4B9Y

Crystal Structure of Apo Agd31B, alpha-transglucosylase in Glycoside Hydrolase Family 31


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.191 
  • R-Value Work: 0.163 
  • R-Value Observed: 0.164 

wwPDB Validation   3D Report Full Report


This is version 1.3 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: https://doi.org/10.1074/jbc.M112.416511
  • Primary Citation of Related Structures:  
    4B9Y, 4B9Z, 4BA0

  • 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 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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
ALPHA-GLUCOSIDASE, PUTATIVE, ADG31B817Cellvibrio japonicusMutation(s): 0 
EC: 3.2.1.20 (PDB Primary Data), 2.4.1.161 (UniProt)
UniProt
Find proteins for B3PEE6 (Cellvibrio japonicus (strain Ueda107))
Explore B3PEE6 
Go to UniProtKB:  B3PEE6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB3PEE6
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PG4
Query on PG4

Download Ideal Coordinates CCD File 
Q [auth A]TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
B [auth A]
C [auth A]
D [auth A]
E [auth A]
F [auth A]
B [auth A],
C [auth A],
D [auth A],
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
OXL
Query on OXL

Download Ideal Coordinates CCD File 
L [auth A]OXALATE ION
C2 O4
MUBZPKHOEPUJKR-UHFFFAOYSA-L
EDO
Query on EDO

Download Ideal Coordinates CCD File 
M [auth A]
N [auth A]
O [auth A]
P [auth A]
R [auth A]
M [auth A],
N [auth A],
O [auth A],
P [auth A],
R [auth A],
S [auth A]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.191 
  • R-Value Work: 0.163 
  • R-Value Observed: 0.164 
  • Space Group: P 6 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 197.329α = 90
b = 197.329β = 90
c = 103.032γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
MOSFLMdata reduction
SCALEPACKdata scaling
autoSHARPphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-11-14
    Type: Initial release
  • Version 1.1: 2012-11-21
    Changes: Database references
  • Version 1.2: 2013-01-16
    Changes: Database references
  • Version 1.3: 2024-10-16
    Changes: Data collection, Database references, Derived calculations, Other, Structure summary