Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: light scattering

Biological Assembly 2  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Biological Assembly 3  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 3 assigned by authors.

Macromolecule Content

• Total Structure Weight: 160.24 kDa 
• Atom Count: 11272 
• Modelled Residue Count: 1424 
• Deposited Residue Count: 1425 
• Unique protein chains: 1

6R2N

Crystal structure of KlGlk1 glucokinase from Kluyveromyces lactis

• PDB DOI: 10.2210/pdb6R2N/pdb

• Classification: TRANSFERASE
• Organism(s): Kluyveromyces lactis
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2019-03-18 Released: 2019-10-16 
• Deposition Author(s): Zak, K., Wator, E., Grudnik, P.
• Funding Organization(s): Polish National Science Centre

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 0.243 
• R-Value Work: 0.204 
• R-Value Observed: 0.205 

Literature

Crystal Structure of Kluyveromyces lactis Glucokinase ( Kl Glk1).

Zak, K.M., Kalinska, M., Wator, E., Kuska, K., Krutyholowa, R., Dubin, G., Popowicz, G.M., Grudnik, P.

(2019) Int J Mol Sci 20

• PubMed: 31569356 
• DOI: 10.3390/ijms20194821
• Primary Citation of Related Structures:  
  6R2N


• PubMed Abstract: 
  

Glucose phosphorylating enzymes are crucial in the regulation of basic cellular processes, including metabolism and gene expression. Glucokinases and hexokinases provide a pool of phosphorylated glucose in an adenosine diphosphate (ADP)- and ATP-dependent manner to shape the cell metabolism. The glucose processing enzymes from Kluyveromyces lactis are poorly characterized despite the emerging contribution of this yeast strain to industrial and laboratory scale biotechnology. The first reports on K. lactis glucokinase ( Kl Glk1) positioned the enzyme as an essential component required for glucose signaling. Nevertheless, no biochemical and structural information was available until now. Here, we present the first crystal structure of Kl Glk1 together with biochemical characterization, including substrate specificity and enzyme kinetics. Additionally, comparative analysis of the presented structure and the prior structures of lactis hexokinase ( Kl Hxk1) demonstrates the potential transitions between open and closed enzyme conformations upon ligand binding.

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Organizational Affiliation: 

Malopolska Centre of Biotechnology, Jagiellonian University, ul. Gronostajowa 7a, 30-387 Krakow, Poland. [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glucokinase-1	A, B, C	475	Kluyveromyces lactis	Mutation(s): 0  Gene Names: GLK1, KLLA0C01155g EC: 2.7.1.2 (PDB Primary Data), 2.7.1.1 (UniProt)
UniProt
Find proteins for Q6CUZ3 (Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37)) Explore Q6CUZ3  Go to UniProtKB:  Q6CUZ3

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BR	O [auth C]	BROMIDE ION Br CPELXLSAUQHCOX-UHFFFAOYSA-M
EDO	D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth B], M [auth B], N [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 0.243 
• R-Value Work: 0.204 
• R-Value Observed: 0.205 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 102.011	α = 90
b = 122.771	β = 90
c = 360.346	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2019-03-18 
• Released Date: 2019-10-16 
Deposition Author(s): Zak, K., Wator, E., Grudnik, P.

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Funding Organization	Location	Grant Number
Polish National Science Centre	Poland	UMO-2015/19/D/NZ1/02009

Revision History  

• Version 1.0: 2019-10-16
  Type: Initial release
  
• Version 1.1: 2020-09-30
  Changes: Database references