5ZCC | pdb_00005zcc

Crystal structure of Alpha-glucosidase in complex with maltose


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 
    0.189 (Depositor), 0.191 (DCC) 
  • R-Value Work: 
    0.164 (Depositor), 0.167 (DCC) 
  • R-Value Observed: 
    0.165 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 2.1 of the entry. See complete history

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

  • 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.


  • Organizational Affiliation
    • Research Faculty of Agriculture, Hokkaido University, Sapporo, Japan.

Macromolecule Content 

  • Total Structure Weight: 65.39 kDa 
  • Atom Count: 5,340 
  • Modeled Residue Count: 545 
  • Deposited Residue Count: 555 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Alpha-glucosidase555Bacillus sp. (in: firmicutes)Mutation(s): 0 
UniProt
Find proteins for A0ACD6B9E0 (Bacillus sp)
Explore A0ACD6B9E0 
Go to UniProtKB:  A0ACD6B9E0
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0ACD6B9E0
Sequence Annotations
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Reference Sequence

Oligosaccharides

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Entity ID: 2
MoleculeChains Length2D Diagram GlycosylationD Interactions
alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose
B
2N/A
Glycosylation Resources
GlyTouCan: G07411ON
GlyCosmos: G07411ON

Biologically Interesting Molecules (External Reference) 

1 Unique

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free:  0.189 (Depositor), 0.191 (DCC) 
  • R-Value Work:  0.164 (Depositor), 0.167 (DCC) 
  • R-Value Observed: 0.165 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 55.046α = 90
b = 84.84β = 90
c = 128.767γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-12-26
    Type: Initial release
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary
  • Version 2.1: 2023-11-22
    Changes: Data collection, Database references, Refinement description, Structure summary