4FZW

Crystal Structure of the PaaF-PaaG Hydratase-Isomerase Complex from E.coli


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.55 Å
  • R-Value Free: 0.321 
  • R-Value Work: 0.280 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Protein-Protein Interactions in the beta-Oxidation Part of the Phenylacetate Utilization Pathway. Crystal Structure of the PaaF-PaaG Hydratase-Isomerase Complex

Grishin, A.M.Ajamian, E.Zhang, L.Rouiller, I.Bostina, M.Cygler, M.

(2012) J.Biol.Chem. 287: 37986-37996

  • DOI: 10.1074/jbc.M112.388231

  • PubMed Abstract: 
  • Microbial anaerobic and so-called hybrid pathways for degradation of aromatic compounds contain β-oxidation-like steps. These reactions convert the product of the opening of the aromatic ring to common metabolites. The hybrid phenylacetate degradatio ...

    Microbial anaerobic and so-called hybrid pathways for degradation of aromatic compounds contain β-oxidation-like steps. These reactions convert the product of the opening of the aromatic ring to common metabolites. The hybrid phenylacetate degradation pathway is encoded in Escherichia coli by the paa operon containing genes for 10 enzymes. Previously, we have analyzed protein-protein interactions among the enzymes catalyzing the initial oxidation steps in the paa pathway (Grishin, A. M., Ajamian, E., Tao, L., Zhang, L., Menard, R., and Cygler, M. (2011) J. Biol. Chem. 286, 10735-10743). Here we report characterization of interactions between the remaining enzymes of this pathway and show another stable complex, PaaFG, an enoyl-CoA hydratase and enoyl-Coa isomerase, both belonging to the crotonase superfamily. These steps are biochemically similar to the well studied fatty acid β-oxidation, which can be catalyzed by individual monofunctional enzymes, multifunctional enzymes comprising several domains, or enzymatic complexes such as the bacterial fatty acid β-oxidation complex. We have determined the structure of the PaaFG complex and determined that although individually PaaF and PaaG are similar to enzymes from the fatty acid β-oxidation pathway, the structure of the complex is dissimilar from bacterial fatty acid β-oxidation complexes. The PaaFG complex has a four-layered structure composed of homotrimeric discs of PaaF and PaaG. The active sites of PaaF and PaaG are adapted to accept the intermediary components of the Paa pathway, different from those of the fatty acid β-oxidation. The association of PaaF and PaaG into a stable complex might serve to speed up the steps of the pathway following the conversion of phenylacetyl-CoA to a toxic and unstable epoxide-CoA by PaaABCE monooxygenase.


    Organizational Affiliation

    Department of Biochemistry, University of Saskatchewan, Saskatoon, Saskatchewan S7N 5E5, Canada.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
2,3-dehydroadipyl-CoA hydratase
A, B
258Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: paaF (ydbR)
EC: 4.2.1.17
Find proteins for P76082 (Escherichia coli (strain K12))
Go to UniProtKB:  P76082
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
1,2-epoxyphenylacetyl-CoA isomerase
C, D
274Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: paaG (ydbT)
EC: 5.3.3.18
Find proteins for P77467 (Escherichia coli (strain K12))
Go to UniProtKB:  P77467
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download SDF File 
Download CCD File 
A, B
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.55 Å
  • R-Value Free: 0.321 
  • R-Value Work: 0.280 
  • Space Group: P 3 2 1
Unit Cell:
Length (Å)Angle (°)
a = 131.976α = 90.00
b = 131.976β = 90.00
c = 153.865γ = 120.00
Software Package:
Software NamePurpose
PHASERphasing
MxDCdata collection
SCALEPACKdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-09-19
    Type: Initial release
  • Version 1.1: 2013-01-16
    Type: Database references
  • Version 1.2: 2017-11-15
    Type: Refinement description