Molecular Diversity

, Volume 17, Issue 2, pp 371–382 | Cite as

Optimizing lactose hydrolysis by computer-guided modification of the catalytic site of a wild-type enzyme

  • Yi-Ning Dong
  • Ling Wang
  • Qiong Gu
  • Haiqin Chen
  • Xiaoming Liu
  • Yuanda Song
  • Wei Chen
  • Arnold T. Hagler
  • Hao Zhang
  • Jun Xu
Full-Length Paper


Lactose intolerance is a serious global health problem. A lactose hydrolysis enzyme, thermostable \(\upbeta \)-galactosidase, BgaB (from Geobacillus stearothermophilus) has attracted the attention of industrial biologists because of its potential application in processing lactose-containing products. However, this enzyme experiences galactose product inhibition. Through homology modeling and molecular dynamics (MD) simulation, we have identified the galactose binding sites in the thermostable \(\upbeta \)-galactosidase BgaB (BgaB). The binding sites are formed from Glu303, Asn310, Trp311, His354, Arg109, Phe341, Try272, Asn147, Glu148, and H354; these residues are all important for enzyme catalysis. A ligand–receptor binding model has been proposed to guide site-directed BgaB mutagenesis experiments. Based upon the model and the MD simulations, we recommend mutating Arg109, Phe341, Trp311, Asn147, Asn310, Try272, and His354 to reduce galactose product inhibition. In vitro site-directed mutagenesis experiments confirmed our predictions. The success rate for mutagenesis was 66.7 %. The best BgaB mutant, F341T, can hydrolyze lactose completely, and is the most promising enzyme for use by the dairy industry. Thus, our study is a successful example of optimizing enzyme catalytic chemical reaction by computer-guided modifying the catalytic site of a wild-type enzyme.


Protein design Lactose hydrolysis  Homology modeling Molecular dynamics simulations Site-directed mutagenesis 



This study was supported in part by the Major Scientific and Technological Special Project of the Ministry of Science and Technology of China (2010ZX09102-305), the National Natural Science Foundation of China (31125021, 31171636), the National High Technology Research and Development Program of China (2011AA100905), and the Anhui provincial university natural science research Project (KJ2013B187)

Supplementary material

11030_2013_9437_MOESM1_ESM.doc (1.2 mb)
Supplementary material 1 (doc 1193 KB)


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Copyright information

© Springer Science+Business Media Dordrecht 2013

Authors and Affiliations

  • Yi-Ning Dong
    • 1
  • Ling Wang
    • 2
  • Qiong Gu
    • 2
  • Haiqin Chen
    • 1
  • Xiaoming Liu
    • 1
  • Yuanda Song
    • 1
  • Wei Chen
    • 1
  • Arnold T. Hagler
    • 3
  • Hao Zhang
    • 1
  • Jun Xu
    • 2
  1. 1.State Key Laboratory of Food Science and TechnologyJiangnan UniversityWuxiPeople’s Republic of China
  2. 2.School of Pharmaceutical Sciences & Institute of Human VirologySun Yat-sen UniversityGuangzhouPeople’s Republic of China
  3. 3.Department of ChemistryUniversity of MassachusettsAmherstUSA

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