1HKC | pdb_00001hkc

RECOMBINANT HUMAN HEXOKINASE TYPE I COMPLEXED WITH GLUCOSE AND PHOSPHATE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 
    0.241 (Depositor) 
  • R-Value Work: 
    0.174 (Depositor), 0.180 (DCC) 
  • R-Value Observed: 
    0.174 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted BGCClick on this verticalbar to view details

This is version 1.5 of the entry. See complete history


Literature

Regulation of hexokinase I: crystal structure of recombinant human brain hexokinase complexed with glucose and phosphate.

Aleshin, A.E.Zeng, C.Bartunik, H.D.Fromm, H.J.Honzatko, R.B.

(1998) J Mol Biology 282: 345-357

  • DOI: https://doi.org/10.1006/jmbi.1998.2017
  • Primary Citation of Related Structures:  
    1HKC

  • PubMed Abstract: 

    Hexokinase I, the pacemaker of glycolysis in brain tissue and red blood cells, is comprised of two similar domains fused into a single polypeptide chain. The C-terminal half of hexokinase I is catalytically active, whereas the N-terminal half is necessary for the relief of product inhibition by phosphate. A crystalline complex of recombinant human hexokinase I with glucose and phosphate (2.8 A resolution) reveals a single binding site for phosphate and glucose at the N-terminal half of the enzyme. Glucose and phosphate stabilize the N-terminal half in a closed conformation. Unexpectedly, glucose binds weakly to the C-terminal half of the enzyme and does not by itself stabilize a closed conformation. Evidently a stable, closed C-terminal half requires either ATP or glucose 6-phosphate along with glucose. The crystal structure here, in conjunction with other studies in crystallography and directed mutation, puts the phosphate regulatory site at the N-terminal half, the site of potent product inhibition at the C-terminal half, and a secondary site for the weak interaction of glucose 6-phosphate at the N-terminal half of the enzyme. The relevance of crystal structures of hexokinase I to the properties of monomeric hexokinase I and oligomers of hexokinase I bound to the surface of mitochondria is discussed.


  • Organizational Affiliation

    Department of Biochemistry and Biophysics, Iowa State University, Ames, IA 50011, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
D-GLUCOSE 6-PHOSPHOTRANSFERASE917Homo sapiensMutation(s): 0 
EC: 2.7.1.1
UniProt & NIH Common Fund Data Resources
Find proteins for P19367 (Homo sapiens)
Explore P19367 
Go to UniProtKB:  P19367
PHAROS:  P19367
GTEx:  ENSG00000156515 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP19367
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free:  0.241 (Depositor) 
  • R-Value Work:  0.174 (Depositor), 0.180 (DCC) 
  • R-Value Observed: 0.174 (Depositor) 
Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 175.09α = 90
b = 175.09β = 90
c = 99.47γ = 120
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORrefinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing

Structure Validation

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Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted BGCClick on this verticalbar to view details

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1998-11-11
    Type: Initial release
  • Version 1.1: 2008-03-03
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Other, Structure summary
  • Version 1.4: 2023-08-09
    Changes: Database references, Refinement description, Structure summary
  • Version 1.5: 2024-05-22
    Changes: Data collection