2X2B

Crystal structure of malonyl-ACP (acyl carrier protein) from Bacillus subtilis


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.69 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.212 
  • R-Value Observed: 0.213 

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

A Novel Role of Malonyl-Acp in Lipid Homeostasis.

Martinez, M.A.Zaballa, M.E.Schaeffer, F.Bellinzoni, M.Albanesi, D.Schujman, G.E.Vila, A.J.Alzari, P.M.De Mendoza, D.

(2010) Biochemistry 49: 3161

  • DOI: https://doi.org/10.1021/bi100136n
  • Primary Citation of Related Structures:  
    2X2B

  • PubMed Abstract: 

    The FapR protein of Bacillus subtilis has been shown to play an important role in membrane lipid homeostasis. FapR acts as a repressor of many genes involved in fatty acid and phospholipid metabolism (the fap regulon). FapR binding to DNA is antagonized by malonyl-CoA, and thus FapR acts as a sensor of the status of fatty acid biosynthesis. However, malonyl-CoA is utilized for fatty acid synthesis only following its conversion to malonyl-ACP, which plays a central role in the initiation and elongation cycles carried out by the type II fatty acid synthase. Using in vitro transcription studies and isothermal titration calorimetry, we show here that malonyl-ACP binds FapR, disrupting the repressor-operator complex with an affinity similar to that of its precursor malonyl-CoA. NMR experiments reveal that there is no protein-protein recognition between ACP and FapR. These findings are consistent with the crystal structure of malonyl-ACP, which shows that the malonyl-phosphopantetheine moiety protrudes away from the protein core and thus can act as an effector ligand. Therefore, FapR regulates the expression of the fap regulon in response to the composition of the malonyl-phosphopantetheine pool. This mechanism ensures that fatty acid biosynthesis in B. subtilis is finely regulated at the transcriptional level by sensing the concentrations of the two first intermediates (malonyl-CoA and malonyl-ACP) in order to balance the production of membrane phospholipids.


  • Organizational Affiliation

    Instituto de Biología Molecular y Celular de Rosario (IBR-CONICET), Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, 2000 Rosario, Argentina.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
ACYL CARRIER PROTEIN78Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
UniProt
Find proteins for P80643 (Bacillus subtilis (strain 168))
Explore P80643 
Go to UniProtKB:  P80643
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP80643
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SXM
Query on SXM

Download Ideal Coordinates CCD File 
B [auth A]3-{[2-({N-[(2S)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanyl}amino)ethyl]sulfanyl}-3-oxopropanoic acid
C14 H25 N2 O10 P S
RNFWAFOKCVKQGB-GFCCVEGCSA-N
PT
Query on PT

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A]
PLATINUM (II) ION
Pt
HRGDZIGMBDGFTC-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.69 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.212 
  • R-Value Observed: 0.213 
  • Space Group: I 41 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 96.944α = 90
b = 96.944β = 90
c = 98.816γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
SHELX-AUTOSHARPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-03-16
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.2: 2011-10-12
    Changes: Database references, Refinement description