3EQA | pdb_00003eqa

Catalytic domain of glucoamylase from aspergillus niger complexed with tris and glycerol

• PDB DOI: https://doi.org/10.2210/pdb3EQA/pdb

• Classification: HYDROLASE
• Organism(s): Aspergillus niger
• Mutation(s): No 


• Deposited: 2008-09-30 Released: 2009-10-13 
• Deposition Author(s): Lee, J., Paetzel, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.229 (Depositor), 0.234 (DCC) 
• R-Value Work: 
  0.181 (Depositor), 0.197 (DCC) 
• R-Value Observed: 
  0.184 (Depositor) 

Starting Model: experimental

Literature

Structure of the catalytic domain of glucoamylase from Aspergillus niger.

Lee, J., Paetzel, M.

(2011) Acta Crystallogr Sect F Struct Biol Cryst Commun 67: 188-192

• PubMed: 21301084 
• DOI: https://doi.org/10.1107/S1744309110049390
• Primary Citation Related Structures: 
  3EQA


• PubMed Abstract: 
  

  Glucoamylase from Aspergillus niger is an industrially important biocatalyst that is utilized in the mass production of glucose from raw starch or soluble oligosaccharides. The G1 isoform consists of a catalytic domain and a starch-binding domain connected by a heavily glycosylated linker region. The amino-terminal catalytic domain of the G1 isoform generated by subtilisin cleavage has been crystallized at pH 8.5, which is a significantly higher pH condition than used for previously characterized glucoamylase crystals. The refined structure at 1.9 Å resolution reveals the active site of the enzyme in complex with both Tris and glycerol molecules. The ligands display both unique and analogous interactions with the substrate-binding site when compared with previous structures of homologous enzymes bound to inhibitors.

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Organizational Affiliation: 
• Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, Canada.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 54.12 kDa 
• Atom Count: 4,107 
• Modeled Residue Count: 458 
• Deposited Residue Count: 470 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glucoamylase	A	470	Aspergillus niger	Mutation(s): 0  EC: 3.2.1.3
UniProt
Find proteins for P69328 (Aspergillus niger) Explore P69328  Go to UniProtKB:  P69328
Glycosylation
Glycosylation Sites: 9

Oligosaccharides

Help  

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
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	4		N-Glycosylation
Glycosylation Resources
GlyTouCan: G81315DD GlyCosmos: G81315DD GlyGen: G81315DD

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
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)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	C	8		N-Glycosylation
Glycosylation Resources
GlyTouCan: G83582BK GlyCosmos: G83582BK GlyGen: G83582BK

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MAN	D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A]	alpha-D-mannopyranose C6 H12 O6 WQZGKKKJIJFFOK-PQMKYFCFSA-N
TRS	K [auth A]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C4 H12 N O3 LENZDBCJOHFCAS-UHFFFAOYSA-O
GOL	L [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.229 (Depositor), 0.234 (DCC) 
• R-Value Work:  0.181 (Depositor), 0.197 (DCC) 
• R-Value Observed: 0.184 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.826	α = 90
b = 73.222	β = 90
c = 106.793	γ = 90

Software Package:

Software Name	Purpose
BOS	data collection
PHASER	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-10-13 
Deposition Author(s): Lee, J., Paetzel, M.

Revision History  

• Version 1.0: 2009-10-13
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 1.2: 2017-10-25
  Changes: Refinement description
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Structure summary
• Version 2.1: 2023-09-06
  Changes: Data collection, Database references, Refinement description, Structure summary
• Version 2.2: 2024-10-30
  Changes: Structure summary