3WLA

Crystal Structure of sOPH Native


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.195 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structural insights into enzymatic degradation of oxidized polyvinyl alcohol

Yang, Y.Ko, T.P.Liu, L.Li, J.Huang, C.H.Chan, H.C.Ren, F.Jia, D.Wang, A.H.-J.Guo, R.T.Chen, J.Du, G.

(2014) Chembiochem 15: 1882-1886

  • DOI: 10.1002/cbic.201402166
  • Primary Citation of Related Structures:  
    3WL5, 3WL6, 3WL7, 3WL8, 3WLA

  • PubMed Abstract: 
  • The ever-increasing production and use of polyvinyl alcohol (PVA) threaten our environment. Yet PVA can be assimilated by microbes in two steps: oxidation and cleavage. Here we report novel α/β-hydrolase structures of oxidized PVA hydrolase (OPH) from two known PVA-degrading organisms, Sphingopyxis sp ...

    The ever-increasing production and use of polyvinyl alcohol (PVA) threaten our environment. Yet PVA can be assimilated by microbes in two steps: oxidation and cleavage. Here we report novel α/β-hydrolase structures of oxidized PVA hydrolase (OPH) from two known PVA-degrading organisms, Sphingopyxis sp. 113P3 and Pseudomonas sp. VM15C, including complexes with substrate analogues, acetylacetone and caprylate. The active site is covered by a lid-like β-ribbon. Unlike other esterase and amidase, OPH is unique in cleaving the CC bond of β-diketone, although it has a catalytic triad similar to that of most α/β-hydrolases. Analysis of the crystal structures suggests a double-oxyanion-hole mechanism, previously only found in thiolase cleaving β-ketoacyl-CoA. Three mutations in the lid region showed enhanced activity, with potential in industrial applications.


    Organizational Affiliation

    Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Lihu Ave. 1800, Wuxi 214122 (China).



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Oxidized polyvinyl alcohol hydrolaseA, B, C336Sphingopyxis sp. 113P3Mutation(s): 0 
Gene Names: oph
EC: 3.7.1.7
UniProt
Find proteins for Q588Z2 (Sphingopyxis sp. (strain 113P3))
Explore Q588Z2 
Go to UniProtKB:  Q588Z2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ588Z2
Protein Feature View
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  • Reference Sequence
Small Molecules
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.195 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 58.34α = 74.04
b = 75.742β = 88.67
c = 75.98γ = 74.01
Software Package:
Software NamePurpose
Blu-Icedata collection
PHASERphasing
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-09-24
    Type: Initial release
  • Version 1.1: 2017-11-22
    Changes: Refinement description