4KEH

Crosslinked Crystal Structure of Type II Fatty Synthase Dehydratase, FabA, and Acyl Carrier Protein, AcpP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.901 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.179 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Trapping the dynamic acyl carrier protein in fatty acid biosynthesis.

Nguyen, C.Haushalter, R.W.Lee, D.J.Markwick, P.R.Bruegger, J.Caldara-Festin, G.Finzel, K.Jackson, D.R.Ishikawa, F.O'Dowd, B.McCammon, J.A.Opella, S.J.Tsai, S.C.Burkart, M.D.

(2014) Nature 505: 427-431

  • DOI: 10.1038/nature12810

  • PubMed Abstract: 
  • Acyl carrier protein (ACP) transports the growing fatty acid chain between enzymatic domains of fatty acid synthase (FAS) during biosynthesis. Because FAS enzymes operate on ACP-bound acyl groups, ACP must stabilize and transport the growing lipid ch ...

    Acyl carrier protein (ACP) transports the growing fatty acid chain between enzymatic domains of fatty acid synthase (FAS) during biosynthesis. Because FAS enzymes operate on ACP-bound acyl groups, ACP must stabilize and transport the growing lipid chain. ACPs have a central role in transporting starting materials and intermediates throughout the fatty acid biosynthetic pathway. The transient nature of ACP-enzyme interactions impose major obstacles to obtaining high-resolution structural information about fatty acid biosynthesis, and a new strategy is required to study protein-protein interactions effectively. Here we describe the application of a mechanism-based probe that allows active site-selective covalent crosslinking of AcpP to FabA, the Escherichia coli ACP and fatty acid 3-hydroxyacyl-ACP dehydratase, respectively. We report the 1.9 Å crystal structure of the crosslinked AcpP-FabA complex as a homodimer in which AcpP exhibits two different conformations, representing probable snapshots of ACP in action: the 4'-phosphopantetheine group of AcpP first binds an arginine-rich groove of FabA, then an AcpP helical conformational change locks AcpP and FabA in place. Residues at the interface of AcpP and FabA are identified and validated by solution nuclear magnetic resonance techniques, including chemical shift perturbations and residual dipolar coupling measurements. These not only support our interpretation of the crystal structures but also provide an animated view of ACP in action during fatty acid dehydration. These techniques, in combination with molecular dynamics simulations, show for the first time that FabA extrudes the sequestered acyl chain from the ACP binding pocket before dehydration by repositioning helix III. Extensive sequence conservation among carrier proteins suggests that the mechanistic insights gleaned from our studies may be broadly applicable to fatty acid, polyketide and non-ribosomal biosynthesis. Here the foundation is laid for defining the dynamic action of carrier-protein activity in primary and secondary metabolism, providing insight into pathways that can have major roles in the treatment of cancer, obesity and infectious disease.


    Organizational Affiliation

    1] Departments of Molecular Biology and Biochemistry, Chemistry, and Pharmaceutical Sciences, University of California, Irvine, California 92697, USA [2].




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
N-{3-[DIHYDROXY(NONYL)-LAMBDA~4~-SULFANYL]PROPYL}-N~3~-[(2R)-2-HYDROXY-3,3-DIMETHYL-4-(PHOSPHONOOXY)BUTANOYL]-BETA-ALANINAMIDE
A, B
171Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: fabA
EC: 4.2.1.59
Find proteins for P0A6Q3 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A6Q3
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Acyl carrier protein
C, D
77N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
1R3
Query on 1R3

Download SDF File 
Download CCD File 
A, B
N-{3-[dihydroxy(nonyl)-lambda~4~-sulfanyl]propyl}-N~3~-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alaninamide
C21 H45 N2 O9 P S
ZGCXUZRDGZYOOW-IBGZPJMESA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.901 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.179 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 84.405α = 90.00
b = 122.178β = 90.00
c = 122.615γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
PHASERphasing
PHENIXrefinement
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-12-25
    Type: Initial release
  • Version 1.1: 2014-01-29
    Type: Database references