Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

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

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

Macromolecule Content

• Total Structure Weight: 241.33 kDa 
• Atom Count: 16541 
• Modelled Residue Count: 2197 
• Deposited Residue Count: 2210 
• Unique protein chains: 2

1WDM

fatty acid beta-oxidation multienzyme complex from Pseudomonas fragi, form I (native3)

• PDB DOI: 10.2210/pdb1WDM/pdb

• Classification: LYASE,OXIDOREDUCTASE/TRANSFERASE
• Organism(s): Pseudomonas fragi
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2004-05-17 Released: 2004-07-27 
• Deposition Author(s): Ishikawa, M., Tsuchiya, D., Oyama, T., Tsunaka, Y., Morikawa, K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.80 Å
• R-Value Free: 0.262 
• R-Value Work: 0.214 
• R-Value Observed: 0.217 

Literature

Structural basis for channelling mechanism of a fatty acid beta-oxidation multienzyme complex

Ishikawa, M., Tsuchiya, D., Oyama, T., Tsunaka, Y., Morikawa, K.

(2004) EMBO J 23: 2745-2754

• PubMed: 15229654 
• DOI: 10.1038/sj.emboj.7600298
• Primary Citation of Related Structures:  
  1WDK, 1WDL, 1WDM


• PubMed Abstract: 
  

The atomic view of the active site coupling termed channelling is a major subject in molecular biology. We have determined two distinct crystal structures of the bacterial multienzyme complex that catalyzes the last three sequential reactions in the fatty acid beta-oxidation cycle. The alpha2beta2 heterotetrameric structure shows the uneven ring architecture, where all the catalytic centers of 2-enoyl-CoA hydratase (ECH), L-3-hydroxyacyl-CoA dehydrogenase (HACD) and 3-ketoacyl-CoA thiolase (KACT) face a large inner solvent region. The substrate, anchored through the 3'-phosphate ADP moiety, allows the fatty acid tail to pivot from the ECH to HACD active sites, and finally to the KACT active site. Coupling with striking domain rearrangements, the incorporation of the tail into the KACT cavity and the relocation of 3'-phosphate ADP bring the reactive C2-C3 bond to the correct position for cleavage. The alpha-helical linker specific for the multienzyme contributes to the pivoting center formation and the substrate transfer through its deformation. This channelling mechanism could be applied to other beta-oxidation multienzymes, as revealed from the homology model of the human mitochondrial trifunctional enzyme complex.

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Related Citations: 

• Reconstitution, morphology and crystallization of a fatty acid beta-oxidation multienzyme complex from Pseudomonas fragi
  Ishikawa, M., Mikami, Y., Usukura, J., Iwasaki, H., Shinagawa, H., Morikawa, K.
  (1997) Biochem J 328: 815

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Organizational Affiliation: 

Biomolecular Engineering Research Institute, Furuedai, Suita, Osaka, Japan.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Fatty oxidation complex alpha subunit	A, B	715	Pseudomonas fragi	Mutation(s): 0  Gene Names: fadB, faoA EC: 4.2.1.17 (PDB Primary Data), 5.3.3.8 (PDB Primary Data), 1.1.1.35 (PDB Primary Data), 5.1.2.3 (PDB Primary Data)
UniProt
Find proteins for P28793 (Pseudomonas fragi) Explore P28793  Go to UniProtKB:  P28793

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
3-ketoacyl-CoA thiolase	C, D	390	Pseudomonas fragi	Mutation(s): 0  Gene Names: fadA, faoB EC: 2.3.1.16
UniProt
Find proteins for P28790 (Pseudomonas fragi) Explore P28790  Go to UniProtKB:  P28790

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ACO	F [auth A], I [auth C], J [auth D]	ACETYL COENZYME *A C23 H38 N7 O17 P3 S ZSLZBFCDCINBPY-ZSJPKINUSA-N
NAD	G [auth A], H [auth B]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C21 H27 N7 O14 P2 BAWFJGJZGIEFAR-NNYOXOHSSA-N
ZN	E [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.80 Å
• R-Value Free: 0.262 
• R-Value Work: 0.214 
• R-Value Observed: 0.217 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 181.453	α = 90
b = 95.462	β = 111.79
c = 161.325	γ = 90

Software Package:

Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
AMoRE	phasing
CNS	refinement
CCP4	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2004-05-17 
• Released Date: 2004-07-27 
Deposition Author(s): Ishikawa, M., Tsuchiya, D., Oyama, T., Tsunaka, Y., Morikawa, K.

Revision History  

• Version 1.0: 2004-07-27
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance