2WC7

Crystal structure of Nostoc Punctiforme Debranching Enzyme(NPDE)(Acarbose soaked)

Summary for 2WC7

• Entry DOI: 10.2210/pdb2wc7/pdb
• Related: 2WCS 2WKG
• Descriptor: ALPHA AMYLASE, CATALYTIC REGION (2 entities in total)
• Functional Keywords: cd/pul-hydrolyzing enzymes, hydrolase, glycosidase, neopullulanse
• Biological source: NOSTOC PUNCTIFORME
• Total number of polymer chains: 1
• Total formula weight: 55629.98

Authors

Dumbrepatil, A.-B.,Song, H.-N.,Choi, J.-H.,Park, K.-H.,Woo, E.-J. (deposition date: 2009-03-10, 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

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

Experimental method

X-RAY DIFFRACTION (2.37 Å)