2NW6 image
Deposition Date 2006-11-14
Release Date 2007-12-04
Last Version Date 2024-10-09
Entry Detail
PDB ID:
2NW6
Title:
Burkholderia cepacia lipase complexed with S-inhibitor
Biological Source:
Source Organism:
Method Details:
Experimental Method:
Resolution:
1.80 Å
R-Value Free:
0.21
R-Value Work:
0.17
R-Value Observed:
0.18
Space Group:
C 1 2 1
Macromolecular Entities
Polymer Type:polypeptide(L)
Molecule:Lipase
Gene (Uniprot):lip
Chain IDs:A
Chain Length:320
Number of Molecules:1
Biological Source:Burkholderia cepacia
Primary Citation
Combined X-ray diffraction and QM/MM study of the Burkholderia cepacia lipase-catalyzed secondary alcohol esterification
J.Phys.Chem.B 112 4876 4883 (2008)
PMID: 18386861 DOI: 10.1021/jp077717u

Abstact

To understand the origin of high enantioselectivity of Burkholderia cepacia lipase (BCL) toward secondary alcohol, (R,S)-1-phenoxy-2-hydroxybutane (1), and its ester (E1), we determined the crystal structure of BCL complexed with phosphonate analogue of S-E1 and accomplished a series of MM, MC, and QM/MM studies. We have found that the inhibitor in the S configuration binds into the BCL active site in the same manner as the R isomer, with an important difference: while in case of the R-inhibitor the H-bond between its alcohol oxygen and catalytic His286 can be formed, in the case of the S-inhibitor this is not possible. Molecular modeling for both E1 enantiomers revealed orientations in which all hydrogen bonds characteristic of productive binding are formed. To check the possibility of chemical transformation, four different orientations of the substrate (two for each enantiomer) were chosen, and a series of ab initio QM/MM calculations were accomplished. Starting from the covalent complex, we modeled the ester (E1) hydrolysis and the alcohol (1) esterification. The calculations revealed that ester release is possible starting with all four covalent complexes. Alcohol release from the BCL-E1 complex in which the S-substrate is bound in the same manner as the S-inhibitor in the crystal structure however is not possible. These results show that the crystallographically determined binding modes should be taken with caution when modeling chemical reactions.

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