Crystal structure of Chaetomium thermophilum Glycerol Kinase in complex with substrate in P1 space group

Experimental Data Snapshot

  • Resolution: 2.02 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.205 
  • R-Value Observed: 0.206 

wwPDB Validation   3D Report Full Report

This is version 1.2 of the entry. See complete history


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

  • 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.

  • Organizational Affiliation

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

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Glycerol kinase-like protein
A, B, C, D, E
A, B, C, D, E, F, G, H
526Thermochaetoides thermophila DSM 1495Mutation(s): 0 
Gene Names: CTHT_0042250
Find proteins for G0SAG9 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
Explore G0SAG9 
Go to UniProtKB:  G0SAG9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupG0SAG9
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on PO4

Download Ideal Coordinates CCD File 
I [auth A]
K [auth B]
M [auth C]
O [auth D]
Q [auth E]
I [auth A],
K [auth B],
M [auth C],
O [auth D],
Q [auth E],
S [auth F]
O4 P
Query on GOL

Download Ideal Coordinates CCD File 
J [auth A]
L [auth B]
N [auth C]
P [auth D]
R [auth E]
J [auth A],
L [auth B],
N [auth C],
P [auth D],
R [auth E],
T [auth F],
U [auth G],
V [auth H]
C3 H8 O3
Experimental Data & Validation

Experimental Data

  • Resolution: 2.02 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.205 
  • R-Value Observed: 0.206 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 61.38α = 85.77
b = 112.82β = 90.04
c = 179.54γ = 85.45
Software Package:
Software NamePurpose
XSCALEdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Polish National Science CentrePolandUMO-2015/19/D/NZ1/02009
Foundation for Polish SciencePolandTEAM TECH CORE FACILITY/2017-4/6

Revision History  (Full details and data files)

  • 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