4KE6

Crystal structure D196N mutant of Monoglyceride lipase from Bacillus sp. H257 in complex with 1-rac-lauroyl glycerol


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.200 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Conformational plasticity and ligand binding of bacterial monoacylglycerol lipase.

Rengachari, S.Aschauer, P.Schittmayer, M.Mayer, N.Gruber, K.Breinbauer, R.Birner-Gruenberger, R.Dreveny, I.Oberer, M.

(2013) J.Biol.Chem. 288: 31093-31104

  • DOI: 10.1074/jbc.M113.491415
  • Primary Citation of Related Structures:  4KE7, 4KE8, 4KE9, 4KEA

  • PubMed Abstract: 
  • Monoacylglycerol lipases (MGLs) play an important role in lipid catabolism across all kingdoms of life by catalyzing the release of free fatty acids from monoacylglycerols. The three-dimensional structures of human and a bacterial MGL were determined ...

    Monoacylglycerol lipases (MGLs) play an important role in lipid catabolism across all kingdoms of life by catalyzing the release of free fatty acids from monoacylglycerols. The three-dimensional structures of human and a bacterial MGL were determined only recently as the first members of this lipase family. In addition to the α/β-hydrolase core, they showed unexpected structural similarities even in the cap region. Nevertheless, the structural basis for substrate binding and conformational changes of MGLs is poorly understood. Here, we present a comprehensive study of five crystal structures of MGL from Bacillus sp. H257 in its free form and in complex with different substrate analogs and the natural substrate 1-lauroylglycerol. The occurrence of different conformations reveals a high degree of conformational plasticity of the cap region. We identify a specific residue, Ile-145, that might act as a gatekeeper restricting access to the binding site. Site-directed mutagenesis of Ile-145 leads to significantly reduced hydrolase activity. Bacterial MGLs in complex with 1-lauroylglycerol, myristoyl, palmitoyl, and stearoyl substrate analogs enable identification of the binding sites for the alkyl chain and the glycerol moiety of the natural ligand. They also provide snapshots of the hydrolytic reaction of a bacterial MGL at different stages. The alkyl chains are buried in a hydrophobic tunnel in an extended conformation. Binding of the glycerol moiety is mediated via Glu-156 and water molecules. Analysis of the structural features responsible for cap plasticity and the binding modes of the ligands suggests conservation of these features also in human MGL.


    Organizational Affiliation

    From the Institute of Molecular Biosciences, University of Graz, Humboldtstrasse 50/3, A-8010 Graz, Austria.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Thermostable monoacylglycerol lipase
A, B, C, D, E, F
270Bacillus sp. (strain H-257)EC: 3.1.1.23
Find proteins for P82597 (Bacillus sp. (strain H-257))
Go to UniProtKB:  P82597
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
1QW
Query on 1QW

Download SDF File 
Download CCD File 
A
(2R)-2,3-dihydroxypropyl dodecanoate
1-Lauroyl-rac-glycerol
C15 H30 O4
ARIWANIATODDMH-CQSZACIVSA-N
 Ligand Interaction
MPD
Query on MPD

Download SDF File 
Download CCD File 
C, E, F
(4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.200 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 39.185α = 90.00
b = 182.878β = 90.00
c = 248.264γ = 90.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
SCALAdata scaling
PHASERphasing
PHENIXrefinement
MOSFLMdata reduction
MAR345data collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-09-18
    Type: Initial release
  • Version 1.1: 2013-10-09
    Type: Database references
  • Version 1.2: 2013-11-20
    Type: Database references
  • Version 1.3: 2017-11-15
    Type: Advisory, Refinement description