2VKZ

Structure of the cerulenin-inhibited fungal fatty acid synthase type I multienzyme complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.00 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.268 
  • R-Value Observed: 0.268 

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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Inhibition of the Fungal Fatty Acid Synthase Type I Multienzyme Complex.

Johansson, P.Wiltschi, B.Kumari, P.Kessler, B.Vonrhein, C.Vonck, J.Oesterhelt, D.Grininger, M.

(2008) Proc Natl Acad Sci U S A 105: 12803

  • DOI: 10.1073/pnas.0805827105
  • Primary Citation of Related Structures:  
    2VKZ

  • PubMed Abstract: 
  • Fatty acids are among the major building blocks of living cells, making lipid biosynthesis a potent target for compounds with antibiotic or antineoplastic properties. We present the crystal structure of the 2.6-MDa Saccharomyces cerevisiae fatty acid synthase (FAS) multienzyme in complex with the antibiotic cerulenin, representing, to our knowledge, the first structure of an inhibited fatty acid megasynthase ...

    Fatty acids are among the major building blocks of living cells, making lipid biosynthesis a potent target for compounds with antibiotic or antineoplastic properties. We present the crystal structure of the 2.6-MDa Saccharomyces cerevisiae fatty acid synthase (FAS) multienzyme in complex with the antibiotic cerulenin, representing, to our knowledge, the first structure of an inhibited fatty acid megasynthase. Cerulenin attacks the FAS ketoacyl synthase (KS) domain, forming a covalent bond to the active site cysteine C1305. The inhibitor binding causes two significant conformational changes of the enzyme. First, phenylalanine F1646, shielding the active site, flips and allows access to the nucleophilic cysteine. Second, methionine M1251, placed in the center of the acyl-binding tunnel, rotates and unlocks the inner part of the fatty acid binding cavity. The importance of the rotational movement of the gatekeeping M1251 side chain is reflected by the cerulenin resistance and the changed product spectrum reported for S. cerevisiae strains mutated in the adjacent glycine G1250. Platensimycin and thiolactomycin are two other potent inhibitors of KSs. However, in contrast to cerulenin, they show selectivity toward the prokaryotic FAS system. Because the flipped F1646 characterizes the catalytic state accessible for platensimycin and thiolactomycin binding, we superimposed structures of inhibited bacterial enzymes onto the S. cerevisiae FAS model. Although almost all side chains involved in inhibitor binding are conserved in the FAS multienzyme, a different conformation of the loop K1413-K1423 of the KS domain might explain the observed low antifungal properties of platensimycin and thiolactomycin.


    Organizational Affiliation

    Department of Membrane Biochemistry, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
FATTY ACID SYNTHASE SUBUNIT ALPHAA, B, C1,887Saccharomyces cerevisiaeMutation(s): 0 
EC: 2.3.1.86 (PDB Primary Data), 2.3.1.41 (PDB Primary Data), 1.1.1.100 (UniProt)
UniProt
Find proteins for P19097 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P19097 
Go to UniProtKB:  P19097
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP19097
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
FATTY ACID SYNTHASE SUBUNIT BETAD [auth G],
E [auth H],
F [auth I]
2,051Saccharomyces cerevisiaeMutation(s): 0 
EC: 2.3.1.86 (PDB Primary Data), 3.1.2.14 (PDB Primary Data), 4.2.1.59 (UniProt), 1.3.1.9 (UniProt), 2.3.1.38 (UniProt), 2.3.1.39 (UniProt)
UniProt
Find proteins for P07149 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P07149 
Go to UniProtKB:  P07149
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP07149
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FMN
Query on FMN

Download Ideal Coordinates CCD File 
J [auth G],
K [auth H],
L [auth I]
FLAVIN MONONUCLEOTIDE
C17 H21 N4 O9 P
FVTCRASFADXXNN-SCRDCRAPSA-N
 Ligand Interaction
CER
Query on CER

Download Ideal Coordinates CCD File 
G [auth A],
H [auth B],
I [auth C]
(2S, 3R)-3-HYDROXY-4-OXO-7,10-TRANS,TRANS-DODECADIENAMIDE
C12 H19 N O3
QEPYZBPOTYDXNA-FECJWDPASA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.00 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.268 
  • R-Value Observed: 0.268 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 231.9α = 90
b = 231.9β = 90
c = 756.8γ = 90
Software Package:
Software NamePurpose
piratemodel building
MOSFLMdata reduction
SCALAdata scaling
SHELXphasing
SHARPphasing
SOLOMONphasing
piratephasing
DMphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-08-12
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-06-21
    Changes: Refinement description