Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content

• Total Structure Weight: 84935.69 
• Atom Count: 5800 
• Residue Count: 726 
• Unique protein chains: 1

5B0S

Beta-1,2-Mannobiose phosphorylase from Listeria innocua - beta-1,2-mannotriose complex

• DOI: 10.2210/pdb5B0S/pdb

• Classification: TRANSFERASE
• Organism(s): Listeria innocua serovar 6a (strain ATCC BAA-680 / CLIP 11262)
• Expression System: Escherichia coli


• Deposited: 2015-11-02 Released: 2015-12-02 
• Deposition Author(s): Tsuda, T., Arakawa, T., Fushinobu, S.
• Funding Organization(s): The Ministry of Agriculture, Forestry and Fisheries, Japan 

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.1 Å
• R-Value Free: 0.215 
• R-Value Work: 0.179 

Literature

Characterization and crystal structure determination of beta-1,2-mannobiose phosphorylase from Listeria innocua

Tsuda, T., Nihira, T., Chiku, K., Suzuki, E., Arakawa, T., Nishimoto, M., Kitaoka, M., Nakai, H., Fushinobu, S.

(2015) Febs Lett. 589: 3816-3821

• PubMed: 26632508 
• DOI: 10.1016/j.febslet.2015.11.034
• Primary Citation of Related Structures:  
  5B0R, 5B0Q, 5B0P


• PubMed Abstract: 
  

Glycoside hydrolase family 130 consists of phosphorylases and hydrolases for β-mannosides. Here, we characterized β-1,2-mannobiose phosphorylase from Listeria innocua (Lin0857) and determined its crystal structures complexed with β-1,2-linked mannooligosaccharides. β-1,2-Mannotriose was bound in a U-shape, interacting with a phosphate analog at both ends. Lin0857 has a unique dimer structure connected by a loop, and a significant open-close loop displacement was observed for substrate entry. A long loop, which is exclusively present in Lin0857, covers the active site to limit the pocket size. A structural basis for substrate recognition and phosphorolysis was provided.

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Organizational Affiliation: 

Department of Biotechnology, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Lin0857 protein	A, B	363	Listeria innocua serovar 6a (strain ATCC BAA-680 / CLIP 11262)	Mutation(s): 0
Find proteins for Q92DF6 (Listeria innocua serovar 6a (strain ATCC BAA-680 / CLIP 11262)) Go to UniProtKB:  Q92DF6

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
SO4	A, B	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	B	GLYCEROL GLYCERIN; PROPANE-1,2,3-TRIOL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
MAN	A, B	ALPHA-D-MANNOSE C6 H12 O6 WQZGKKKJIJFFOK-PQMKYFCFSA-N
BMA	A, B	BETA-D-MANNOSE C6 H12 O6 WQZGKKKJIJFFOK-RWOPYEJCSA-N
MES	A, B	2-(N-MORPHOLINO)-ETHANESULFONIC ACID C6 H13 N O4 S SXGZJKUKBWWHRA-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.1 Å
• R-Value Free: 0.215 
• R-Value Work: 0.179 
• Space Group: P 3₁ 2 1

Unit Cell:

Length (Å)	Angle (°)
a = 145.545	α = 90.00
b = 145.545	β = 90.00
c = 105.744	γ = 120.00

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2015-11-02 
• Released Date: 2015-12-02 
• Deposition Author(s): Tsuda, T., Arakawa, T., Fushinobu, S.

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Funding Organization	Location	Grant Number
The Ministry of Agriculture, Forestry and Fisheries, Japan	Japan	25010A

Revision History 

• Version 1.0: 2015-12-02
  Type: Initial release
• Version 1.1: 2015-12-23
  Type: Database references