2WC7

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.37 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.215 
  • R-Value Observed: 0.215 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

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: 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/P ...

    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.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
ALPHA AMYLASE, CATALYTIC REGIONA488Nostoc punctiformeMutation(s): 0 
EC: 3.2.1.54
Find proteins for B2IUW9 (Nostoc punctiforme (strain ATCC 29133 / PCC 73102))
Explore B2IUW9 
Go to UniProtKB:  B2IUW9
Protein Feature View
Expand
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • 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
CNSrefinement
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • 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