA complex, establishing the structural basis for hormone recognition. We also elucidate the mechanism for DNA release upon hormone binding through the single-particle cryo-electron microscopy structure of an MmfR-operator complex. DNA binding and release assays with MmfR mutants and synthetic AHFCA analogues define the role of individual amino acid residues and hormone functional groups in ligand recognition and DNA release. These findings will facilitate the exploitation of actinobacterial hormones and their associated TFTRs in synthetic biology and in the discovery of new antibiotics.


  • Organizational Affiliation

    Department of Chemistry, University of Warwick, Coventry, UK.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
TetR family transcriptional regulator214Streptomyces coelicolorMutation(s): 0 
Gene Names: mmfR
UniProt
Find proteins for Q9JN89 (Streptomyces coelicolor)
Explore Q9JN89 
Go to UniProtKB:  Q9JN89
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9JN89
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
LUB (Subject of Investigation/LOI)
Query on LUB

Download Ideal Coordinates CCD File 
B [auth A]4-(Hydroxymethyl)-2-propylfuran-3-carboxylic acid
C9 H14 O4
ZQVNOVXAPYHZNS-ZETCQYMHSA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
C [auth A]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.174 
  • R-Value Observed: 0.175 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 67.21α = 90
b = 67.21β = 90
c = 92.82γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
XDSdata scaling
SOLVEphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data

  • Released Date: 2020-09-30 
  • Deposition Author(s): Fulop, V.

Funding OrganizationLocationGrant Number
Royal SocietyUnited KingdomUF090255
Biotechnology and Biological Sciences Research CouncilUnited KingdomBB/M022765/1
Biotechnology and Biological Sciences Research CouncilUnited KingdomBB/M017982/1

Revision History  (Full details and data files)

  • Version 1.0: 2020-09-30
    Type: Initial release
  • Version 1.1: 2021-02-24
    Changes: Database references
  • Version 1.2: 2021-03-03
    Changes: Database references