1WDK

fatty acid beta-oxidation multienzyme complex from Pseudomonas fragi, form I (native2)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.203 
  • R-Value Observed: 0.206 

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


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

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

  • 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 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.


    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

    Organizational Affiliation

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



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Fatty oxidation complex alpha subunitA, B715Pseudomonas fragiMutation(s): 0 
Gene Names: fadBfaoA
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
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
3-ketoacyl-CoA thiolaseC, D390Pseudomonas fragiMutation(s): 0 
Gene Names: fadAfaoB
EC: 2.3.1.16
UniProt
Find proteins for P28790 (Pseudomonas fragi)
Explore P28790 
Go to UniProtKB:  P28790
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ACO (Subject of Investigation/LOI)
Query on ACO

Download Ideal Coordinates CCD File 
M [auth C], O [auth D]ACETYL COENZYME *A
C23 H38 N7 O17 P3 S
ZSLZBFCDCINBPY-ZSJPKINUSA-N
 Ligand Interaction
NAD (Subject of Investigation/LOI)
Query on NAD

Download Ideal Coordinates CCD File 
F [auth A], I [auth B]NICOTINAMIDE-ADENINE-DINUCLEOTIDE
C21 H27 N7 O14 P2
BAWFJGJZGIEFAR-NNYOXOHSSA-N
 Ligand Interaction
N8E (Subject of Investigation/LOI)
Query on N8E

Download Ideal Coordinates CCD File 
G [auth A], H [auth A], J [auth B], K [auth B]3,6,9,12,15-PENTAOXATRICOSAN-1-OL
C18 H38 O6
MJELOWOAIAAUJT-UHFFFAOYSA-N
 Ligand Interaction
HG
Query on HG

Download Ideal Coordinates CCD File 
L [auth C], N [auth D]MERCURY (II) ION
Hg
BQPIGGFYSBELGY-UHFFFAOYSA-N
 Ligand Interaction
ZN
Query on ZN

Download Ideal Coordinates CCD File 
E [auth A]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.203 
  • R-Value Observed: 0.206 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 180.705α = 90
b = 94.578β = 111.45
c = 160.001γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
SHARPphasing
CNSrefinement
CCP4data scaling

Structure Validation

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Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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