2FAD

Crystal structure of E. coli heptanoyl-ACP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.209 

Starting Model: experimental
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Ligand Structure Quality Assessment 

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This is version 1.4 of the entry. See complete history


Literature

Structural Studies of Fatty Acyl-(Acyl Carrier Protein) Thioesters Reveal a Hydrophobic Binding Cavity that Can Expand to Fit Longer Substrates.

Roujeinikova, A.Simon, W.J.Gilroy, J.Rice, D.W.Rafferty, J.B.Slabas, A.R.

(2007) J Mol Biol 365: 135-145

  • DOI: https://doi.org/10.1016/j.jmb.2006.09.049
  • Primary Citation of Related Structures:  
    2FAC, 2FAD, 2FAE

  • PubMed Abstract: 

    A knowledge of the structures of acyl chain loaded species of the acyl carrier protein (ACP) as used in fatty acid biosynthesis and a range of other metabolic events, is essential for a full understanding of the molecular recognition at the heart of these processes. To date the only crystal structure of an acylated species of ACP is that of a butyryl derivative of Escherichia coli ACP. We have now determined the structures of a family of acylated E. coli ACPs of varying acyl chain length. The acyl moiety is attached via a thioester bond to a phosphopantetheine linker that is in turn bound to a serine residue in ACP. The growing acyl chain can be accommodated within a central cavity in the ACP for transport during the elongation stages of lipid synthesis through changes in the conformation of a four alpha-helix bundle. The results not only clarify the means by which a substrate of varying size and complexity is transported in the cell but also suggest a mechanism by which interacting enzymes can recognize the loaded ACP through recognition of surface features including the conformation of the phosphopantetheine linker.


  • Organizational Affiliation

    Krebs Institute for Biomolecular Research, Department of Molecular Biology and Biotechnology, The University of Sheffield, Sheffield S10 2TN, UK.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Acyl carrier protein
A, B
77Escherichia coliMutation(s): 0 
Gene Names: acpP
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
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PM5
Query on PM5

Download Ideal Coordinates CCD File 
K [auth A],
M [auth B]
S-(2-{[N-(2-HYDROXY-4-{[HYDROXY(OXIDO)PHOSPHINO]OXY}-3,3-DIMETHYLBUTANOYL)-BETA-ALANYL]AMINO}ETHYL) HEPTANETHIOATE
C18 H35 N2 O7 P S
IPSBILXXAVXCDA-INIZCTEOSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
D [auth A]
E [auth A]
F [auth A]
G [auth A]
H [auth A]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
NA
Query on NA

Download Ideal Coordinates CCD File 
C [auth A]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.209 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 49.257α = 90
b = 106.244β = 90
c = 28.195γ = 90
Software Package:
Software NamePurpose
CNSrefinement
PDB_EXTRACTdata extraction
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing

Structure Validation

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Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted PM5Click on this verticalbar to view details

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-09-26
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 1.3: 2023-08-30
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.4: 2024-10-30
    Changes: Structure summary