5B0P | pdb_00005b0p

Beta-1,2-Mannobiose phosphorylase from Listeria innocua - glycerol complex

• PDB DOI: https://doi.org/10.2210/pdb5B0P/pdb

• Classification: TRANSFERASE
• Organism(s): Listeria innocua Clip11262
• Expression System: Escherichia coli
• Mutation(s): No 


• 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: 1.90 Å
• R-Value Free: 
  0.197 (Depositor), 0.208 (DCC) 
• R-Value Work: 
  0.165 (Depositor), 0.177 (DCC) 
• R-Value Observed: 
  0.166 (Depositor) 

Starting Model: experimental

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: https://doi.org/10.1016/j.febslet.2015.11.034
• Primary Citation Related Structures: 
  5B0P, 5B0Q, 5B0R, 5B0S


• 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.
Faculty of Agriculture, Niigata University, Niigata 950-2181, Japan.
National Food Research Institute, National Agriculture and Food Research Organization, Tsukuba, Ibaraki 305-8642, Japan.
Faculty of Agriculture, Niigata University, Niigata 950-2181, Japan. Electronic address: [e-mail].
Department of Biotechnology, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan. Electronic address: [e-mail].

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 84.04 kDa 
• Atom Count: 6,447 
• Modeled Residue Count: 709 
• Deposited Residue Count: 726 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lin0857 protein	A, B	363	Listeria innocua Clip11262	Mutation(s): 0  Gene Names: lin0857 EC: 2.4.1.339
UniProt
Find proteins for Q92DF6 (Listeria innocua serovar 6a (strain ATCC BAA-680 / CLIP 11262)) Explore Q92DF6  Go to UniProtKB:  Q92DF6

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MES	I [auth A], J [auth A], P [auth B], Q [auth B]	2-(N-MORPHOLINO)-ETHANESULFONIC ACID C6 H13 N O4 S SXGZJKUKBWWHRA-UHFFFAOYSA-N
SO4	C [auth A], D [auth A], E [auth A], K [auth B], L [auth B], M [auth B], N [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	F [auth A], G [auth A], H [auth A], O [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.197 (Depositor), 0.208 (DCC) 
• R-Value Work:  0.165 (Depositor), 0.177 (DCC) 
• R-Value Observed: 0.166 (Depositor) 

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 146.559	α = 90
b = 146.559	β = 90
c = 106.324	γ = 120

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

• 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
  Changes: Database references
• Version 1.2: 2020-02-26
  Changes: Data collection, Database references, Derived calculations
• Version 1.3: 2023-11-08
  Changes: Data collection, Database references, Refinement description