Clostridium thermocellum cellodextrin phosphorylase ligand free form

Experimental Data Snapshot

  • Resolution: 2.30 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.191 
  • R-Value Observed: 0.192 

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This is version 1.2 of the entry. See complete history


Cellodextrin phosphorylase from Ruminiclostridium thermocellum: X-ray crystal structure and substrate specificity analysis.

O'Neill, E.C.Pergolizzi, G.Stevenson, C.E.M.Lawson, D.M.Nepogodiev, S.A.Field, R.A.

(2017) Carbohydr Res 451: 118-132

  • DOI: https://doi.org/10.1016/j.carres.2017.07.005
  • Primary Citation of Related Structures:  
    5NZ7, 5NZ8

  • PubMed Abstract: 

    The GH94 glycoside hydrolase cellodextrin phosphorylase (CDP, EC produces cellodextrin oligomers from short β-1→4-glucans and α-D-glucose 1-phosphate. Compared to cellobiose phosphorylase (CBP), which produces cellobiose from glucose and α-D-glucose 1-phosphate, CDP is biochemically less well characterised. Herein, we investigate the donor and acceptor substrate specificity of recombinant CDP from Ruminiclostridium thermocellum and we isolate and characterise a glucosamine addition product to the cellobiose acceptor with the non-natural donor α-D-glucosamine 1-phosphate. In addition, we report the first X-ray crystal structure of CDP, along with comparison to the available structures from CBPs and other closely related enzymes, which contributes to understanding of the key structural features necessary to discriminate between monosaccharide (CBP) and oligosaccharide (CDP) acceptor substrates.

  • 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
Cellodextrin phosphorylase
A, B
1,009Acetivibrio thermocellusMutation(s): 0 
Gene Names: cdp-ym4
Find proteins for Q93HT8 (Acetivibrio thermocellus)
Explore Q93HT8 
Go to UniProtKB:  Q93HT8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ93HT8
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.30 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.191 
  • R-Value Observed: 0.192 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 84.64α = 90
b = 151.81β = 114.6
c = 91.97γ = 90
Software Package:
Software NamePurpose
Aimlessdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Biotechnology and Biological Sciences Research CouncilUnited KingdomBB/J004561/1 (MET)
EPSRC and InnovateUKUnited KingdomBB/M02903411
John Innes FoundationUnited Kingdom--

Revision History  (Full details and data files)

  • Version 1.0: 2017-08-09
    Type: Initial release
  • Version 1.1: 2017-11-01
    Changes: Database references
  • Version 1.2: 2024-05-08
    Changes: Data collection, Database references, Refinement description