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.

Macromolecule Content

• Total Structure Weight: 103.87 kDa 
• Atom Count: 7256 
• Modelled Residue Count: 898 
• Deposited Residue Count: 917 
• Unique protein chains: 1

1DGK

MUTANT MONOMER OF RECOMBINANT HUMAN HEXOKINASE TYPE I WITH GLUCOSE AND ADP IN THE ACTIVE SITE

• PDB DOI: 10.2210/pdb1DGK/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 1999-11-24 Released: 2000-03-08 
• Deposition Author(s): Aleshin, A.E., Liu, X., Kirby, C., Bourenkov, G.P., Bartunik, H.D., Fromm, H.J., Honzatko, R.B.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.308 
• R-Value Work: 0.258 
• R-Value Observed: 0.260 

Literature

Crystal structures of mutant monomeric hexokinase I reveal multiple ADP binding sites and conformational changes relevant to allosteric regulation.

Aleshin, A.E., Kirby, C., Liu, X., Bourenkov, G.P., Bartunik, H.D., Fromm, H.J., Honzatko, R.B.

(2000) J Mol Biol 296: 1001-1015

• PubMed: 10686099 
• DOI: 10.1006/jmbi.1999.3494
• Primary Citation of Related Structures:  
  1CZA, 1DGK


• PubMed Abstract: 
  

Hexokinase I, the pacemaker of glycolysis in brain tissue, is composed of two structurally similar halves connected by an alpha-helix. The enzyme dimerizes at elevated protein concentrations in solution and in crystal structures; however, almost all published data reflect the properties of a hexokinase I monomer in solution. Crystal structures of mutant forms of recombinant human hexokinase I, presented here, reveal the enzyme monomer for the first time. The mutant hexokinases bind both glucose 6-phosphate and glucose with high affinity to their N and C-terminal halves, and ADP, also with high affinity, to a site near the N terminus of the polypeptide chain. Exposure of the monomer crystals to ADP in the complete absence of glucose 6-phosphate reveals a second binding site for adenine nucleotides at the putative active site (C-half), with conformational changes extending 15 A to the contact interface between the N and C-halves. The structures reveal distinct conformational states for the C-half and a rigid-body rotation of the N-half, as possible elements of a structure-based mechanism for allosteric regulation of catalysis.

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Related Citations: 

• 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 Biol 282: 345

• The Mechanism of Regulation of Hexokinase: New Insights from the Crystal Structure of Recombinant Human Brain Hexokinase Complexed with Glucose and Glucose-6-Phosphate
  Aleshin, A.E., Zeng, C., Bartunik, H.D., Fromm, H.J., Honzatko, R.B.
  (1998) Structure 6: 39

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HEXOKINASE TYPE I	A [auth N]	917	Homo sapiens	Mutation(s): 4  Gene Names: HK1 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

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ADP	E [auth N], F [auth N]	ADENOSINE-5'-DIPHOSPHATE C10 H15 N5 O10 P2 XTWYTFMLZFPYCI-KQYNXXCUSA-N
GLC	B [auth N], C [auth N]	alpha-D-glucopyranose C6 H12 O6 WQZGKKKJIJFFOK-DVKNGEFBSA-N
PO4	D [auth N]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.308 
• R-Value Work: 0.258 
• R-Value Observed: 0.260 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 145.78	α = 90
b = 146.83	β = 90
c = 58.59	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: 1999-11-24 
• Released Date: 2000-03-08 
Deposition Author(s): Aleshin, A.E., Liu, X., Kirby, C., Bourenkov, G.P., Bartunik, H.D., Fromm, H.J., Honzatko, R.B.

Revision History  

• Version 1.0: 2000-03-08
  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: 2018-01-31
  Changes: Database references
• Version 1.4: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Database references, Derived calculations, Structure summary
• Version 1.5: 2021-11-03
  Changes: Database references, Structure summary