Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 94.76 kDa 
• Atom Count: 6,804 
• Modelled Residue Count: 780 
• Deposited Residue Count: 817 
• Unique protein chains: 1

 4B9Z

Crystal Structure of Agd31B, alpha-transglucosylase, complexed with Acarbose

• PDB DOI: 10.2210/pdb4B9Z/pdb

• Classification: HYDROLASE
• Organism(s): Cellvibrio japonicus
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2012-09-09 Released: 2012-11-14 
• Deposition Author(s): Larsbrink, J., Izumi, A., Hemsworth, G.R., Davies, G.J., Brumer, H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.187 
• R-Value Work: 0.161 
• R-Value Observed: 0.162 

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

• PubMed: 23132856 
• DOI: 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.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ALPHA-GLUCOSIDASE, PUTATIVE, ADG31B	A	817	Cellvibrio japonicus	Mutation(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

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
4,6-dideoxy-4-{[(1S,4R,5S,6S)-4,5,6-trihydroxy-3-(hydroxymethyl)cyclohex-2-en-1-yl]amino}-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose	B	3	N/A	N/A
Glycosylation Resources
GlyTouCan:  G66431MI GlyCosmos:  G66431MI

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PEG	I [auth A]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
SO4	C [auth A], D [auth A], E [auth A], F [auth A], G [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
OXL	H [auth A]	OXALATE ION C2 O4 MUBZPKHOEPUJKR-UHFFFAOYSA-L
EDO	J [auth A], K [auth A], L [auth A], M [auth A], N [auth A], O [auth A], P [auth A], Q [auth A], R [auth A], S [auth A], T [auth A], U [auth A], V [auth A], W [auth A], X [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900007	B	alpha-acarbose	Oligosaccharide / Inhibitor		Ligand Interaction

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.187 
• R-Value Work: 0.161 
• R-Value Observed: 0.162 
• Space Group: P 6 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 196.88	α = 90
b = 196.88	β = 90
c = 102.76	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
MOSFLM	data reduction
SCALEPACK	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-11-14 
Deposition Author(s): Larsbrink, J., Izumi, A., Hemsworth, G.R., Davies, G.J., Brumer, H.

Revision History  

• 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 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Non-polymer description, Other, Structure summary