6P2D | pdb_00006p2d

Structure of mouse ketohexokinase-C in complex with fructose and ADP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.79 Å
  • R-Value Free: 
    0.220 (Depositor), 0.217 (DCC) 
  • R-Value Work: 
    0.170 (Depositor), 0.170 (DCC) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 2.2 of the entry. See complete history

Literature

Michaelis-like complex of mouse ketohexokinase isoform C.

Gasper, W.C.Gardner, S.Ross, A.Oppelt, S.A.Allen, K.N.Tolan, D.R.

(2024) Acta Crystallogr D Struct Biol 80: 377-385

  • DOI: https://doi.org/10.1107/S2059798324003723
  • Primary Citation Related Structures: 
    6P2D

  • PubMed Abstract: 

    Over the past forty years there has been a drastic increase in fructose-related diseases, including obesity, heart disease and diabetes. Ketohexokinase (KHK), the first enzyme in the liver fructolysis pathway, catalyzes the ATP-dependent phosphorylation of fructose to fructose 1-phosphate. Understanding the role of KHK in disease-related processes is crucial for the management and prevention of this growing epidemic. Molecular insight into the structure-function relationship in ligand binding and catalysis by KHK is needed for the design of therapeutic inhibitory ligands. Ketohexokinase has two isoforms: ketohexokinase A (KHK-A) is produced ubiquitously at low levels, whereas ketohexokinase C (KHK-C) is found at much higher levels, specifically in the liver, kidneys and intestines. Structures of the unliganded and liganded human isoforms KHK-A and KHK-C are known, as well as structures of unliganded and inhibitor-bound mouse KHK-C (mKHK-C), which shares 90% sequence identity with human KHK-C. Here, a high-resolution X-ray crystal structure of mKHK-C refined to 1.79 Å resolution is presented. The structure was determined in a complex with both the substrate fructose and the product of catalysis, ADP, providing a view of the Michaelis-like complex of the mouse ortholog. Comparison to unliganded structures suggests that KHK undergoes a conformational change upon binding of substrates that places the enzyme in a catalytically competent form in which the β-sheet domain from one subunit rotates by 16.2°, acting as a lid for the opposing active site. Similar kinetic parameters were calculated for the mouse and human enzymes and indicate that mice may be a suitable animal model for the study of fructose-related diseases. Knowledge of the similarity between the mouse and human enzymes is important for understanding preclinical efforts towards targeting this enzyme, and this ground-state, Michaelis-like complex suggests that a conformational change plays a role in the catalytic function of KHK-C.


  • Organizational Affiliation
    • Program in Biochemistry and Molecular Biology, Boston University, Boston, MA 02215, USA.

Macromolecule Content 

  • Total Structure Weight: 35.5 kDa 
  • Atom Count: 2,726 
  • Modeled Residue Count: 296 
  • Deposited Residue Count: 315 
  • Unique protein chains: 1

Macromolecules

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Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Ketohexokinase315Mus musculusMutation(s): 0 
Gene Names: KhkmCG_23498
EC: 2.7.1.3
UniProt
Find proteins for P97328 (Mus musculus)
Explore P97328 
Go to UniProtKB:  P97328
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP97328
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.79 Å
  • R-Value Free:  0.220 (Depositor), 0.217 (DCC) 
  • R-Value Work:  0.170 (Depositor), 0.170 (DCC) 
Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 42.252α = 90
b = 78.446β = 90
c = 150.772γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PHENIXrefinement
SADABSdata scaling
PDB_EXTRACTdata extraction
SAINTdata reduction
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2020-06-03
    Type: Initial release
  • Version 1.1: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary
  • Version 1.2: 2023-10-11
    Changes: Data collection, Database references, Refinement description, Structure summary
  • Version 2.0: 2024-05-29
    Type: Coordinate replacement
    Reason: Model orientation/position
    Changes: Advisory, Atomic model, Author supporting evidence, Data collection, Database references, Derived calculations, Non-polymer description, Refinement description, Source and taxonomy, Structure summary
  • Version 2.1: 2024-10-09
    Changes: Structure summary
  • Version 2.2: 2025-11-12
    Changes: Database references