1GAI

GLUCOAMYLASE-471 COMPLEXED WITH D-GLUCO-DIHYDROACARBOSE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.167 
  • R-Value Work: 0.147 
  • R-Value Observed: 0.147 

wwPDB Validation 3D Report Full Report



Literature

Crystallographic complexes of glucoamylase with maltooligosaccharide analogs: relationship of stereochemical distortions at the nonreducing end to the catalytic mechanism.

Aleshin, A.E.Stoffer, B.Firsov, L.M.Svensson, B.Honzatko, R.B.

(1996) Biochemistry 35: 8319-8328

  • DOI: 10.1021/bi960321g
  • Primary Citation of Related Structures:  
    1GAI, 1GAH

  • PubMed Abstract: 
  • Crystal structures at pH 4 of complexes of glucoamylase from Aspergillus awamori var. X100 with the pseudotetrasaccharides D-gluco-dihydroacarbose and acarbose have been refined to R-factors of 0.147 and 0.131 against data to 1.7- and 2.0-A resolutio ...

    Crystal structures at pH 4 of complexes of glucoamylase from Aspergillus awamori var. X100 with the pseudotetrasaccharides D-gluco-dihydroacarbose and acarbose have been refined to R-factors of 0.147 and 0.131 against data to 1.7- and 2.0-A resolution, respectively. The two inhibitors bind in nearly identical manners, each exhibiting a dual binding mode with respect to the location of the last sugar residues. The reduced affinity of D-gluco-dihydroacarbose (K1 = 10(-8) M) relative to acarbose (K1 = 10(-12) M) may stem in part from the weakening of hydrogen bonds of the catalytic water (Wat 500) to the enzyme. Steric contacts between the nonreducing end of D-gluco-dihydroacarbose and the catalytic water perturb Wat 500 from its site of optimal hydrogen bonding to the active site. Interactions within the active site displace the 6-hydroxymethyl group of the nonreducing end of both acarbose and D-gluco-dihydroacarbose toward a more axial position. In the case of D-gluco-dihydroacarbose the shift in the position of the 6-hydroxymethyl group occurs with a 12 degrees change in two dihedral angles of the glucopyranose ring toward a half-chair conformation. The observed conformational distortion of the first residue of D-gluco-dihydroacarbose is consistent with the generation of a glucopyranosyl cation in the transition state. Comparable distortions of stereochemistry in model compounds require approximately 2 kcal/mol, not more than 25% of the energy necessary to form the half-chair conformation in glucose. The magnitude of stereochemical distortion observed in the active site of glucoamylase suggests that favorable electrostatic interactions between the putative glucopyranosyl cation intermediate and the active site must be more important in stabilizing the transition state than mechanical distortion of the substrate.


    Related Citations: 
    • Refined Structure for the Complex of D-Gluco-Dihydroacarbose with Glucoamylase from Aspergillus Awamori Var. X100 to 2.2 A Resolution: Dual Conformations for Extended Inhibitors Bound to the Active Site of Glucoamylase
      Stoffer, B., Aleshin, A.E., Firsov, L.M., Svensson, B., Honzatko, R.B.
      (1995) FEBS Lett 358: 57
    • Refined Crystal Structures of Glucoamylase from Aspergillus Awamori Var. X100
      Aleshin, A.E., Hoffman, C., Firsov, L.M., Honzatko, R.B.
      (1994) J Mol Biol 238: 575
    • Refined Structure for the Complex of Acarbose with Glucoamylase from Aspergillus Awamori Var. X100 to 2.4-A Resolution
      Aleshin, A.E., Firsov, L.M., Honzatko, R.B.
      (1994) J Biol Chem 269: 15631
    • Refined Structure for the Complex of 1-Deoxynojirimycin with Glucoamylase from Aspergillus Awamori Var. X100 to 2.4-A Resolution
      Harris, E.M., Aleshin, A.E., Firsov, L.M., Honzatko, R.B.
      (1993) Biochemistry 32: 1618
    • Crystal Structure of Glucoamylase from Aspergillus Awamori Var. X100 to 2.2-A Resolution
      Aleshin, A., Golubev, A., Firsov, L.M., Honzatko, R.B.
      (1992) J Biol Chem 267: 19291

    Organizational Affiliation

    Department of Biochemistry and Biophysics, Iowa State University, Ames, 50011, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
GLUCOAMYLASE-471A472Aspergillus awamoriMutation(s): 0 
Gene Names: GLAA
EC: 3.2.1.3
Find proteins for P69327 (Aspergillus awamori)
Explore P69327 
Go to UniProtKB:  P69327
Protein Feature View
Expand
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChainsChain Length2D Diagram Glycosylation
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
B
5 N-Glycosylation
Entity ID: 3
MoleculeChainsChain Length2D Diagram Glycosylation
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
C
9 N-Glycosylation
Entity ID: 4
MoleculeChainsChain Length2D Diagram Glycosylation
4,6-dideoxy-4-{[(1S,2S,3S,4R,5R)-2,3,4-trihydroxy-5-(hydroxymethyl)cyclohexyl]amino}-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose
D
3 N/A N/A
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MAN
Query on MAN

Download CCD File 
A
alpha-D-mannopyranose
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
GACKi :  10   nM  PDBBind
GACKi:  10   nM  Binding MOAD
Biologically Interesting Molecules (External Reference) 1 Unique
Entity ID: 4
IDChainsNameType/Class2D Diagram3D Interactions
PRD_900061
Query on PRD_900061
Ddihydro-alpha-acarboseOligosaccharide /  Inhibitor

--

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.167 
  • R-Value Work: 0.147 
  • R-Value Observed: 0.147 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 116.9α = 90
b = 104.4β = 90
c = 48.4γ = 90
Software Package:
Software NamePurpose
XENGENdata collection
XENGENdata reduction
X-PLORmodel building
X-PLORrefinement
XENGENdata scaling
X-PLORphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1996-08-17
    Type: Initial release
  • Version 1.1: 2008-03-10
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Atomic model, Version format compliance
  • Version 1.3: 2011-10-05
    Changes: Derived calculations
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Other, Structure summary