3WEO

Sugar beet alpha-glucosidase with acarviosyl-maltohexaose


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free: 0.150 
  • R-Value Work: 0.123 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Structural advantage of sugar beet alpha-glucosidase to stabilize the Michaelis complex with long-chain substrate

Tagami, T.Yamashita, K.Okuyama, M.Mori, H.Yao, M.Kimura, A.

(2014) J.Biol.Chem. 290: 1796-1803

  • DOI: 10.1074/jbc.M114.606939
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The α-glucosidase from sugar beet (SBG) is an exo-type glycosidase. The enzyme has a pocket-shaped active site, but efficiently hydrolyzes longer maltooligosaccharides and soluble starch due to lower Km and higher kcat/Km for such substrates. To obta ...

    The α-glucosidase from sugar beet (SBG) is an exo-type glycosidase. The enzyme has a pocket-shaped active site, but efficiently hydrolyzes longer maltooligosaccharides and soluble starch due to lower Km and higher kcat/Km for such substrates. To obtain structural insights into the mechanism governing its unique substrate specificity, a series of acarviosyl-maltooligosaccharides was employed for steady-state kinetic and structural analyses. The acarviosyl-maltooligosaccharides have a longer maltooligosaccharide moiety compared with the maltose moiety of acarbose, which is known to be the transition state analog of α-glycosidases. The clear correlation obtained between log Ki of the acarviosyl-maltooligosaccharides and log(Km/kcat) for hydrolysis of maltooligosaccharides suggests that the acarviosyl-maltooligosaccharides are transition state mimics. The crystal structure of the enzyme bound with acarviosyl-maltohexaose reveals that substrate binding at a distance from the active site is maintained largely by van der Waals interactions, with the four glucose residues at the reducing terminus of acarviosyl-maltohexaose retaining a left-handed single-helical conformation, as also observed in cycloamyloses and single helical V-amyloses. The kinetic behavior and structural features suggest that the subsite structure suitable for the stable conformation of amylose lowers the Km for long-chain substrates, which in turn is responsible for higher specificity of the longer substrates.


    Organizational Affiliation

    From the Research Faculty of Agriculture, okuyama@abs.agr.hokudai.ac.jp.,Graduate School of Life Science, and Faculty of Advanced Life Science, Hokkaido University, Sapporo 060-8589, Japan.,From the Research Faculty of Agriculture, kimura@abs.agr.hokudai.ac.jp.,Graduate School of Life Science, and.,From the Research Faculty of Agriculture.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Alpha-glucosidase
A
913Beta vulgarisMutation(s): 0 
Gene Names: Agl
EC: 3.2.1.20
Find proteins for L0N7E5 (Beta vulgaris)
Go to UniProtKB:  L0N7E5
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

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A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

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A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
FUC
Query on FUC

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A
ALPHA-L-FUCOSE
C6 H12 O5
SHZGCJCMOBCMKK-SXUWKVJYSA-N
 Ligand Interaction
GLC
Query on GLC

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A
ALPHA-D-GLUCOSE
C6 H12 O6
WQZGKKKJIJFFOK-DVKNGEFBSA-N
 Ligand Interaction
NAG
Query on NAG

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A
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
ACR
Query on ACR

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A
ALPHA-ACARBOSE
1,4-DEOXY-4-((5-HYDROXYMETHYL-2,3,4-TRIHYDROXYCYCLOHEX-5,6-ENYL)AMINO)FRUCTOSE
C25 H43 N O18
XUFXOAAUWZOOIT-WVJZLWNXSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free: 0.150 
  • R-Value Work: 0.123 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 86.166α = 90.00
b = 99.154β = 90.00
c = 107.354γ = 90.00
Software Package:
Software NamePurpose
XSCALEdata scaling
XDSdata scaling
PHENIXphasing
PHENIXrefinement
PDB_EXTRACTdata extraction
BSSdata collection
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-07-16
    Type: Initial release
  • Version 1.1: 2014-07-30
    Type: Other
  • Version 1.2: 2014-12-31
    Type: Database references
  • Version 1.3: 2015-02-04
    Type: Database references