4BA0

Crystal Structure of Agd31B, alpha-transglucosylase, complexed with 5F-alpha-GlcF


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.193 
  • R-Value Work: 0.167 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural Enzymology of Cellvibrio Japonicus Agd31B Reveals Alpha-Transglucosylase Activity in Glycoside Hydrolase Family 31

Larsbrink, J.Izumi, A.Hemsworth, G.R.Davies, G.J.Brumer, H.

(2012) J.Biol.Chem. 287: 43288

  • DOI: 10.1074/jbc.M112.416511
  • Primary Citation of Related Structures:  4B9Y, 4B9Z

  • PubMed Abstract: 
  • The metabolism of the storage polysaccharides glycogen and starch is of vital importance to organisms from all domains of life. In bacteria, utilization of these α-glucans requires the concerted action of a variety of enzymes, including glycoside hyd ...

    The metabolism of the storage polysaccharides glycogen and starch is of vital importance to organisms from all domains of life. In bacteria, utilization of these α-glucans requires the concerted action of a variety of enzymes, including glycoside hydrolases, glycoside phosphorylases, and transglycosylases. In particular, transglycosylases from glycoside hydrolase family 13 (GH13) and GH77 play well established roles in α-glucan side chain (de)branching, regulation of oligo- and polysaccharide chain length, and formation of cyclic dextrans. Here, we present the biochemical and tertiary structural characterization of a new type of bacterial 1,4-α-glucan 4-α-glucosyltransferase from GH31. Distinct from 1,4-α-glucan 6-α-glucosyltransferases (EC 2.4.1.24) and 4-α-glucanotransferases (EC 2.4.1.25), this enzyme strictly transferred one glucosyl residue from α(1→4)-glucans in disproportionation reactions. Substrate hydrolysis was undetectable for a series of malto-oligosaccharides except maltose for which transglycosylation nonetheless dominated across a range of substrate concentrations. Crystallographic analysis of the enzyme in free, acarbose-complexed, and trapped 5-fluoro-β-glucosyl-enzyme intermediate forms revealed extended substrate interactions across one negative and up to three positive subsites, thus providing structural rationalization for the unique, single monosaccharide transferase activity of the enzyme.


    Organizational Affiliation

    Division of Glycoscience, School of Biotechnology, Royal Institute of Technology, AlbaNova University Centre, 106 91 Stockholm, Sweden.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
ALPHA-GLUCOSIDASE, PUTATIVE, ADG31B
A
817Cellvibrio japonicus (strain Ueda107)Gene Names: agd31B
EC: 2.4.1.161
Find proteins for B3PEE6 (Cellvibrio japonicus (strain Ueda107))
Go to UniProtKB:  B3PEE6
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
5GF
Query on 5GF

Download SDF File 
Download CCD File 
A
5-FLUORO-BETA-D-GLUCOPYRANOSE
C6 H11 F O6
YQZCKDSOGGIGPL-VFUOTHLCSA-N
 Ligand Interaction
EDO
Query on EDO

Download SDF File 
Download CCD File 
A
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
PGE
Query on PGE

Download SDF File 
Download CCD File 
A
TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
 Ligand Interaction
ARG
Query on ARG

Download SDF File 
Download CCD File 
A
ARGININE
C6 H15 N4 O2
ODKSFYDXXFIFQN-BYPYZUCNSA-O
 Ligand Interaction
PEG
Query on PEG

Download SDF File 
Download CCD File 
A
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.193 
  • R-Value Work: 0.167 
  • Space Group: P 6 2 2
Unit Cell:
Length (Å)Angle (°)
a = 197.230α = 90.00
b = 197.230β = 90.00
c = 103.060γ = 120.00
Software Package:
Software NamePurpose
MOSFLMdata reduction
MOLREPphasing
PHENIXrefinement
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-11-14
    Type: Initial release
  • Version 1.1: 2012-11-21
    Type: Database references
  • Version 1.2: 2013-01-16
    Type: Database references