3GLY

REFINED CRYSTAL STRUCTURES OF GLUCOAMYLASE FROM ASPERGILLUS AWAMORI VAR. X100


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

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: 575-591

  • DOI: 10.1006/jmbi.1994.1316
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The refined crystal structures of a proteolytic fragment of glucoamylase from Aspergillus awamori var. X100 have been determined at pH 6 and 4 to a resolution of 2.2 A and 2.4 A, respectively. The models include the equivalent of residues 1 to 471 of ...

    The refined crystal structures of a proteolytic fragment of glucoamylase from Aspergillus awamori var. X100 have been determined at pH 6 and 4 to a resolution of 2.2 A and 2.4 A, respectively. The models include the equivalent of residues 1 to 471 of glucoamylase from Aspergillus niger and a complete interpretation of the solvent structure. The R-factors of the pH 6 and 4 structures are 0.14 and 0.12, respectively, with root-mean-square deviations of 0.014 A and 0.012 A from expected bondlengths. The enzyme has the general shape of a doughnut. The "hole" of the doughnut consists of a barrier of hydrophobic residues at the center, which separates two water-filled voids, one of which serves as the active site. Three clusters of water molecules extend laterally from the active site. One of the lateral clusters connects the deepest recess of the active site to the surface of the enzyme. The most significant difference in the pH 4 and 6 structures is the thermal parameter of water 500, the putative nucleophile in the hydrolysis of maltooligosaccharides. Water 500 is associated more tightly with the enzyme at pH 4 (the pH of optimum catalysis) than at pH 6. In contrast to water 500, Glu179, the putative catalytic acid of glucoamylase, retains the same conformation in both structures and is in an environment that would favor the ionized, rather than the acid form of the side-chain. Glycosyl chains of 5 and 8 sugar residues are linked to Asparagines 171 and 395, respectively. The conformations of the two glycosyl chains are similar, being superimposable on each other with a root-mean-square discrepancy of 1.9 A. The N-glycosyl chains hydrogen bond to the surface of the protein through their terminal sugars, but otherwise do not interact strongly with the enzyme. The structures have ten serine/threonine residues, to each of which is linked a single mannose sugar. The structure of the ten O-glycosylated residues taken together suggests a well-defined conformation for proteins that have extensive O-glycosylation of their polypeptide chain.


    Related Citations: 
    • Refined Structure for the Complex of Acarbose with Glucoamylase from Aspergillus Awamori Var. X100 to 2.4 Angstroms Resolution
      Aleshin, A.E.,Firsov, L.M.,Honzatko, R.B.
      (1994) J.Biol.Chem. 269: 15631
    • 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
    • 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


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
GLUCOAMYLASE-471
A
470Aspergillus awamoriMutation(s): 0 
Gene Names: GLAA
EC: 3.2.1.3
Find proteins for P69327 (Aspergillus awamori)
Go to UniProtKB:  P69327
Small Molecules
Ligands 3 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

Download SDF File 
Download CCD File 
A
BETA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-RWOPYEJCSA-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
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 116.700α = 90.00
b = 104.300β = 90.00
c = 48.490γ = 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: 1994-11-01
    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