5O22

E. coli FolD in complex with carolacton


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.175 
  • R-Value Observed: 0.176 

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:  
    5O22, 5O2A, 5O28

  • 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-dependent C1 metabolism ...

    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

    German Centre for Infection Research (DZIF), Partner Site Hannover, 38124, Braunschweig, Germany. rolf.mueller@helmholtz-hzi.de.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Bifunctional protein FolDA289Escherichia coli K-12Mutation(s): 0 
Gene Names: folDadsb0529JW0518
EC: 1.5.1.5 (PDB Primary Data), 3.5.4.9 (PDB Primary Data)
Find proteins for P24186 (Escherichia coli (strain K12))
Explore P24186 
Go to UniProtKB:  P24186
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Bifunctional protein FolDB289Escherichia coli K-12Mutation(s): 0 
Gene Names: folDadsb0529JW0518
EC: 1.5.1.5 (PDB Primary Data), 3.5.4.9 (PDB Primary Data)
Find proteins for P24186 (Escherichia coli (strain K12))
Explore P24186 
Go to UniProtKB:  P24186
Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Bifunctional protein FolDC289Escherichia coli K-12Mutation(s): 0 
Gene Names: folDadsb0529JW0518
EC: 1.5.1.5 (PDB Primary Data), 3.5.4.9 (PDB Primary Data)
Find proteins for P24186 (Escherichia coli (strain K12))
Explore P24186 
Go to UniProtKB:  P24186
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Bifunctional protein FolDD289Escherichia coli K-12Mutation(s): 0 
Gene Names: folDadsb0529JW0518
EC: 1.5.1.5 (PDB Primary Data), 3.5.4.9 (PDB Primary Data)
Find proteins for P24186 (Escherichia coli (strain K12))
Explore P24186 
Go to UniProtKB:  P24186
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
C3R
Query on C3R

Download Ideal Coordinates CCD File 
E [auth A], F [auth B], G [auth C], H [auth D]Carolacton
C25 H40 O8
WCKOGWVWLFJJJX-ZCXGUVEESA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MLY
Query on MLY
AL-PEPTIDE LINKINGC8 H18 N2 O2LYS
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
C3RKd:  10   nM  Binding MOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.175 
  • R-Value Observed: 0.176 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 99.64α = 90
b = 81.016β = 112.95
c = 100.935γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
SCALEPACKdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research FoundationGermanyKO4116_3_1

Revision History  (Full details and data files)

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