1AGM

Refined structure for the complex of acarbose with glucoamylase from Aspergillus awamori var. x100 to 2.4 angstroms resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

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: 15631-15639


  • PubMed Abstract: 
  • The three-dimensional structure of the pseudotetrasaccharide acarbose complexed with glucoamylase II(471) from Aspergillus awamori var. X100 has been determined to 2.4-A resolution. The model includes residues corresponding to 1-471 of glucoamylase I ...

    The three-dimensional structure of the pseudotetrasaccharide acarbose complexed with glucoamylase II(471) from Aspergillus awamori var. X100 has been determined to 2.4-A resolution. The model includes residues corresponding to 1-471 of glucoamylase I from Aspergillus niger, a single molecule of bound acarbose, and 535 sites for water molecules. The crystallographic R factor from refinement is 0.124, and the root-mean-squared deviation in bond distances is 0.013 A. Electron density for a single molecule of bound acarbose defines what may be the first four subsites in the binding of extended maltooligosaccharides. Hydrogen bonds between acarbose and the enzyme involve Arg54, Asp55, Arg305, carbonyl177, main chain amide121, Glu179, Glu180, and carbonyl179. Glu179 forms a salt link to the imino linkage between the first and second residues of acarbose. This buried salt link probably contributes significantly to the unusually tight association (Kd approximately 10(-12) M) of acarbose with glucoamylase. In addition, a significant hydrophobic contact between the third residue of acarbose and the side chain of Trp120 distorts the three-center angle of the glucosidic linkage between the second and third residues of acarbose. A water molecule (water500) hydrogen bonds to Glu400 and the 6-hydroxyl of the valienamine moiety of acarbose and is at an approximate distance of 3.7 A from the "anomeric" carbon of the inhibitor. The relevance of the acarbose-glucoamylase complex to the mechanism of enzymic hydrolysis of oligosaccharides is discussed.


    Related Citations: 
    • 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
    • Crystal Structure of Glucoamylase from Aspergillus Awamori Var. X100 to 2.2 Angstroms Resolution
      Aleshin, A.E.,Golubev, A.,Firsov, L.M.,Honzatko, R.B.
      (1992) J.Biol.Chem. 267: 19291
    • Refined Structure of the Complex of 1-Deoxynojirimycin with Glucoamylase from Aspergillus Awamori Var. X100 to 2.4 Angstroms Resolution
      Harris, E.M.S.,Aleshin, A.E.,Firsov, L.M.,Honzatko, R.B.
      (1993) Biochemistry 32: 1618


    Organizational Affiliation

    Department of Molecular Biology, St. Petersburg Nuclear Physics Institute, Russia.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
GLUCOAMYLASE-471
A
470Aspergillus 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
NAG
Query on NAG

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Download CCD File 
A
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
ACR
Query on ACR

Download SDF File 
Download CCD File 
A
ALPHA-ACARBOSE
1,4-DEOXY-4-((5-HYDROXYMETHYL-2,3,4-TRIHYDROXYCYCLOHEX-5,6-ENYL)AMINO)FRUCTOSE
C25 H43 N O18
XUFXOAAUWZOOIT-WVJZLWNXSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
ACRKd: ~0.001 nM BINDINGMOAD
ACRKi: 0.001 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 116.700α = 90.00
b = 103.900β = 90.00
c = 48.340γ = 90.00
Software Package:
Software NamePurpose
PROLSQrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1994-09-30
    Type: Initial release
  • Version 1.1: 2008-03-03
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Non-polymer description, Version format compliance
  • Version 1.3: 2017-11-29
    Type: Derived calculations, Other