3WL5

Crystal structure of pOPH S172C


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.187 
  • R-Value Work: 0.159 
  • R-Value Observed: 0.161 

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: https://doi.org/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. 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
MoleculeChains Sequence LengthOrganismDetailsImage
Oxidized polyvinyl alcohol hydrolase364Pseudomonas sp.Mutation(s): 1 
Gene Names: pvaB
EC: 3.7.1.7
UniProt
Find proteins for Q9LCQ7 (Pseudomonas sp)
Explore Q9LCQ7 
Go to UniProtKB:  Q9LCQ7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9LCQ7
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CIT
Query on CIT

Download Ideal Coordinates CCD File 
B [auth A]CITRIC ACID
C6 H8 O7
KRKNYBCHXYNGOX-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
OCS
Query on OCS
A
L-PEPTIDE LINKINGC3 H7 N O5 SCYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.187 
  • R-Value Work: 0.159 
  • R-Value Observed: 0.161 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 58.537α = 90
b = 65.426β = 90
c = 84.195γ = 90
Software Package:
Software NamePurpose
Blu-Icedata collection
OASISmodel building
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
OASISphasing

Structure Validation

View Full Validation Report



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