1LF6

CRYSTAL STRUCTURE OF BACTERIAL GLUCOAMYLASE

• PDB DOI: https://doi.org/10.2210/pdb1LF6/pdb

• Classification: HYDROLASE
• Organism(s): Thermoanaerobacterium thermosaccharolyticum
• Mutation(s): No 


• Deposited: 2002-04-10 Released: 2003-02-25 
• Deposition Author(s): Aleshin, A.E., Feng, P.-H., Honzatko, R.B., Reilly, P.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.232 
• R-Value Work: 0.194 

Literature

Crystal structure and evolution of prokaryotic glucoamylase

Aleshin, A.E., Feng, P.-H., Honzatko, R.B., Reilly, P.J.

(2003) J Mol Biol 327: 61-73

• PubMed: 12614608 
• DOI: https://doi.org/10.1016/s0022-2836(03)00084-6
• Primary Citation of Related Structures:  
  1LF6, 1LF9


• PubMed Abstract: 
  

  The first crystal structures of a two-domain, prokaryotic glucoamylase were determined to high resolution from the clostridial species Thermoanaerobacterium thermosaccharolyticum with and without acarbose. The N-terminal domain has 18 antiparallel strands arranged in beta-sheets of a super-beta-sandwich. The C-terminal domain is an (alpha/alpha)(6) barrel, lacking the peripheral subdomain of eukaryotic glucoamylases. Interdomain contacts are common to all prokaryotic Family GH15 proteins. Domains similar to those of prokaryotic glucoamylases in maltose phosphorylases (Family GH65) and glycoaminoglycan lyases (Family PL8) suggest evolution from a common ancestor. Eukaryotic glucoamylases may have evolved from prokaryotic glucoamylases by the substitution of the N-terminal domain with the peripheral subdomain and by the addition of a starch-binding domain.

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Organizational Affiliation: 

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

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 153.37 kDa 
• Atom Count: 11,584 
• Modelled Residue Count: 1,348 
• Deposited Residue Count: 1,368 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
glucoamylase	A, B	684	Thermoanaerobacterium thermosaccharolyticum	Mutation(s): 0  EC: 3.2.1.3
UniProt
Find proteins for O85672 (Thermoanaerobacterium thermosaccharolyticum) Explore O85672  Go to UniProtKB:  O85672

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	C [auth A], D [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.232 
• R-Value Work: 0.194 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 81.186	α = 90
b = 102.513	β = 90
c = 164.82	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
SOLVE	phasing
CNS	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2003-02-25 
Deposition Author(s): Aleshin, A.E., Feng, P.-H., Honzatko, R.B., Reilly, P.J.

Revision History  

• Version 1.0: 2003-02-25
  Type: Initial release
  
• Version 1.1: 2008-04-28
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2018-01-31
  Changes: Experimental preparation
• Version 1.4: 2024-02-14
  Changes: Data collection, Database references, Derived calculations