Structural features of the Nostoc punctiforme debranching enzyme reveal the basis of its mechanism and substrate specificity
Arti Baban Dumbrepatil
Department of Food Science and Technology, Chungbuk National University, Chungju, 361-763, Korea
Medical Proteomics Research Center, Korea Research Institute of Biosciences and Biotechnology, 111 Gwahango, Yuseong-gu, Daejon 305-806, Korea
Search for more papers by this authorJi-Hye Choi
Center for Agricultural Biomaterials and Department of Food Science and Biotechnology, Seoul National University, Seoul 151-192, Korea
Department of Smart Foods and Drugs, Graduate School of Inje University, Gimhae 621-740, Korea
Search for more papers by this authorJong Tae Park
Center for Agricultural Biomaterials and Department of Food Science and Biotechnology, Seoul National University, Seoul 151-192, Korea
Department of Biology, University of Incheon, Incheon 402-749, Korea
Search for more papers by this authorMyo-Jeong Kim
Department of Smart Foods and Drugs, Graduate School of Inje University, Gimhae 621-740, Korea
Search for more papers by this authorTae Jip Kim
Department of Food Science and Technology, Chungbuk National University, Chungju, 361-763, Korea
Search for more papers by this authorCorresponding Author
Eui-Jeon Woo
Medical Proteomics Research Center, Korea Research Institute of Biosciences and Biotechnology, 111 Gwahango, Yuseong-gu, Daejon 305-806, Korea
Eui-Jeon Woo, Medical Proteomics Research Center, Korea Research Institute of Biosciences and Biotechnology, 111 Gwahango, Yuseong-gu, Daejon 305-806, Korea===
Kwan Hwa Park, Center for Agricultural Biomaterials and Department of Food Science and Biotechnology, Seoul National University, Seoul 151-192, Korea===
Search for more papers by this authorCorresponding Author
Kwan Hwa Park
Center for Agricultural Biomaterials and Department of Food Science and Biotechnology, Seoul National University, Seoul 151-192, Korea
Department of Biology, University of Incheon, Incheon 402-749, Korea
Eui-Jeon Woo, Medical Proteomics Research Center, Korea Research Institute of Biosciences and Biotechnology, 111 Gwahango, Yuseong-gu, Daejon 305-806, Korea===
Kwan Hwa Park, Center for Agricultural Biomaterials and Department of Food Science and Biotechnology, Seoul National University, Seoul 151-192, Korea===
Search for more papers by this authorArti Baban Dumbrepatil
Department of Food Science and Technology, Chungbuk National University, Chungju, 361-763, Korea
Medical Proteomics Research Center, Korea Research Institute of Biosciences and Biotechnology, 111 Gwahango, Yuseong-gu, Daejon 305-806, Korea
Search for more papers by this authorJi-Hye Choi
Center for Agricultural Biomaterials and Department of Food Science and Biotechnology, Seoul National University, Seoul 151-192, Korea
Department of Smart Foods and Drugs, Graduate School of Inje University, Gimhae 621-740, Korea
Search for more papers by this authorJong Tae Park
Center for Agricultural Biomaterials and Department of Food Science and Biotechnology, Seoul National University, Seoul 151-192, Korea
Department of Biology, University of Incheon, Incheon 402-749, Korea
Search for more papers by this authorMyo-Jeong Kim
Department of Smart Foods and Drugs, Graduate School of Inje University, Gimhae 621-740, Korea
Search for more papers by this authorTae Jip Kim
Department of Food Science and Technology, Chungbuk National University, Chungju, 361-763, Korea
Search for more papers by this authorCorresponding Author
Eui-Jeon Woo
Medical Proteomics Research Center, Korea Research Institute of Biosciences and Biotechnology, 111 Gwahango, Yuseong-gu, Daejon 305-806, Korea
Eui-Jeon Woo, Medical Proteomics Research Center, Korea Research Institute of Biosciences and Biotechnology, 111 Gwahango, Yuseong-gu, Daejon 305-806, Korea===
Kwan Hwa Park, Center for Agricultural Biomaterials and Department of Food Science and Biotechnology, Seoul National University, Seoul 151-192, Korea===
Search for more papers by this authorCorresponding Author
Kwan Hwa Park
Center for Agricultural Biomaterials and Department of Food Science and Biotechnology, Seoul National University, Seoul 151-192, Korea
Department of Biology, University of Incheon, Incheon 402-749, Korea
Eui-Jeon Woo, Medical Proteomics Research Center, Korea Research Institute of Biosciences and Biotechnology, 111 Gwahango, Yuseong-gu, Daejon 305-806, Korea===
Kwan Hwa Park, Center for Agricultural Biomaterials and Department of Food Science and Biotechnology, Seoul National University, Seoul 151-192, Korea===
Search for more papers by this authorAbstract
The debranching enzyme Nostoc punctiforme debranching enzyme (NPDE) from the cyanobacterium Nostoc punctiforme (PCC73102) hydrolyzes the α-1,6 glycosidic linkages of malto-oligosaccharides. Despite its high homology to cyclodextrin/pullulan (CD/PUL)-hydrolyzing enzymes from glycosyl hydrolase 13 family (GH-13), NPDE exhibits a unique catalytic preference for longer malto-oligosaccharides (>G8), performing hydrolysis without the transgylcosylation or CD-hydrolyzing activities of other GH-13 enzymes. To investigate the molecular basis for the property of NPDE, we determined the structure of NPDE at 2.37-Å resolution. NPDE lacks the typical N-terminal domain of other CD/PUL-hydrolyzing enzymes and forms an elongated dimer in a head-to-head configuration. The unique orientation of residues 25–55 in NPDE yields an extended substrate binding groove from the catalytic center to the dimeric interface. The substrate binding groove with a lengthy cavity beyond the −1 subsite exhibits a suitable architecture for binding longer malto-oligosaccharides (>G8). These structural results may provide a molecular basis for the substrate specificity and catalytic function of this cyanobacterial enzyme, distinguishing it from the classical neopullulanases and CD/PUL-hydrolyzing enzymes. Proteins 2010. © 2009 Wiley-Liss, Inc.
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