3W37

Sugar beet alpha-glucosidase with acarbose


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.182 
  • R-Value Work: 0.154 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Molecular basis for the recognition of long-chain substrates by plant & alpha-glucosidase

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

(2013) J.Biol.Chem. 288: 19296-19303

  • DOI: 10.1074/jbc.M113.465211
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Sugar beet α-glucosidase (SBG), a member of glycoside hydrolase family 31, shows exceptional long-chain specificity, exhibiting higher kcat/Km values for longer malto-oligosaccharides. However, its amino acid sequence is similar to those of other sho ...

    Sugar beet α-glucosidase (SBG), a member of glycoside hydrolase family 31, shows exceptional long-chain specificity, exhibiting higher kcat/Km values for longer malto-oligosaccharides. However, its amino acid sequence is similar to those of other short chain-specific α-glucosidases. To gain structural insights into the long-chain substrate recognition of SBG, a crystal structure complex with the pseudotetrasaccharide acarbose was determined at 1.7 Å resolution. The active site pocket of SBG is formed by a (β/α)8 barrel domain and a long loop (N-loop) bulging from the N-terminal domain similar to other related enzymes. Two residues (Phe-236 and Asn-237) in the N-loop are important for the long-chain specificity. Kinetic analysis of an Asn-237 mutant enzyme and a previous study of a Phe-236 mutant enzyme demonstrated that these residues create subsites +2 and +3. The structure also indicates that Phe-236 and Asn-237 guide the reducing end of long substrates to subdomain b2, which is an additional element inserted into the (β/α)8 barrel domain. Subdomain b2 of SBG includes Ser-497, which was identified as the residue at subsite +4 by site-directed mutagenesis.


    Organizational Affiliation

    Research Faculty of Agriculture, Hokkaido University, Sapporo 060-8589, Japan.




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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Download CCD File 
A
ALPHA-L-FUCOSE
C6 H12 O5
SHZGCJCMOBCMKK-SXUWKVJYSA-N
 Ligand Interaction
NAG
Query on NAG

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Download CCD File 
A
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
ACY
Query on ACY

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A
ACETIC ACID
C2 H4 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-N
 Ligand Interaction
ACR
Query on ACR

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Download CCD File 
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
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
ACRKi: 6680 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.182 
  • R-Value Work: 0.154 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 86.360α = 90.00
b = 98.200β = 90.00
c = 108.750γ = 90.00
Software Package:
Software NamePurpose
XSCALEdata scaling
PDB_EXTRACTdata extraction
BSSdata collection
XDSdata reduction
PHASERphasing
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-05-29
    Type: Initial release
  • Version 1.1: 2013-06-12
    Type: Database references
  • Version 1.2: 2013-07-17
    Type: Database references
  • Version 1.3: 2014-07-30
    Type: Other