3REN

CPF_2247, a novel alpha-amylase from Clostridium perfringens

• PDB DOI: https://doi.org/10.2210/pdb3REN/pdb

• Classification: HYDROLASE
• Organism(s): Clostridium perfringens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2011-04-04 Released: 2011-05-18 
• Deposition Author(s): Ficko-Blean, E., Stuart, C.P., Boraston, A.B.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.224 
• R-Value Work: 0.169 
• R-Value Observed: 0.172 

Literature

Structural analysis of CPF_2247, a novel alpha-amylase from Clostridium perfringens.

Ficko-Blean, E., Stuart, C.P., Boraston, A.B.

(2011) Proteins 79: 2771-2777

• PubMed: 21905105 
• DOI: https://doi.org/10.1002/prot.23116
• Primary Citation of Related Structures:  
  3REN


• PubMed Abstract: 
  

  CPF_2247 from Clostridium perfringens ATCC 13124 was identified as a putative carbohydrate-active enzyme by its low sequence identity to endo-β-1,4-glucanases belonging to family 8 of the glycoside hydrolase classification. The X-ray crystal structure of CPF_2247 determined to 2.0 Å resolution by single-wavelength anomalous dispersion using seleno-methionine-substituted protein revealed an (α/α)(6) barrel fold. A large cleft on the surface of the protein contains residues that are structurally conserved with key elements of the catalytic machinery in clan GH-M glycoside hydrolases. Assessment of CPF_2247 as a carbohydrate-active enzyme disclosed α-glucanase activity on amylose, glycogen, and malto-oligosaccharides.

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Organizational Affiliation: 

Department of Biochemistry & Microbiology, University of Victoria, Victoria, 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)

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 82.3 kDa 
• Atom Count: 6,107 
• Modelled Residue Count: 669 
• Deposited Residue Count: 700 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glycosyl hydrolase, family 8	A, B	350	Clostridium perfringens	Mutation(s): 0  Gene Names: CPF_2247
UniProt
Find proteins for A0A0H2YP60 (Clostridium perfringens (strain ATCC 13124 / DSM 756 / JCM 1290 / NCIMB 6125 / NCTC 8237 / Type A)) Explore A0A0H2YP60  Go to UniProtKB:  A0A0H2YP60

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	E [auth A], N [auth B], O [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
EDO	F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], P [auth B], Q [auth B], R [auth B], S [auth B], T [auth B], U [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
MG	C [auth A], D [auth A], M [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.224 
• R-Value Work: 0.169 
• R-Value Observed: 0.172 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 65.35	α = 90
b = 75.06	β = 90
c = 158.54	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-05-18 
Deposition Author(s): Ficko-Blean, E., Stuart, C.P., Boraston, A.B.

Revision History  

• Version 1.0: 2011-05-18
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2013-09-04
  Changes: Database references
• Version 1.3: 2024-11-06
  Changes: Data collection, Database references, Derived calculations, Structure summary