1KUL

GLUCOAMYLASE, GRANULAR STARCH-BINDING DOMAIN, NMR, 5 STRUCTURES


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 100 
  • Conformers Submitted: 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Solution structure of the granular starch binding domain of glucoamylase from Aspergillus niger by nuclear magnetic resonance spectroscopy.

Sorimachi, K.Jacks, A.J.Le Gal-Coeffet, M.F.Williamson, G.Archer, D.B.Williamson, M.P.

(1996) J Mol Biol 259: 970-987

  • DOI: 10.1006/jmbi.1996.0374
  • Primary Citation of Related Structures:  
    1KUL, 1KUM

  • PubMed Abstract: 
  • The solution structure of the granular starch binding domain (SBD) of glucoamylase 1 from Aspergillus niger has been determined by heteronuclear multidimensional nuclear magnetic resonance spectroscopy and simulated annealing. A total of 1092 nuclear Overhauser enhancement-derived 1H-1H distance constraints, 137 dihedral constraints and 86 hydrogen bond constraints were incorporated into an X-PLOR simulated annealing and refinement protocol ...

    The solution structure of the granular starch binding domain (SBD) of glucoamylase 1 from Aspergillus niger has been determined by heteronuclear multidimensional nuclear magnetic resonance spectroscopy and simulated annealing. A total of 1092 nuclear Overhauser enhancement-derived 1H-1H distance constraints, 137 dihedral constraints and 86 hydrogen bond constraints were incorporated into an X-PLOR simulated annealing and refinement protocol. The family of calculated structures shows a well defined beta-sheet structure consisting of one parallel and six antiparallel pairs of beta-strands which forms an open-sided beta-barrel. The root-mean-square deviation (rmsd) of 53 individual structures to the calculated average structure for the backbone atoms of residues excluding the N terminus and two mobile loops is 0.57(+/-0.10) A while the rmsd for backbone atoms in beta-strands is 0.45(+/-0.08) A. Structural features of the SBD in solution are compared to the X-ray crystal structure of a homologous domain of cyclodextrin glycosyltransferase (CGTase) in the free and bound forms. Titration studies with two ligands, maltoheptaose and beta-cyclodextrin, show the existence of two binding sites. Examination of the tertiary structures shows these two sites to be at one end of the molecule on opposite faces. The majority of residues showing the largest 1H and 15N chemical shift changes are located in loop regions. Many residues implicated in binding, based on these changes, are similar in location to previously identified binding site residues in the crystal structures of CGTase. Overall, the shift changes are small indicating that the SBD does not undergo large conformational changes upon ligand binding.


    Related Citations: 
    • 1H and 15N Assignments and Secondary Structure of the Starch-Binding Domain of Glucoamylase from Aspergillus Niger
      Jacks, A.J., Sorimachi, K., Le Gal-Coeffet, M.F., Williamson, G., Archer, D.B., Williamson, M.P.
      (1995) Eur J Biochem 233: 568

    Organizational Affiliation

    Krebs Institute for Biomolecular Research, Department of Molecular Biology and Biotechnology, University of Sheffield, UK.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
GLUCOAMYLASEA108Aspergillus nigerMutation(s): 0 
Gene Names: A. NIGER GLAAGLAA
EC: 3.2.1.3
UniProt
Find proteins for P69328 (Aspergillus niger)
Explore P69328 
Go to UniProtKB:  P69328
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP69328
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 100 
  • Conformers Submitted: 

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1996-07-11
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2022-02-23
    Changes: Database references, Derived calculations, Other