4BC5

Crystal structure of human D-xylulokinase in complex with inhibitor 5- deoxy-5-fluoro-D-xylulose


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.98 Å
  • R-Value Free: 0.192 
  • R-Value Work: 0.172 
  • R-Value Observed: 0.173 

Starting Model: experimental
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This is version 1.4 of the entry. See complete history


Literature

Structure and Function of Human Xylulokinase, an Enzyme with Important Roles in Carbohydrate Metabolism

Bunker, R.D.Bulloch, E.M.M.Dickson, J.M.J.Loomes, K.M.Baker, E.N.

(2013) J Biol Chem 288: 1643

  • DOI: https://doi.org/10.1074/jbc.M112.427997
  • Primary Citation of Related Structures:  
    4BC2, 4BC3, 4BC4, 4BC5

  • PubMed Abstract: 

    D-Xylulokinase (XK; EC 2.7.1.17) catalyzes the ATP-dependent phosphorylation of d-xylulose (Xu) to produce xylulose 5-phosphate (Xu5P). In mammals, XK is the last enzyme in the glucuronate-xylulose pathway, active in the liver and kidneys, and is linked through its product Xu5P to the pentose-phosphate pathway. XK may play an important role in metabolic disease, given that Xu5P is a key regulator of glucose metabolism and lipogenesis. We have expressed the product of a putative human XK gene and identified it as the authentic human d-xylulokinase (hXK). NMR studies with a variety of sugars showed that hXK acts only on d-xylulose, and a coupled photometric assay established its key kinetic parameters as K(m)(Xu) = 24 ± 3 μm and k(cat) = 35 ± 5 s(-1). Crystal structures were determined for hXK, on its own and in complexes with Xu, ADP, and a fluorinated inhibitor. These reveal that hXK has a two-domain fold characteristic of the sugar kinase/hsp70/actin superfamily, with glycerol kinase as its closest relative. Xu binds to domain-I and ADP to domain-II, but in this open form of hXK they are 10 Å apart, implying that a large scale conformational change is required for catalysis. Xu binds in its linear keto-form, sandwiched between a Trp side chain and polar side chains that provide exquisite hydrogen bonding recognition. The hXK structure provides a basis for the design of specific inhibitors with which to probe its roles in sugar metabolism and metabolic disease.


  • Organizational Affiliation

    Maurice Wilkins Centre for Molecular Biodiscovery and School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland 1142, New Zealand.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
XYLULOSE KINASE
A, B, C
538Homo sapiensMutation(s): 0 
EC: 2.7.1.17
UniProt & NIH Common Fund Data Resources
Find proteins for O75191 (Homo sapiens)
Explore O75191 
Go to UniProtKB:  O75191
PHAROS:  O75191
GTEx:  ENSG00000093217 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO75191
Sequence Annotations
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  • Reference Sequence
Small Molecules
Binding Affinity Annotations 
IDSourceBinding Affinity
5FX PDBBind:  4BC5 Ki: 2.50e+4 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.98 Å
  • R-Value Free: 0.192 
  • R-Value Work: 0.172 
  • R-Value Observed: 0.173 
  • Space Group: P 32
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 102.109α = 90
b = 102.109β = 90
c = 159.101γ = 120
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-11-28
    Type: Initial release
  • Version 1.1: 2012-12-05
    Changes: Database references
  • Version 1.2: 2012-12-19
    Changes: Atomic model, Database references, Other
  • Version 1.3: 2013-01-30
    Changes: Database references
  • Version 1.4: 2024-05-01
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description