3GBD

Crystal structure of the isomaltulose synthase SmuA from Protaminobacter rubrum

• PDB DOI: https://doi.org/10.2210/pdb3GBD/pdb

• Classification: ISOMERASE
• Organism(s): Serratia plymuthica
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-02-19 Released: 2009-05-26 
• Deposition Author(s): Ravaud, S., Robert, X., Haser, R., Aghajari, N.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 0.224 
• R-Value Work: 0.179 
• R-Value Observed: 0.179 

Literature

Structural determinants of product specificity of sucrose isomerases

Ravaud, S., Robert, X., Watzlawick, H., Haser, R., Mattes, R., Aghajari, N.

(2009) FEBS Lett 583: 1964-1968

• PubMed: 19427862 
• DOI: https://doi.org/10.1016/j.febslet.2009.05.002
• Primary Citation of Related Structures:  
  3GBD, 3GBE


• PubMed Abstract: 
  

  The healthy sweetener isomaltulose is industrially produced from the conversion of sucrose by the sucrose isomerase SmuA from Protaminobacter rubrum. Crystal structures of SmuA in native and deoxynojirimycin complexed forms completed with modeling studies unravel the characteristics of the isomaltulose synthases catalytic pocket and their substrate binding mode. Comparison with the trehalulose synthase MutB highlights the role of Arg(298) and Arg(306) active site residues and surface charges in controlling product specificity of sucrose isomerases (isomaltulose versus trehalulose). The results provide a rationale for the specific design of optimized enzymes.

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Organizational Affiliation: 

Institut de Biologie et Chimie des Protéines, UMR 5086-CNRS/Université de Lyon, IFR128 BioSciences Gerland-Lyon Sud, Lyon, France.

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: 66.37 kDa 
• Atom Count: 5,446 
• Modelled Residue Count: 558 
• Deposited Residue Count: 558 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Sucrose isomerase SmuA from Protaminobacter rubrum	A	558	Serratia plymuthica	Mutation(s): 0  Gene Names: smuA EC: 5.4.99.11
UniProt
Find proteins for D0VX20 (Serratia plymuthica) Explore D0VX20  Go to UniProtKB:  D0VX20

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FLC	J [auth A]	CITRATE ANION C6 H5 O7 KRKNYBCHXYNGOX-UHFFFAOYSA-K
EDO	B [auth A], C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 0.224 
• R-Value Work: 0.179 
• R-Value Observed: 0.179 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 61.63	α = 90
b = 81.39	β = 90
c = 135.57	γ = 90

Software Package:

Software Name	Purpose
DNA	data collection
AMoRE	phasing
CNS	refinement
XDS	data reduction
XSCALE	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-05-26 
Deposition Author(s): Ravaud, S., Robert, X., Haser, R., Aghajari, N.

Revision History  

• Version 1.0: 2009-05-26
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2023-11-01
  Changes: Data collection, Database references, Derived calculations, Refinement description