Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

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

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

Macromolecule Content

• Total Structure Weight: 51.50 kDa 
• Atom Count: 4287 
• Modelled Residue Count: 448 
• Deposited Residue Count: 456 
• Unique protein chains: 1

3OM2

Crystal structure of B. megaterium levansucrase mutant D257A

• PDB DOI: 10.2210/pdb3OM2/pdb

• Classification: TRANSFERASE
• Organism(s): Priestia megaterium
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2010-08-26 Released: 2011-03-23 
• Deposition Author(s): Strube, C.P., Homann, A., Gamer, M., Jahn, D., Seibel, J., Heinz, D.W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.217 
• R-Value Work: 0.161 
• R-Value Observed: 0.163 

Literature

Polysaccharide Synthesis of the Levansucrase SacB from Bacillus megaterium Is Controlled by Distinct Surface Motifs.

Strube, C.P., Homann, A., Gamer, M., Jahn, D., Seibel, J., Heinz, D.W.

(2011) J Biol Chem 286: 17593-17600

• PubMed: 21454585 
• DOI: 10.1074/jbc.M110.203166
• Primary Citation of Related Structures:  
  3OM2, 3OM5, 3OM6, 3OM7


• PubMed Abstract: 
  

Despite the widespread biological function of carbohydrates, the polysaccharide synthesis mechanisms of glycosyltransferases remain largely unexplored. Bacterial levansucrases (glycoside hydrolase family 68) synthesize high molecular weight, β-(2,6)-linked levan from sucrose by transfer of fructosyl units. The kinetic and biochemical characterization of Bacillus megaterium levansucrase SacB variants Y247A, Y247W, N252A, D257A, and K373A reveal novel surface motifs remote from the sucrose binding site with distinct influence on the polysaccharide product spectrum. The wild type activity (k(cat)) and substrate affinity (K(m)) are maintained. The structures of the SacB variants reveal clearly distinguishable subsites for polysaccharide synthesis as well as an intact active site architecture. These results lead to a new understanding of polysaccharide synthesis mechanisms. The identified surface motifs are discussed in the context of related glycosyltransferases.

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Organizational Affiliation: 

Department of Molecular Structural Biology, Helmholtz-Centre for Infection Research, Inhoffenstrasse 7B, 38124 Braunschweig, Germany.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Levansucrase	A	456	Priestia megaterium	Mutation(s): 1  Gene Names: sacB EC: 2.4.1.10
UniProt
Find proteins for D5DC07 (Priestia megaterium (strain DSM 319 / IMG 1521)) Explore D5DC07  Go to UniProtKB:  D5DC07

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CIT	C [auth A], E [auth A]	CITRIC ACID C6 H8 O7 KRKNYBCHXYNGOX-UHFFFAOYSA-N
CA	B [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
MG	D [auth A], F [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.217 
• R-Value Work: 0.161 
• R-Value Observed: 0.163 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 49.003	α = 90
b = 55.289	β = 90
c = 163.614	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
DNA	data collection
XDS	data reduction
SCALA	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2010-08-26 
• Released Date: 2011-03-23 
Deposition Author(s): Strube, C.P., Homann, A., Gamer, M., Jahn, D., Seibel, J., Heinz, D.W.

Revision History  

• Version 1.0: 2011-03-23
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance