2D3T

Fatty Acid beta-oxidation multienzyme complex from Pseudomonas Fragi, Form V


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.4 Å
  • R-Value Free: 0.295 
  • R-Value Work: 0.242 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Ligand-Induced Domain Rearrangement of Fatty Acid beta-Oxidation Multienzyme Complex

Tsuchiya, D.Shimizu, N.Ishikawa, M.Suzuki, Y.Morikawa, K.

(2006) Structure 14: 237-246

  • DOI: 10.1016/j.str.2005.10.011

  • PubMed Abstract: 
  • The quaternary structure of a fatty acid beta-oxidation multienzyme complex, catalyzing three sequential reactions, was investigated by X-ray crystallographic and small-angle X-ray solution scattering analyses. X-ray crystallography revealed an inter ...

    The quaternary structure of a fatty acid beta-oxidation multienzyme complex, catalyzing three sequential reactions, was investigated by X-ray crystallographic and small-angle X-ray solution scattering analyses. X-ray crystallography revealed an intermediate structure of the complex among the previously reported structures. However, the theoretical scattering curves calculated from the crystal structures remarkably disagree with the experimental profiles. Instead, an ensemble of the atomic models, which were all calculated by rigid-body optimization, reasonably explained the experimental data. These structures significantly differ from those in the crystals, but they maintain the substrate binding pocket at the domain boundary. Comparisons among these structures indicated that binding of 3-hydroxyhexadecanoyl-CoA or nicotinamide adenine dinucleotide induces domain rearrangements in the complex. The conformational changes suggest the structural events occurring during the chain reaction catalyzed by the multienzyme complex.


    Related Citations: 
    • 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


    Organizational Affiliation

    Biomolecular Engineering Research Institute, 6-2-3 Furuedai, Suita, Osaka 565-0874, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Fatty oxidation complex alpha subunit
A, B
715Pseudomonas fragiGene Names: fadB (faoA)
EC: 5.1.2.3, 5.3.3.8, 1.1.1.35, 4.2.1.17
Find proteins for P28793 (Pseudomonas fragi)
Go to UniProtKB:  P28793
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
3-ketoacyl-CoA thiolase
C, D
390Pseudomonas fragiGene Names: fadA (faoB)
EC: 2.3.1.16
Find proteins for P28790 (Pseudomonas fragi)
Go to UniProtKB:  P28790
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ACO
Query on ACO

Download SDF File 
Download CCD File 
C, D
ACETYL COENZYME *A
C23 H38 N7 O17 P3 S
ZSLZBFCDCINBPY-ZSJPKINUSA-N
 Ligand Interaction
NAD
Query on NAD

Download SDF File 
Download CCD File 
A, B
NICOTINAMIDE-ADENINE-DINUCLEOTIDE
C21 H27 N7 O14 P2
BAWFJGJZGIEFAR-NNYOXOHSSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.4 Å
  • R-Value Free: 0.295 
  • R-Value Work: 0.242 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 95.227α = 90.00
b = 137.552β = 90.00
c = 198.139γ = 90.00
Software Package:
Software NamePurpose
CNSrefinement
SCALEPACKdata scaling
AMoREphasing
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-02-21
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance