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

Experimental Data Snapshot

  • Resolution: 2.37 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.215 
  • R-Value Observed: 0.215 

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Structural Features of the Nostoc Punctiforme Debranching Enzyme Reveal the Basis of its Mechanism and Substrate Specificity.

Dumbrepatil, A.-B.Choi, J.-H.Park, J.T.Kim, M.J.Kim, T.J.Woo, E.-J.Park, K.-H.

(2010) Proteins 78: 348

  • DOI: https://doi.org/10.1002/prot.22548
  • Primary Citation of Related Structures:  
    2WC7, 2WCS, 2WKG

  • 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.

  • Organizational Affiliation

    Department of Food Science and Technology, Chungbuk National University, Chungju, 361-763, Korea.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
ALPHA AMYLASE, CATALYTIC REGION488Nostoc punctiformeMutation(s): 0 
Find proteins for B2IUW9 (Nostoc punctiforme (strain ATCC 29133 / PCC 73102))
Explore B2IUW9 
Go to UniProtKB:  B2IUW9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB2IUW9
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.37 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.215 
  • R-Value Observed: 0.215 
  • Space Group: P 61 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 86.968α = 90
b = 86.968β = 90
c = 262.393γ = 120
Software Package:
Software NamePurpose

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-09-29
    Type: Initial release
  • Version 1.1: 2011-06-16
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2023-12-13
    Changes: Data collection, Database references, Other, Refinement description