5B0S

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


Experimental Data Snapshot

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

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

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

  • DOI: 10.1016/j.febslet.2015.11.034
  • Primary Citation of Related Structures:  

  • 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 mannool ...

    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.


    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
MoleculeChainsSequence LengthOrganismDetails
Lin0857 protein
A, B
363Listeria 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
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

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Download CCD File 
B
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
MAN
Query on MAN

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Download CCD File 
A, B
ALPHA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
 Ligand Interaction
BMA
Query on BMA

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Download CCD File 
A, B
BETA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-RWOPYEJCSA-N
 Ligand Interaction
MES
Query on MES

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Download CCD File 
A, B
2-(N-MORPHOLINO)-ETHANESULFONIC ACID
C6 H13 N O4 S
SXGZJKUKBWWHRA-UHFFFAOYSA-N
 Ligand Interaction
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 = 145.545α = 90.00
b = 145.545β = 90.00
c = 105.744γ = 120.00
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
The Ministry of Agriculture, Forestry and Fisheries, JapanJapan25010A

Revision History 

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