8XI1 | pdb_00008xi1

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

PDB DOI: https://doi.org/10.2210/pdb8XI1/pdb
Entry: 8XI1 supersedes: 8H2K

Classification: CARBOHYDRATE
Organism(s): Acetivibrio thermocellus
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2023-12-19 Released: 2024-12-25
Deposition Author(s): Kuga, T., Sunagawa, N., Igarashi, K.
Funding Organization(s): Japan Society for the Promotion of Science (JSPS), Ministry of Education, Culture, Sports, Science and Technology (Japan)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.37 Å
R-Value Free:
0.200 (Depositor), 0.201 (DCC)
R-Value Work:
0.174 (Depositor), 0.175 (DCC)
R-Value Observed:
0.176 (Depositor)

Starting Model: in silico
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 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

PubMed: 38863949 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.5458/jag.jag.JAG-2023_0011
Primary Citation 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.

Macromolecule Content

Total Structure Weight: 226.15 kDa
Atom Count: 18,830
Modeled Residue Count: 1,968
Deposited Residue Count: 1,984
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
cellodextrin phosphorylase variant	A, B	992	Acetivibrio thermocellus	Mutation(s): 0
UniProt
Find proteins for Q93HT8 (Acetivibrio thermocellus) Explore Q93HT8 Go to UniProtKB: Q93HT8
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q93HT8
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PEG (Subject of Investigation/LOI) Query on PEG Download:Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A] mmCIF format, chain E [auth A]	E [auth A]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]
GOL (Subject of Investigation/LOI) Query on GOL Download:Ideal Coordinates CCD File SDF format, chain J [auth B] SDF format, chain H [auth B] SDF format, chain D [auth A] SDF format, chain C [auth A] MOL2 format, chain J [auth B] MOL2 format, chain H [auth B] MOL2 format, chain D [auth A] MOL2 format, chain C [auth A] mmCIF format, chain J [auth B] mmCIF format, chain H [auth B] mmCIF format, chain D [auth A] mmCIF format, chain C [auth A]	C [auth A], D [auth A], H [auth B], J [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain H [auth B] Focus chain J [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain H [auth B] Focus chain J [auth B]
ACT (Subject of Investigation/LOI) Query on ACT Download:Ideal Coordinates CCD File SDF format, chain L [auth B] SDF format, chain K [auth B] SDF format, chain I [auth B] MOL2 format, chain L [auth B] MOL2 format, chain K [auth B] MOL2 format, chain I [auth B] mmCIF format, chain L [auth B] mmCIF format, chain K [auth B] mmCIF format, chain I [auth B]	I [auth B], K [auth B], L [auth B]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain I [auth B] Focus chain K [auth B] Focus chain L [auth B] Interactions & Density Focus chain I [auth B] Focus chain K [auth B] Focus chain L [auth B]
CL (Subject of Investigation/LOI) Query on CL Download:Ideal Coordinates CCD File SDF format, chain N [auth B] SDF format, chain M [auth B] SDF format, chain G [auth A] SDF format, chain F [auth A] MOL2 format, chain N [auth B] MOL2 format, chain M [auth B] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] mmCIF format, chain N [auth B] mmCIF format, chain M [auth B] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A]	F [auth A], G [auth A], M [auth B], N [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain M [auth B] Focus chain N [auth B] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain M [auth B] Focus chain N [auth B]