5O28

E. coli FolD apo


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.89 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.184 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

The natural product carolacton inhibits folate-dependent C1 metabolism by targeting FolD/MTHFD.

Fu, C.Sikandar, A.Donner, J.Zaburannyi, N.Herrmann, J.Reck, M.Wagner-Dobler, I.Koehnke, J.Muller, R.

(2017) Nat Commun 8: 1529-1529

  • DOI: 10.1038/s41467-017-01671-5
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The natural product carolacton is a macrolide keto-carboxylic acid produced by the myxobacterium Sorangium cellulosum, and was originally described as an antibacterial compound. Here we show that carolacton targets FolD, a key enzyme from the folate- ...

    The natural product carolacton is a macrolide keto-carboxylic acid produced by the myxobacterium Sorangium cellulosum, and was originally described as an antibacterial compound. Here we show that carolacton targets FolD, a key enzyme from the folate-dependent C1 metabolism. We characterize the interaction between bacterial FolD and carolacton biophysically, structurally and biochemically. Carolacton binds FolD with nanomolar affinity, and the crystal structure of the FolD-carolacton complex reveals the mode of binding. We show that the human FolD orthologs, MTHFD1 and MTHFD2, are also inhibited in the low nM range, and that micromolar concentrations of carolacton inhibit the growth of cancer cell lines. As mitochondrial MTHFD2 is known to be upregulated in cancer cells, it may be possible to use carolacton as an inhibitor tool compound to assess MTHFD2 as an anti-cancer target.


    Organizational Affiliation

    Department of Microbial Natural Products, Helmholtz Centre for Infection Research and Department of Pharmaceutical Biotechnology, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Saarland University, Campus E8.1, 66123, Saarbr├╝cken, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Bifunctional protein FolD
A
289Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: folD (ads)
Find proteins for P24186 (Escherichia coli (strain K12))
Go to UniProtKB:  P24186
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Bifunctional protein FolD
B
289Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: folD (ads)
Find proteins for P24186 (Escherichia coli (strain K12))
Go to UniProtKB:  P24186
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Bifunctional protein FolD
C, D
289Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: folD (ads)
Find proteins for P24186 (Escherichia coli (strain K12))
Go to UniProtKB:  P24186
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MLY
Query on MLY
A, B, C, D
L-PEPTIDE LINKINGC8 H18 N2 O2LYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.89 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.184 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 99.590α = 90.00
b = 79.840β = 113.26
c = 101.410γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
xia2data reduction
PHASERphasing
xia2data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research FoundationGermanyKO4116_3_1

Revision History 

  • Version 1.0: 2018-02-28
    Type: Initial release