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 
  • R-Value Observed: 0.282 

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
  • Structures With Same Primary Citation

  • 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 hydrataseA, B258Escherichia coli K-12Mutation(s): 0 
Gene Names: b1393JW1388paaFydbR
EC: 4.2.1.17
Find proteins for P76082 (Escherichia coli (strain K12))
Explore P76082 
Go to UniProtKB:  P76082
Protein Feature View
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  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
1,2-epoxyphenylacetyl-CoA isomeraseC, D274Escherichia coli K-12Mutation(s): 0 
Gene Names: paaGydbTb1394JW1389
EC: 5.3.3.18
Find proteins for P77467 (Escherichia coli (strain K12))
Explore P77467 
Go to UniProtKB:  P77467
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download CCD File 
A, B
GLYCEROL
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 
  • R-Value Observed: 0.282 
  • Space Group: P 3 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 131.976α = 90
b = 131.976β = 90
c = 153.865γ = 120
Software Package:
Software NamePurpose
SCALEPACKdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction
MxDCdata collection
DENZOdata reduction

Structure Validation

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Entry History 

Deposition Data

Revision History 

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