3WL8

Crystal Structure of pOPH S172A with octanoic acid


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.175 
  • R-Value Work: 0.148 

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:  

  • 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) fro ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Oxidized polyvinyl alcohol hydrolase
A
364Pseudomonas spMutation(s): 1 
Gene Names: pvaB
EC: 3.7.1.7
Find proteins for Q9LCQ7 (Pseudomonas sp)
Go to UniProtKB:  Q9LCQ7
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CIT
Query on CIT

Download SDF File 
Download CCD File 
A
CITRIC ACID
C6 H8 O7
KRKNYBCHXYNGOX-UHFFFAOYSA-N
 Ligand Interaction
OCA
Query on OCA

Download SDF File 
Download CCD File 
A
OCTANOIC ACID (CAPRYLIC ACID)
C8 H16 O2
WWZKQHOCKIZLMA-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.175 
  • R-Value Work: 0.148 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 58.392α = 90.00
b = 65.295β = 90.00
c = 83.972γ = 90.00
Software Package:
Software NamePurpose
CNSrefinement
HKL-2000data scaling
Blu-Icedata collection
PHASERphasing
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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