2WCS
Crystal Structure of Debranching enzyme from Nostoc punctiforme (NPDE)
Summary for 2WCS
Entry DOI | 10.2210/pdb2wcs/pdb |
Related | 2WC7 2WKG |
Descriptor | ALPHA AMYLASE, CATALYTIC REGION (2 entities in total) |
Functional Keywords | maltooligosaccharides, hydrolase, glycosidase, cyanobacteria |
Biological source | NOSTOC PUNCTIFORME |
Total number of polymer chains | 1 |
Total formula weight | 55629.98 |
Authors | Dumbrepatil, A.B.,Choi, J.H.,Nam, S.H.,Park, K.H.,Woo, E.J. (deposition date: 2009-03-16, release date: 2009-09-29, Last modification date: 2023-12-13) |
Primary citation | Dumbrepatil, A.B.,Choi, J.H.,Park, J.T.,Kim, M.J.,Kim, T.J.,Woo, E.J.,Park, K.H. Structural Features of the Nostoc Punctiforme Debranching Enzyme Reveal the Basis of its Mechanism and Substrate Specificity. Proteins, 78:348-, 2010 Cited by PubMed 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. PubMed: 19768689DOI: 10.1002/PROT.22548 PDB entries with the same primary citation |
Experimental method | X-RAY DIFFRACTION (2.8 Å) |
Structure validation
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