Paenibacillus sp. YM1 laminaribiose phosphorylase with sulphate bound

Experimental Data Snapshot

  • Resolution: 1.95 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.202 
  • R-Value Observed: 0.203 

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This is version 1.1 of the entry. See complete history


Unravelling the Specificity of Laminaribiose Phosphorylase from Paenibacillus sp. YM-1 towards Donor Substrates Glucose/Mannose 1-Phosphate by Using X-ray Crystallography and Saturation Transfer Difference NMR Spectroscopy.

Kuhaudomlarp, S.Walpole, S.Stevenson, C.E.M.Nepogodiev, S.A.Lawson, D.M.Angulo, J.Field, R.A.

(2019) Chembiochem 20: 181-192

  • DOI: https://doi.org/10.1002/cbic.201800260
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Glycoside phosphorylases (GPs) carry out a reversible phosphorolysis of carbohydrates into oligosaccharide acceptors and the corresponding sugar 1-phosphates. The reversibility of the reaction enables the use of GPs as biocatalysts for carbohydrate synthesis. Glycosyl hydrolase family 94 (GH94), which only comprises GPs, is one of the most studied GP families that have been used as biocatalysts for carbohydrate synthesis, in academic research and in industrial production. Understanding the mechanism of GH94 enzymes is a crucial step towards enzyme engineering to improve and expand the applications of these enzymes in synthesis. In this work with a GH94 laminaribiose phosphorylase from Paenibacillus sp. YM-1 (PsLBP), we have demonstrated an enzymatic synthesis of disaccharide 1 (β-d-mannopyranosyl-(1→3)-d-glucopyranose) by using a natural acceptor glucose and noncognate donor substrate α-mannose 1-phosphate (Man1P). To investigate how the enzyme recognises different sugar 1-phosphates, the X-ray crystal structures of PsLBP in complex with Glc1P and Man1P have been solved, providing the first molecular detail of the recognition of a noncognate donor substrate by GPs, which revealed the importance of hydrogen bonding between the active site residues and hydroxy groups at C2, C4, and C6 of sugar 1-phosphates. Furthermore, we used saturation transfer difference NMR spectroscopy to support crystallographic studies on the sugar 1-phosphates, as well as to provide further insights into the PsLBP recognition of the acceptors and disaccharide products.

  • Organizational Affiliation

    Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Laminaribiose phosphorylase
A, B
913Paenibacillus sp. YM1Mutation(s): 0 
Gene Names: lbpA
Find proteins for D7UT17 (Paenibacillus sp. YM1)
Explore D7UT17 
Go to UniProtKB:  D7UT17
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupD7UT17
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on SO4

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A],
K [auth B],
L [auth B]
O4 S
Query on EDO

Download Ideal Coordinates CCD File 
E [auth A]
F [auth A]
G [auth A]
H [auth A]
M [auth B]
E [auth A],
F [auth A],
G [auth A],
H [auth A],
M [auth B],
N [auth B],
O [auth B],
P [auth B],
Q [auth B],
R [auth B]
C2 H6 O2
Query on CL

Download Ideal Coordinates CCD File 
I [auth A],
J [auth A],
S [auth B],
T [auth B]
Experimental Data & Validation

Experimental Data

  • Resolution: 1.95 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.202 
  • R-Value Observed: 0.203 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 146.704α = 90
b = 146.704β = 90
c = 222.95γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Biotechnology and Biological Sciences Research CouncilUnited KingdomBB/J004561/1
Biotechnology and Biological Sciences Research CouncilUnited KingdomBB/P010660/1
Engineering and Physical Sciences Research CouncilUnited KingdomBB/M02903411

Revision History  (Full details and data files)

  • Version 1.0: 2018-06-13
    Type: Initial release
  • Version 1.1: 2019-04-24
    Changes: Data collection, Database references