4I45

Crystal Structure of Orf6 protein from Photobacterium profundum, Mg2+-bound form


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.4 Å
  • R-Value Free: 0.196 
  • R-Value Work: 0.148 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structure, Activity, and Substrate Selectivity of the Orf6 Thioesterase from Photobacterium profundum.

Rodriguez-Guilbe, M.Oyola-Robles, D.Schreiter, E.R.Baerga-Ortiz, A.

(2013) J.Biol.Chem. 288: 10841-10848

  • DOI: 10.1074/jbc.M112.446765
  • Primary Citation of Related Structures:  3R87

  • PubMed Abstract: 
  • Thioesterase activity is typically required for the release of products from polyketide synthase enzymes, but no such enzyme has been characterized in deep-sea bacteria associated with the production of polyunsaturated fatty acids. In this work, we h ...

    Thioesterase activity is typically required for the release of products from polyketide synthase enzymes, but no such enzyme has been characterized in deep-sea bacteria associated with the production of polyunsaturated fatty acids. In this work, we have expressed and purified the Orf6 thioesterase from Photobacterium profundum. Enzyme assays revealed that Orf6 has a higher specific activity toward long-chain fatty acyl-CoA substrates (palmitoyl-CoA and eicosapentaenoyl-CoA) than toward short-chain or aromatic acyl-CoA substrates. We determined a high resolution (1.05 Å) structure of Orf6 that reveals a hotdog hydrolase fold arranged as a dimer of dimers. The putative active site of this structure is occupied by additional electron density not accounted for by the protein sequence, consistent with the presence of an elongated compound. A second crystal structure (1.40 Å) was obtained from a crystal that was grown in the presence of Mg(2+), which reveals the presence of a binding site for divalent cations at a crystal contact. The Mg(2+)-bound structure shows localized conformational changes (root mean square deviation of 1.63 Å), and its active site is unoccupied, suggesting a mechanism to open the active site for substrate entry or product release. These findings reveal a new thioesterase enzyme with a preference for long-chain CoA substrates in a deep-sea bacterium whose potential range of applications includes bioremediation and the production of biofuels.


    Organizational Affiliation

    Department of Biochemistry, University of Puerto Rico School of Medicine, San Juan, Puerto Rico.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
ORF6 thioesterase
A
135Photobacterium profundumN/A
Find proteins for Q93CG9 (Photobacterium profundum)
Go to UniProtKB:  Q93CG9
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

Download SDF File 
Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.4 Å
  • R-Value Free: 0.196 
  • R-Value Work: 0.148 
  • Space Group: I 2 2 2
Unit Cell:
Length (Å)Angle (°)
a = 51.292α = 90.00
b = 54.362β = 90.00
c = 88.363γ = 90.00
Software Package:
Software NamePurpose
d*TREKdata scaling
ADSCdata collection
PHASERphasing
d*TREKdata reduction
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-02-27
    Type: Initial release
  • Version 1.1: 2013-05-01
    Type: Database references