1GAI

GLUCOAMYLASE-471 COMPLEXED WITH D-GLUCO-DIHYDROACARBOSE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.167 
  • R-Value Work: 0.147 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

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:  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 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
    • 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
    • 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
    • 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 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


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
GLUCOAMYLASE-471
A
472Aspergillus awamoriGene Names: GLAA
EC: 3.2.1.3
Find proteins for P69327 (Aspergillus awamori)
Go to UniProtKB:  P69327
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MAN
Query on MAN

Download SDF File 
Download CCD File 
A
ALPHA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
 Ligand Interaction
BMA
Query on BMA

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Download CCD File 
A
BETA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-RWOPYEJCSA-N
 Ligand Interaction
GAC
Query on GAC

Download SDF File 
Download CCD File 
A
DIHYDRO-ACARBOSE
C25 H45 N O18
CUAQESWNTOXZJZ-RTNAABQMSA-N
 Ligand Interaction
NAG
Query on NAG

Download SDF File 
Download CCD File 
A
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
GACKi: 10 nM BINDINGMOAD
GACKi: 10 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.167 
  • R-Value Work: 0.147 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 116.900α = 90.00
b = 104.400β = 90.00
c = 48.400γ = 90.00
Software Package:
Software NamePurpose
XENGENdata scaling
X-PLORrefinement
X-PLORmodel building
X-PLORphasing
XENGENdata collection
XENGENdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1996-08-17
    Type: Initial release
  • Version 1.1: 2008-03-10
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Atomic model, Version format compliance
  • Version 1.3: 2011-10-05
    Type: Derived calculations