5AH0

STRUCTURE OF LIPASE 1 FROM PELOSINUS FERMENTANS


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.196 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Characterization of a Poly(Butylene Adipate-Co-Terephthalate)-Hydrolyzing Lipase from Pelosinus Fermentans.

Biundo, A.Hromic, A.Pavkov-Keller, T.Gruber, K.Quartinello, F.Haernvall, K.Perz, V.Arrell, M.S.Zinn, M.Ribitsch, D.Guebitz, G.M.

(2016) Appl Microbiol Biotechnol 100: 1753

  • DOI: https://doi.org/10.1007/s00253-015-7031-1
  • Primary Citation of Related Structures:  
    5AH0

  • PubMed Abstract: 

    Certain α/β hydrolases have the ability to hydrolyze synthetic polyesters. While their partial hydrolysis has a potential for surface functionalization, complete hydrolysis allows recycling of valuable building blocks. Although knowledge about biodegradation of these materials is important regarding their fate in the environment, it is currently limited to aerobic organisms. A lipase from the anaerobic groundwater organism Pelosinus fermentans DSM 17108(PfL1) was cloned and expressed in Escherichia coli BL21-Gold (DE3) and purified from the cell extract. Biochemical characterization with small substrates showed thermoalkalophilic properties (Topt=50 °C, pHopt=7.5) and higher activity towards para-nitrophenyl octanoate (12.7 U mg(-1)) compared to longer and shorter chain lengths (C14 0.7 U mg(-1) and C2 4.3 U mg(-1), respectively). Crystallization and determination of the 3-D structure displayed the presence of a lid structure and a zinc ion surrounded by an extra domain. These properties classify the enzyme into the I.5 lipase family. PfL1 is able to hydrolyze poly(1,4-butylene adipate-co-terephthalate) (PBAT) polymeric substrates. The hydrolysis of PBAT showed the release of small building blocks as detected by liquid chromatography mass spectrometry (LC-MS). Protein dynamics seem to be involved with lid opening for the hydrolysis of PBAT by PfL1.


  • Organizational Affiliation

    Institute of Environmental Biotechnology, University of Natural Resources and Life Science (BOKU), Konrad Lorenz Strasse 22, 3430, Tulln an der Donau, Austria.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
LIPASE
A, B
387Pelosinus fermentans DSM 17108Mutation(s): 0 
EC: 3.1.1.3
UniProt
Find proteins for A0A0A0YMQ9 (Pelosinus fermentans DSM 17108)
Explore A0A0A0YMQ9 
Go to UniProtKB:  A0A0A0YMQ9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0A0YMQ9
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.196 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 91.8α = 90
b = 91.8β = 90
c = 215.9γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-11-04
    Type: Initial release
  • Version 1.1: 2016-06-15
    Changes: Database references
  • Version 1.2: 2017-12-06
    Changes: Refinement description
  • Version 1.3: 2024-01-10
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description