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2WCS

Crystal Structure of Debranching enzyme from Nostoc punctiforme (NPDE)

Summary for 2WCS
Entry DOI10.2210/pdb2wcs/pdb
Related2WC7 2WKG
DescriptorALPHA AMYLASE, CATALYTIC REGION (2 entities in total)
Functional Keywordsmaltooligosaccharides, hydrolase, glycosidase, cyanobacteria
Biological sourceNOSTOC PUNCTIFORME
Total number of polymer chains1
Total formula weight55629.98
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 citationDumbrepatil, 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: 19768689
DOI: 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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