Abstract: The gene of pgd S and ggt were cloned from Bacillus subtilis 115 genome DNA by PCR. Physical and chemical properties,trans- membrane domains,sub- cellular localization,secondary structures,and three dimensional structure modeling of Pgd S and GGT were analyzed using the software of Ex PASy- Prot Param,Server3.0 Signal P,TMHMM Server and Tmpred,PSORTB,Predict Protein,Swiss- Model Workspace,respectively. The results showed that the pgd S genes contained 1242 nucleotides and code 414 amino acids. The ggt genes contained 1764 nucleotides and code 588 amino acids. By amino acid sequence analysis,there was a strong transmembrane domain in the N side of GGT. Pgd S and GGT were stable hydrophilic proteins,existence signal peptide and its subcellular localization in the cell wall and outside of cell,respectively. The secondary structure of Pgd S and GGT were mainly loop,which accounted for 53.27% and 52.47% respectively.The process of γ- PGA synthesis and related research were effectively controlled through the analysis of the structure characteristics of theγ- PGA degradation enzyme.