4LIP

PSEUDOMONAS LIPASE COMPLEXED WITH RC-(RP, SP)-DIBUTYLCARBAMOYLGLYCERO-3-O-BUTYLPHOSPHONATE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.202 
  • R-Value Work: 0.178 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural basis of the chiral selectivity of Pseudomonas cepacia lipase

Lang, D.A.Mannesse, M.L.M.De Haas, G.Verheij, H.M.Dijkstra, B.W.

(1998) Eur.J.Biochem. 254: 333-340

  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • To investigate the enantioselectivity of Pseudomonas cepacia lipase, inhibition studies were performed with Sc- and Rc-(Rp,Sp)-1,2-dialkylcarbamoylglycero-3-O-p-nitrophenyl alkylphosphonates of different alkyl chain lengths. P. cepacia lipase was mos ...

    To investigate the enantioselectivity of Pseudomonas cepacia lipase, inhibition studies were performed with Sc- and Rc-(Rp,Sp)-1,2-dialkylcarbamoylglycero-3-O-p-nitrophenyl alkylphosphonates of different alkyl chain lengths. P. cepacia lipase was most rapidly inactivated by Rc-(Rp,Sp)-1,2-dioctylcarbamoylglycero-3-O-p-nitrophenyl octylphosphonate (Rc-trioctyl) with an inactivation half-time of 75 min, while that for the Sc-(Rp,Sp)-1,2-dioctylcarbamoylglycero-3-O-p-nitrophenyl octyl-phosphonate (Sc-trioctyl) compound was 530 min. X-ray structures were obtained of P. cepacia lipase after reaction with Rc-trioctyl to 0.29-nm resolution at pH 4 and covalently modified with Rc-(Rp,Sp)-1,2-dibutylcarbamoylglycero-3-O-p-nitrophenyl butyl-phosphonate (Rc-tributyl) to 0.175-nm resolution at pH 8.5. The three-dimensional structures reveal that both triacylglycerol analogues had reacted with the active-site Ser87, forming a covalent complex. The bound phosphorus atom shows the same chirality (Sp) in both complexes despite the use of a racemic (Rp,Sp) mixture at the phosphorus atom of the triacylglycerol analogues. In the structure of Rc-tributyl-complexed P. cepacia lipase, the diacylglycerol moiety has been lost due to an aging reaction, and only the butyl phosphonate remains visible in the electron density. In the Rc-trioctyl complex the complete inhibitor is clearly defined; it adopts a bent tuning fork conformation. Unambiguously, four binding pockets for the triacylglycerol could be detected: an oxyanion hole and three pockets which accommodate the sn-1, sn-2, and sn-3 fatty acid chains. Van der Waals' interactions are the main forces that keep the radyl groups of the triacylglycerol analogue in position and, in addition, a hydrogen bond to the carbonyl oxygen of the sn-2 chain contributes to fixing the position of the inhibitor.


    Related Citations: 
    • The Open Conformation of a Pseudomonas Lipase
      Schrag, J.D.,Li, Y.,Cygler, M.,Lang, D.,Burgdorf, T.,Hecht, H.J.,Schmid, R.,Schomburg, D.,Rydel, T.J.,Oliver, J.D.,Strickland, L.C.,Dunaway, C.M.,Larson, S.B.,Day, J.,McPherson, A.
      (1997) Structure 5: 187
    • Extracellular Lipase of Pseudomonas Sp. Strain Atcc 21808: Purification, Characterization, Crystallization, and Preliminary X-Ray Diffraction Data
      Kordel, M.,Hofmann, B.,Schomburg, D.,Schmid, R.D.
      (1991) J.Bacteriol. 173: 4836


    Organizational Affiliation

    BIOSON Research Institute and Laboratory of Biophysical Chemistry, University of Groningen, The Netherlands.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
TRIACYL-GLYCEROL-HYDROLASE
D, E
320Burkholderia cepaciaMutation(s): 0 
Gene Names: lip (lipA)
EC: 3.1.1.3
Find proteins for P22088 (Burkholderia cepacia)
Go to UniProtKB:  P22088
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CCP
Query on CCP

Download SDF File 
Download CCD File 
D, E
BUTYLPHOSPHONATE
C4 H11 O3 P
UOKRBSXOBUKDGE-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

Download SDF File 
Download CCD File 
D, E
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.202 
  • R-Value Work: 0.178 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 84.040α = 90.00
b = 46.360β = 116.53
c = 85.380γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
X-PLORrefinement
SCALEPACKdata scaling
AMoREphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1998-08-19
    Type: Initial release
  • Version 1.1: 2008-03-25
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance