5VCB

Crystal structure of holo-(acyl-carrier-protein) synthase:holo(acyl-carrier-protein) complex from Escherichia Coli.

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.10 Å
  • R-Value Free: 0.297 
  • R-Value Work: 0.278 
  • R-Value Observed: 0.279 

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Literature

Structure, High Affinity, and Negative Cooperativity of the Escherichia coli Holo-(Acyl Carrier Protein):Holo-(Acyl Carrier Protein) Synthase Complex.

Marcella, A.M., Culbertson, S.J., Shogren-Knaak, M.A., Barb, A.W.

(2017) J Mol Biol 429: 3763-3775

  • DOI: 10.1016/j.jmb.2017.10.015
  • Primary Citation of Related Structures:  
    5VBX, 5VCB

  • PubMed Abstract: 

    • The Escherichia coli holo-(acyl carrier protein) synthase (ACPS) catalyzes the coenzyme A-dependent activation of apo-ACPP to generate holo-(acyl carrier protein) (holo-ACPP) in an early step of fatty acid biosynthesis. E. coli ACPS is sufficiently different from the human fatty acid synthase to justify the development of novel ACPS-targeting antibiotics ...

    The Escherichia coli holo-(acyl carrier protein) synthase (ACPS) catalyzes the coenzyme A-dependent activation of apo-ACPP to generate holo-(acyl carrier protein) (holo-ACPP) in an early step of fatty acid biosynthesis. E. coli ACPS is sufficiently different from the human fatty acid synthase to justify the development of novel ACPS-targeting antibiotics. Models of E. coli ACPS in unliganded and holo-ACPP-bound forms solved by X-ray crystallography to 2.05and 4.10Å, respectively, revealed that ACPS bound three product holo-ACPP molecules to form a 3:3 hexamer. Solution NMR spectroscopy experiments validated the ACPS binding interface on holo-ACPP using chemical shift perturbations and by determining the relative orientation of holo-ACPP to ACPS by fitting residual dipolar couplings. The binding interface is organized to arrange contacts between positively charged ACPS residues and the holo-ACPP phosphopantetheine moiety, indicating product contains more stabilizing interactions than expected in the enzyme:substrate complex. Indeed, holo-ACPP bound the enzyme with greater affinity than the substrate, apo-ACPP, and with negative cooperativity. The first equivalent of holo-ACPP bound with a K D =62±13nM, followed by the binding of two more equivalents of holo-ACPP with K D =1.2±0.2μM. Cooperativity was not observed for apo-ACPP which bound with K D =2.4±0.1μM. Strong product binding and high levels of holo-ACPP in the cell identify a potential regulatory role of ACPS in fatty acid biosynthesis.

    Organizational Affiliation: 

    Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, 2437 Pammel Drive, Molecular Biology Building, rm 4210, Iowa State University, Ames, IA 50011, United States. Electronic address: abarb@iastate.edu.



Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Holo-[acyl-carrier-protein] synthase126Escherichia coli K-12Mutation(s): 0 
Gene Names: acpS, dpj, b2563, JW2547
EC: 2.7.8.7
UniProt
Find proteins for P24224 (Escherichia coli (strain K12))
Explore P24224 
Go to UniProtKB:  P24224
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP24224
Protein Feature View
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  • Reference Sequence
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(by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Acyl carrier protein79Escherichia coli S88Mutation(s): 0 
Gene Names: acpP, ECS88_1108
UniProt
Find proteins for P0A6A8 (Escherichia coli (strain K12))
Explore P0A6A8 
Go to UniProtKB:  P0A6A8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0A6A8
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.10 Å
  • R-Value Free: 0.297 
  • R-Value Work: 0.278 
  • R-Value Observed: 0.279 
  • Space Group: P 43
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 251.424α = 90
b = 251.424β = 90
c = 58.939γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
Aimlessdata scaling
PHENIXphasing

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Science Foundation (NSF, United States)United StatesEEC-0813570
Argonne National Laboratory's (Beam time)United StatesGUP-48455

Revision History  (Full details and data files)

  • Version 1.0: 2017-11-01
    Type: Initial release
  • Version 1.1: 2017-11-29
    Changes: Database references
  • Version 1.2: 2019-11-27
    Changes: Author supporting evidence