3WL5 | pdb_00003wl5

Crystal structure of pOPH S172C

• PDB DOI: https://doi.org/10.2210/pdb3WL5/pdb

• Classification: HYDROLASE
• Organism(s): Pseudomonas sp.
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2013-11-07 Released: 2014-09-24 
• Deposition Author(s): Yang, Y., Ko, T.P., Li, J.H., Liu, L., Huang, C.H., Chan, H.C., Ren, F.F., Jia, D.X., Wang, A.H.-J., Guo, R.T., Chen, J., Du, G.C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 
  0.187 (Depositor), 0.187 (DCC) 
• R-Value Work: 
  0.159 (Depositor), 0.158 (DCC) 
• R-Value Observed: 
  0.161 (Depositor) 

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

• PubMed: 25044912 
• DOI: https://doi.org/10.1002/cbic.201402166
• Primary Citation 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.

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

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 39.52 kDa 
• Atom Count: 3,021 
• Modeled Residue Count: 338 
• Deposited Residue Count: 364 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Oxidized polyvinyl alcohol hydrolase	A	364	Pseudomonas 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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CIT	B [auth A]	CITRIC ACID C6 H8 O7 KRKNYBCHXYNGOX-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
OCS	A	L-PEPTIDE LINKING	C3 H7 N O5 S		CYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free:  0.187 (Depositor), 0.187 (DCC) 
• R-Value Work:  0.159 (Depositor), 0.158 (DCC) 
• R-Value Observed: 0.161 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.537	α = 90
b = 65.426	β = 90
c = 84.195	γ = 90

Software Package:

Software Name	Purpose
Blu-Ice	data collection
OASIS	model building
CNS	refinement
HKL-2000	data reduction
HKL-2000	data scaling
OASIS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-09-24 
Deposition Author(s): Yang, Y., Ko, T.P., Li, J.H., Liu, L., Huang, C.H., Chan, H.C., Ren, F.F., Jia, D.X., Wang, A.H.-J., Guo, R.T., Chen, J., Du, G.C.

Revision History  

• Version 1.0: 2014-09-24
  Type: Initial release
  
• Version 1.1: 2017-11-22
  Changes: Refinement description
• Version 1.2: 2025-03-26
  Changes: Data collection, Database references, Derived calculations, Structure summary