5Z70

Crystal structure of oleate hydratase from Stenotrophomonas sp. KCTC 12332


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.91 Å
  • R-Value Free: 0.290 
  • R-Value Work: 0.227 
  • R-Value Observed: 0.230 

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This is version 1.2 of the entry. See complete history


Literature

Crystal structure of oleate hydratase from Stenotrophomonas sp. KCTC 12332 reveals conformational plasticity surrounding the FAD binding site.

Park, A.K.Lee, G.H.Kim, D.W.Jang, E.H.Kwon, H.T.Chi, Y.M.

(2018) Biochem Biophys Res Commun 499: 772-776

  • DOI: https://doi.org/10.1016/j.bbrc.2018.03.220
  • Primary Citation of Related Structures:  
    5Z70

  • PubMed Abstract: 

    Unsaturated fatty acids are toxic to various bacteria, causing their death or growth inhibition. To prevent this toxicity, unsaturated fatty acids should be converted into saturated fatty acids via hydrogenation reaction, which is the complete reduction of double bonds on the carbon chain. In a recent report, we observed that Stenotrophomonas sp. KCTC 12332 exhibited a high biotransformation activity of oleic acid (OA) in 10-hydroxystearic acid and identified the gene encoding oleate hydratase (OhySt) by complete genomic analysis. In the present study, to further investigate the structural features of OhySt, the recombinant protein was expressed in Escherichia coli, and then purified and crystallized. Biochemical assay showed that OhySt produces 10-hydroxystearic acid in a flavin adenosine dinucleotide (FAD)-dependent manner, indicating that it requires FAD as a cofactor. The OhySt structure, which is determined in its apo state, allows for a structural comparison with the previously reported FAD bound structure of oleate hydratase. The comparison of structures indicates remarkable conformational change of the loop region surrounding the FAD molecule upon binding of FAD. This change forces one of the important catalytic residues into position for catalysis.


  • Organizational Affiliation

    Division of Biotechnology, College of Life Sciences, Korea University, Seoul, 02841, Republic of Korea; Unit of Polar Genomics, Korea Polar Research Institute, Yeonsu-gu, Incheon, 21990, Republic of Korea.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Oleate hydratase
A, B
605Stenotrophomonas sp. KCTC 12332Mutation(s): 0 
Gene Names: AXG53_12705
UniProt
Find proteins for A0A126NKL7 (Stenotrophomonas sp. KCTC 12332)
Explore A0A126NKL7 
Go to UniProtKB:  A0A126NKL7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A126NKL7
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.91 Å
  • R-Value Free: 0.290 
  • R-Value Work: 0.227 
  • R-Value Observed: 0.230 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 62.061α = 90
b = 235.252β = 90
c = 176.372γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

  • Released Date: 2018-09-05 
  • Deposition Author(s): Park, A.K.

Revision History  (Full details and data files)

  • Version 1.0: 2018-09-05
    Type: Initial release
  • Version 1.1: 2019-08-28
    Changes: Data collection, Structure summary
  • Version 1.2: 2023-11-22
    Changes: Data collection, Database references, Refinement description