6OKG | pdb_00006okg

Crosslinked Crystal Structure of Type II Fatty Acid Synthase Ketosynthase, FabF, and C16-crypto Acyl Carrier Protein, AcpP

• PDB DOI: https://doi.org/10.2210/pdb6OKG/pdb

• Classification: TRANSFERASE
• Organism(s): Escherichia coli K-12
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2019-04-12 Released: 2020-04-22 
• Deposition Author(s): Mindrebo, J.T., Kim, W.E., Bartholow, T.G., Chen, A., Davis, T.D., La Clair, J., Burkart, M.D., Noel, J.P.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), Howard Hughes Medical Institute (HHMI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 
  0.228 (Depositor), 0.228 (DCC) 
• R-Value Work: 
  0.194 (Depositor), 0.195 (DCC) 
• R-Value Observed: 
  0.196 (Depositor) 

Starting Models: experimental

Literature

Gating mechanism of elongating beta-ketoacyl-ACP synthases.

Mindrebo, J.T., Patel, A., Kim, W.E., Davis, T.D., Chen, A., Bartholow, T.G., La Clair, J.J., McCammon, J.A., Noel, J.P., Burkart, M.D.

(2020) Nat Commun 11: 1727-1727

• PubMed: 32265440 
• DOI: https://doi.org/10.1038/s41467-020-15455-x
• Primary Citation Related Structures: 
  6OKC, 6OKF, 6OKG, 6OLT


• PubMed Abstract: 
  

  Carbon-carbon bond forming reactions are essential transformations in natural product biosynthesis. During de novo fatty acid and polyketide biosynthesis, β-ketoacyl-acyl carrier protein (ACP) synthases (KS), catalyze this process via a decarboxylative Claisen-like condensation reaction. KSs must recognize multiple chemically distinct ACPs and choreograph a ping-pong mechanism, often in an iterative fashion. Here, we report crystal structures of substrate mimetic bearing ACPs in complex with the elongating KSs from Escherichia coli, FabF and FabB, in order to better understand the stereochemical features governing substrate discrimination by KSs. Complemented by molecular dynamics (MD) simulations and mutagenesis studies, these structures reveal conformational states accessed during KS catalysis. These data taken together support a gating mechanism that regulates acyl-ACP binding and substrate delivery to the KS active site. Two active site loops undergo large conformational excursions during this dynamic gating mechanism and are likely evolutionarily conserved features in elongating KSs.

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Organizational Affiliation: 
• Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093-0358, USA.
Jack H. Skirball Center for Chemical Biology and Proteomics, Salk Institute for Biological Studies, La Jolla, CA, 92037, USA.
Department of Pharmacology, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA.
Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093-0358, USA. [e-mail].
Jack H. Skirball Center for Chemical Biology and Proteomics, Salk Institute for Biological Studies, La Jolla, CA, 92037, USA. [e-mail].
Howard Hughes Medical Institute, Salk Institute for Biological Studies, La Jolla, CA, 92037, USA. [e-mail].
Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093-0358, USA. [e-mail].

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)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 52.34 kDa 
• Atom Count: 3,904 
• Modeled Residue Count: 488 
• Deposited Residue Count: 491 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3-oxoacyl-[acyl-carrier-protein] synthase 2	A	413	Escherichia coli K-12	Mutation(s): 0  Gene Names: fabF, fabJ, b1095, JW1081 EC: 2.3.1.179
UniProt
Find proteins for P0AAI5 (Escherichia coli (strain K12)) Explore P0AAI5  Go to UniProtKB:  P0AAI5

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Acyl carrier protein	B	78	Escherichia coli K-12	Mutation(s): 0  Gene Names: acpP, b1094, JW1080
UniProt
Find proteins for P0A6A8 (Escherichia coli (strain K12)) Explore P0A6A8  Go to UniProtKB:  P0A6A8

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MU4 (Subject of Investigation/LOI)	D [auth A]	N-[2-(hexadecanoylamino)ethyl]-N~3~-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alaninamide C27 H54 N3 O8 P KCTLTWRYJGTZMN-VWLOTQADSA-N
NA	C [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.228 (Depositor), 0.228 (DCC) 
• R-Value Work:  0.194 (Depositor), 0.195 (DCC) 
• R-Value Observed: 0.196 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 86.89	α = 90
b = 86.89	β = 90
c = 113.729	γ = 90

Software Package:

Software Name	Purpose
MOSFLM	data reduction
Aimless	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2020-04-22 
Deposition Author(s): Mindrebo, J.T., Kim, W.E., Bartholow, T.G., Chen, A., Davis, T.D., La Clair, J., Burkart, M.D., Noel, J.P.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	5R01GM095970-06
Howard Hughes Medical Institute (HHMI)	United States	--

Revision History  

• Version 1.0: 2020-04-22
  Type: Initial release
  
• Version 1.1: 2023-10-11
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.2: 2024-11-06
  Changes: Structure summary