Biological Assembly 1  

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

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 54.10 kDa 
• Atom Count: 4117 
• Modelled Residue Count: 469 
• Deposited Residue Count: 486 
• Unique protein chains: 1

1IG8

Crystal Structure of Yeast Hexokinase PII with the correct amino acid sequence

• PDB DOI: 10.2210/pdb1IG8/pdb

• Classification: TRANSFERASE
• Organism(s): Saccharomyces cerevisiae
• Mutation(s): No 


• Deposited: 2001-04-17 Released: 2001-05-02 
• Deposition Author(s): Kuser, P.R., Krauchenco, S., Antunes, O.A., Polikarpov, I.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.246 
• R-Value Work: 0.162 

Literature

The high resolution crystal structure of yeast hexokinase PII with the correct primary sequence provides new insights into its mechanism of action.

Kuser, P.R., Krauchenco, S., Antunes, O.A., Polikarpov, I.

(2000) J Biol Chem 275: 20814-20821

• PubMed: 10749890 
• DOI: 10.1074/jbc.M910412199
• Primary Citation of Related Structures:  
  1IG8


• PubMed Abstract: 
  

Hexokinase is the first enzyme in the glycolytic pathway, catalyzing the transfer of a phosphoryl group from ATP to glucose to form glucose 6-phosphate and ADP. Two yeast hexokinase isozymes are known, namely PI and PII. The crystal structure of yeast hexokinase PII from Saccharomyces cerevisiae without substrate or competitive inhibitor is determined and refined in a tetragonal crystal form at 2.2-A resolution. The folding of the peptide chain is very similar to that of Schistosoma mansoni and previous yeast hexokinase models despite only 30% sequence identity between them. Distinct differences in conformation are found that account for the absence of glucose in the binding site. Comparison of the current model with S. mansoni and yeast hexokinase PI structures both complexed with glucose shows in atomic detail the rigid body domain closure and specific loop movements as glucose binds. A hydrophobic channel formed by strictly conserved hydrophobic residues in the small domain of the hexokinase is identified. The channel's mouth is close to the active site and passes through the small domain to its surface. The possible role of the observed channel in proton transfer is discussed.

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Related Citations: 

• Crystallization and Preliminary Crystal Analysis of Yeast Hexokinase PI and PII
  Kuser, P.R., Golubev, A.M., Polikarpov, I.
  (1999) Acta Crystallogr D Biol Crystallogr 55: 2047

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Organizational Affiliation: 

Laboratório Nacional de Luz Sincrotron, Campinas, São Paulo, Brazil.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
hexokinase PII	A	486	Saccharomyces cerevisiae	Mutation(s): 0  EC: 2.7.1.1
UniProt
Find proteins for P04807 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P04807  Go to UniProtKB:  P04807

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	B [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.246 
• R-Value Work: 0.162 
• Space Group: I 4

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 142.809	α = 90
b = 142.809	β = 90
c = 58.462	γ = 90

Software Package:

Software Name	Purpose
AMoRE	phasing
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2001-04-17 
• Released Date: 2001-05-02 
Deposition Author(s): Kuser, P.R., Krauchenco, S., Antunes, O.A., Polikarpov, I.

Revision History  

• Version 1.0: 2001-05-02
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance