4ZWN

Crystal Structure of a Soluble Variant of the Monoglyceride Lipase from Saccharomyces Cerevisiae


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.49 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.188 
  • R-Value Observed: 0.190 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Crystal structure of the Saccharomyces cerevisiae monoglyceride lipase Yju3p.

Aschauer, P.Rengachari, S.Lichtenegger, J.Schittmayer, M.Das, K.M.Mayer, N.Breinbauer, R.Birner-Gruenberger, R.Gruber, C.C.Zimmermann, R.Gruber, K.Oberer, M.

(2016) Biochim Biophys Acta 1861: 462-470

  • DOI: 10.1016/j.bbalip.2016.02.005
  • Primary Citation of Related Structures:  
    4ZWN, 4ZXF

  • PubMed Abstract: 
  • Monoglyceride lipases (MGLs) are a group of α/β-hydrolases that catalyze the hydrolysis of monoglycerides (MGs) into free fatty acids and glycerol. This reaction serves different physiological functions, namely in the last step of phospholipid and tr ...

    Monoglyceride lipases (MGLs) are a group of α/β-hydrolases that catalyze the hydrolysis of monoglycerides (MGs) into free fatty acids and glycerol. This reaction serves different physiological functions, namely in the last step of phospholipid and triglyceride degradation, in mammalian endocannabinoid and arachidonic acid metabolism, and in detoxification processes in microbes. Previous crystal structures of MGLs from humans and bacteria revealed conformational plasticity in the cap region of this protein and gave insight into substrate binding. In this study, we present the structure of a MGL from Saccharomyces cerevisiae called Yju3p in its free form and in complex with a covalently bound substrate analog mimicking the tetrahedral intermediate of MG hydrolysis. These structures reveal a high conservation of the overall shape of the MGL cap region and also provide evidence for conformational changes in the cap of Yju3p. The complex structure reveals that, despite the high structural similarity, Yju3p seems to have an additional opening to the substrate binding pocket at a different position compared to human and bacterial MGL. Substrate specificities towards MGs with saturated and unsaturated alkyl chains of different lengths were tested and revealed highest activity towards MG containing a C18:1 fatty acid.


    Organizational Affiliation

    Institute of Molecular Biosciences, University of Graz, Humboldtstraße 50/3, 8010 Graz, Austria. Electronic address: m.oberer@uni-graz.at.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Monoglyceride lipaseABCD334Saccharomyces cerevisiae S288CMutation(s): 2 
Gene Names: YJU3YKL094WYKL441
EC: 3.1.1.23
Find proteins for P28321 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P28321 
Go to UniProtKB:  P28321
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download CCD File 
B, C
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
NO3
Query on NO3

Download CCD File 
A
NITRATE ION
N O3
NHNBFGGVMKEFGY-UHFFFAOYSA-N
 Ligand Interaction
NA
Query on NA

Download CCD File 
D
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.49 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.188 
  • R-Value Observed: 0.190 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 77.196α = 90
b = 108.566β = 90
c = 167.667γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
Auto-Rickshawphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Austrian Science FundAustriaP24857
DK Molecular EnzymologyAustriaW901-B12

Revision History 

  • Version 1.0: 2016-04-27
    Type: Initial release
  • Version 1.1: 2016-05-25
    Changes: Database references
  • Version 1.2: 2017-09-06
    Changes: Author supporting evidence