5KOF | pdb_00005kof

Crosslinked Crystal Structure of Type II Fatty Acid Synthase Ketosynthase, FabB, and Acyl Carrier Protein, AcpP

• PDB DOI: https://doi.org/10.2210/pdb5KOF/pdb

• Classification: TRANSFERASE
• Organism(s): Escherichia coli
• Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
• Mutation(s): No 


• Deposited: 2016-06-30 Released: 2018-01-24 
• Deposition Author(s): Milligan, J.C., Jackson, D.R., Barajas, J.F., Tsai, S.C.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 
  0.229 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.209 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.210 (Depositor) 

Starting Model: experimental

Literature

Molecular basis for interactions between an acyl carrier protein and a ketosynthase.

Milligan, J.C., Lee, D.J., Jackson, D.R., Schaub, A.J., Beld, J., Barajas, J.F., Hale, J.J., Luo, R., Burkart, M.D., Tsai, S.C.

(2019) Nat Chem Biol 15: 669-671

• PubMed: 31209348 
• DOI: https://doi.org/10.1038/s41589-019-0301-y
• Primary Citation of Related Structures:  
  5KOF


• PubMed Abstract: 
  

  Fatty acid synthases are dynamic ensembles of enzymes that can biosynthesize long hydrocarbon chains efficiently. Here we visualize the interaction between the Escherichia coli acyl carrier protein (AcpP) and β-ketoacyl-ACP-synthase I (FabB) using X-ray crystallography, NMR, and molecular dynamics simulations. We leveraged this structural information to alter lipid profiles in vivo and provide a molecular basis for how protein-protein interactions can regulate the fatty acid profile in E. coli.

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Organizational Affiliation: 

Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, CA, USA.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 4-mer - A2B2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 103.54 kDa 
• Atom Count: 7,268 
• Modelled Residue Count: 963 
• Deposited Residue Count: 970 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3-oxoacyl-[acyl-carrier-protein] synthase 1	A [auth B], C [auth A]	407	Escherichia coli	Mutation(s): 0  EC: 2.3.1.41
UniProt
Find proteins for P0A953 (Escherichia coli (strain K12)) Explore P0A953  Go to UniProtKB:  P0A953

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Acyl carrier protein	B [auth C], D	78	Escherichia coli	Mutation(s): 0
UniProt
Find proteins for P0A6A8 (Escherichia coli (strain K12)) Explore P0A6A8  Go to UniProtKB:  P0A6A8

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
6W5	E [auth C], F [auth D]	[(3~{S})-2,2-dimethyl-3-oxidanyl-4-oxidanylidene-4-[[3-oxidanylidene-3-[2-(prop-2-enoylamino)ethylamino]propyl]amino]butyl] dihydrogen phosphate C14 H26 N3 O8 P BHBIKTJIKWGGMD-GFCCVEGCSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free:  0.229 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.209 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.210 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 59.33	α = 90
b = 103.92	β = 110.61
c = 83.4	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
iMOSFLM	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2018-01-24 
Deposition Author(s): Milligan, J.C., Jackson, D.R., Barajas, J.F., Tsai, S.C.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	--

Revision History  

• Version 1.0: 2018-01-24
  Type: Initial release
  
• Version 1.1: 2019-08-07
  Changes: Data collection, Database references
• Version 1.2: 2019-12-04
  Changes: Author supporting evidence
• Version 1.3: 2023-10-04
  Changes: Data collection, Database references, Refinement description
• Version 1.4: 2024-11-06
  Changes: Structure summary