6ZQ8

Crystal structure of Chaetomium thermophilum Glycerol Kinase in P3221 space group

• PDB DOI: https://doi.org/10.2210/pdb6ZQ8/pdb

• Classification: TRANSFERASE
• Organism(s): Thermochaetoides thermophila DSM 1495
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2020-07-09 Released: 2020-12-23 
• Deposition Author(s): Wilk, P., Wator, E., Malecki, P., Tokarz, P., Grudnik, P.
• Funding Organization(s): Polish National Science Centre, Foundation for Polish Science

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.38 Å
• R-Value Free: 0.284 
• R-Value Work: 0.244 
• R-Value Observed: 0.246 

Literature

Structural Characterization of Glycerol Kinase from the Thermophilic Fungus Chaetomium thermophilum .

Wilk, P., Kuska, K., Wator, E., Malecki, P.H., Wos, K., Tokarz, P., Dubin, G., Grudnik, P.

(2020) Int J Mol Sci 21

• PubMed: 33339113 
• DOI: https://doi.org/10.3390/ijms21249570
• Primary Citation of Related Structures:  
  6ZQ4, 6ZQ5, 6ZQ6, 6ZQ7, 6ZQ8


• PubMed Abstract: 
  

  Glycerol is an organic compound that can be utilized as an alternative source of carbon by various organisms. One of the ways to assimilate glycerol by the cell is the phosphorylative catabolic pathway in which its activation is catalyzed by glycerol kinase (GK) and glycerol-3-phosphate (G3P) is formed. To date, several GK crystal structures from bacteria, archaea, and unicellular eukaryotic parasites have been solved. Herein, we present a series of crystal structures of GK from Chaetomium thermophilum (CtGK) in apo and glycerol-bound forms. In addition, we show the feasibility of an ADP-dependent glucokinase (ADPGK)-coupled enzymatic assay to measure the CtGK activity. New structures described in our work provide structural insights into the GK catalyzed reaction in the filamentous fungus and set the foundation for understanding the glycerol metabolism in eukaryotes.

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Organizational Affiliation: 

Malopolska Centre of Biotechnology, Jagiellonian University, 7a Gronostajowa St., 30-387 Kraków, Poland.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: light scattering

Macromolecule Content

• Total Structure Weight: 114.13 kDa 
• Atom Count: 7,883 
• Modelled Residue Count: 1,021 
• Deposited Residue Count: 1,052 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glycerol kinase-like protein	A [auth B], B [auth A]	526	Thermochaetoides thermophila DSM 1495	Mutation(s): 0  Gene Names: CTHT_0042250
UniProt
Find proteins for G0SAG9 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719)) Explore G0SAG9  Go to UniProtKB:  G0SAG9

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.38 Å
• R-Value Free: 0.284 
• R-Value Work: 0.244 
• R-Value Observed: 0.246 
• Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 92.145	α = 90
b = 92.145	β = 90
c = 232.954	γ = 120

Software Package:

Software Name	Purpose
XDS	data reduction
XSCALE	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2020-12-23 
Deposition Author(s): Wilk, P., Wator, E., Malecki, P., Tokarz, P., Grudnik, P.

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Funding Organization	Location	Grant Number
Polish National Science Centre	Poland	UMO-2015/19/D/NZ1/02009
Foundation for Polish Science	Poland	TEAM TECH CORE FACILITY/2017-4/6

Revision History  

• Version 1.0: 2020-12-23
  Type: Initial release
  
• Version 1.1: 2020-12-30
  Changes: Database references
• Version 1.2: 2024-01-31
  Changes: Data collection, Database references, Refinement description