8XIS | pdb_00008xis

Cellodextrin phosphorylase from Clostridium thermocellum mutant - all cysteine residues were substituted with serines


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.68 Å
  • R-Value Free: 
    0.230 (Depositor), 0.230 (DCC) 
  • R-Value Work: 
    0.188 (Depositor), 0.188 (DCC) 
  • R-Value Observed: 
    0.190 (Depositor) 

Starting Model: in silico
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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Effect of Free Cysteine Residues to Serine Mutation on Cellodextrin Phosphorylase.

Kuga, T.Sunagawa, N.Igarashi, K.

(2024) J Appl Glycosci (1999) 71: 37-46

  • DOI: https://doi.org/10.5458/jag.jag.JAG-2023_0011
  • Primary Citation of Related Structures:  
    8XI1, 8XIL, 8XIS

  • PubMed Abstract: 

    Cellodextrin phosphorylase (CDP) plays a key role in energy-efficient cellulose metabolism of anaerobic bacteria by catalyzing phosphorolysis of cellodextrin to produce cellobiose and glucose 1-phosphate, which can be utilized for glycolysis without consumption of additional ATP. As the enzymatic phosphorolysis reaction is reversible, CDP is also employed to produce cellulosic materials in vitro. However, the enzyme is rapidly inactivated by oxidation, which hinders in vitro utilization in aerobic environments. It has been suggested that the cysteine residues of CDP, which do not form disulfide bonds, are responsible for the loss of activity, and the aim of the present work was to test this idea. For this purpose, we replaced all 11 free cysteine residues of CDP from Acetivibrio thermocellus (formerly known as Clostridium thermocellum ) with serine, which structurally resembles cysteine in our previous work. Herein, we show that the resulting CDP variant, named CDP-CS, has comparable activity to the wild-type enzyme, but shows increased stability to oxidation during long-term storage. X-Ray crystallography indicated that the mutations did not markedly alter the overall structure of the enzyme. Ensemble refinement of the crystal structures of CDP and CDP-CS indicated that the C372S and C625S mutations reduce structural fluctuations in the protein main chain, which may contribute to the increased stability of CDP-CS to oxidation.


  • Organizational Affiliation
    • 1 Department of Biomaterial Sciences, Graduate School of Agricultural and Life Sciences, The University of Tokyo.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
cellodextrin phosphorylase variant
A, B
992Acetivibrio thermocellusMutation(s): 0 
UniProt
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
Expand
  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
BGC (Subject of Investigation/LOI)
Query on BGC

Download Ideal Coordinates CCD File 
D [auth A],
V [auth B]
beta-D-glucopyranose
C6 H12 O6
WQZGKKKJIJFFOK-VFUOTHLCSA-N
PEG
Query on PEG

Download Ideal Coordinates CCD File 
GA [auth B],
M [auth A],
O [auth A]
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
PO4 (Subject of Investigation/LOI)
Query on PO4

Download Ideal Coordinates CCD File 
C [auth A],
U [auth B]
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
GOL
Query on GOL

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CA [auth B]
DA [auth B]
E [auth A]
EA [auth B]
FA [auth B]
CA [auth B],
DA [auth B],
E [auth A],
EA [auth B],
FA [auth B],
HA [auth B],
J [auth A],
K [auth A],
LA [auth B],
MA [auth B],
R [auth A],
S [auth A],
T [auth A],
X [auth B],
Z [auth B]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
ACT
Query on ACT

Download Ideal Coordinates CCD File 
AA [auth B]
BA [auth B]
F [auth A]
G [auth A]
H [auth A]
AA [auth B],
BA [auth B],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
IA [auth B],
L [auth A],
N [auth A],
W [auth B],
Y [auth B]
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
CL (Subject of Investigation/LOI)
Query on CL

Download Ideal Coordinates CCD File 
JA [auth B],
KA [auth B],
P [auth A],
Q [auth A]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.68 Å
  • R-Value Free:  0.230 (Depositor), 0.230 (DCC) 
  • R-Value Work:  0.188 (Depositor), 0.188 (DCC) 
  • R-Value Observed: 0.190 (Depositor) 
Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 82.277α = 98.407
b = 88.52β = 110.691
c = 88.54γ = 110.652
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan Society for the Promotion of Science (JSPS)Japan22J12566
Ministry of Education, Culture, Sports, Science and Technology (Japan)Japan18H05494

Revision History  (Full details and data files)

  • Version 1.0: 2024-12-25
    Type: Initial release
  • Version 1.1: 2025-07-09
    Changes: Database references