title: Structural features of the Nostoc punctiforme debranching enzyme reveal the basis of its mechanism and substrate specificity.
abstract: The debranching enzyme Nostoc punctiforme debranching enzyme (NPDE) from the cyanobacterium Nostoc punctiforme (PCC73102) hydrolyzes the alpha-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-A 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.
authors.affiliation: Department of Food Science and Technology, Chungbuk National University, Chungju, 361-763, Korea.
authors.forename: Arti Baban
authors.initials: AB
authors.lastname: Dumbrepatil
authors.forename: Ji-Hye
authors.initials: JH
authors.lastname: Choi
authors.forename: Jong Tae
authors.initials: JT
authors.lastname: Park
authors.forename: Myo-Jeong
authors.initials: MJ
authors.lastname: Kim
authors.forename: Tae Jip
authors.initials: TJ
authors.lastname: Kim
authors.forename: Eui-Jeon
authors.initials: EJ
authors.lastname: Woo
authors.forename: Kwan Hwa
authors.initials: KH
authors.lastname: Park
mesh_terms: D000595:Amino Acid Sequence; D001426:Bacterial Proteins / Q000737:chemistry*; D020134:Catalytic Domain; D018360:Crystallography, X-Ray; D008958:Models, Molecular; D008969:Molecular Sequence Data; D046937:Nostoc / Q000201:enzymology*; D011487:Protein Conformation; D055503:Protein Multimerization; D016415:Sequence Alignment; D013379:Substrate Specificity
chemical_list: D001426:Bacterial Proteins