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

Experimental Data Snapshot

  • Resolution: 2.20 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.162 

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This is version 1.3 of the entry. See complete history


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

  • DOI: https://doi.org/10.1074/jbc.M910412199
  • Primary Citation of Related Structures:  

  • 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.

  • Organizational Affiliation

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

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
hexokinase PII486Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for P04807 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P04807 
Go to UniProtKB:  P04807
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP04807
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on SO4

Download Ideal Coordinates CCD File 
O4 S
Experimental Data & Validation

Experimental Data

  • Resolution: 2.20 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.162 
  • Space Group: I 4
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 142.809α = 90
b = 142.809β = 90
c = 58.462γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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
  • Version 1.3: 2024-02-07
    Changes: Data collection, Database references, Derived calculations