5ZCB | pdb_00005zcb

Crystal structure of Alpha-glucosidase

• PDB DOI: https://doi.org/10.2210/pdb5ZCB/pdb

• Classification: HYDROLASE
• Organism(s): Bacillus sp. (in: firmicutes)
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2018-02-16 Released: 2018-12-26 
• Deposition Author(s): Kato, K., Saburi, W., Yao, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 
  0.215 (Depositor), 0.218 (DCC) 
• R-Value Work: 
  0.179 (Depositor), 0.186 (DCC) 
• R-Value Observed: 
  0.181 (Depositor) 

Starting Model: experimental

Literature

Function and structure of GH13_31 alpha-glucosidase with high alpha-(1→4)-glucosidic linkage specificity and transglucosylation activity.

Auiewiriyanukul, W., Saburi, W., Kato, K., Yao, M., Mori, H.

(2018) FEBS Lett 592: 2268-2281

• PubMed: 29870070 
• DOI: https://doi.org/10.1002/1873-3468.13126
• Primary Citation Related Structures: 
  5ZCB, 5ZCC, 5ZCD, 5ZCE


• PubMed Abstract: 
  

  α-Glucosidase hydrolyzes α-glucosides and transfers α-glucosyl residues to an acceptor through transglucosylation. In this study, GH13_31 α-glucosidase BspAG13_31A with high transglucosylation activity is reported in Bacillus sp. AHU2216 and biochemically and structurally characterized. This enzyme is specific to α-(1→4)-glucosidic linkage as substrates and transglucosylation products. Maltose is the most preferred substrate. Crystal structures of BspAG13_31A wild-type for the substrate-free form and inactive acid/base mutant E256Q in complexes with maltooligosaccharides were solved at 1.6-2.5 Å resolution. BspAG13_31A has a catalytic domain folded by an (β/α) ₈ -barrel. In subsite +1, Ala200 and His203 on β→α loop 4 and Asn258 on β→α loop 5 are involved in the recognition of maltooligosaccharides. Structural basis for specificity of GH13_31 enzymes to α-(1→4)-glucosidic linkage is first described.

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Organizational Affiliation: 
• Research Faculty of Agriculture, Hokkaido University, Sapporo, Japan.
Faculty of Advanced Life Science, Hokkaido University, Sapporo, Japan.

Biological Assembly 1  

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

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 65.05 kDa 
• Atom Count: 4,708 
• Modeled Residue Count: 546 
• Deposited Residue Count: 555 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Alpha-glucosidase	A	555	Bacillus sp. (in: firmicutes)	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CA	B [auth A], C [auth A], D [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free:  0.215 (Depositor), 0.218 (DCC) 
• R-Value Work:  0.179 (Depositor), 0.186 (DCC) 
• R-Value Observed: 0.181 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.893	α = 90
b = 84.856	β = 90
c = 128.429	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-12-26 
Deposition Author(s): Kato, K., Saburi, W., Yao, M.

Revision History  

• Version 1.0: 2018-12-26
  Type: Initial release
  
• Version 1.1: 2023-11-22
  Changes: Data collection, Database references, Refinement description