Structure and function of human xylulokinase, an enzyme with important roles in carbohydrate metabolism

J Biol Chem. 2013 Jan 18;288(3):1643-52. doi: 10.1074/jbc.M112.427997. Epub 2012 Nov 23.


D-Xylulokinase (XK; EC 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.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Adenosine Diphosphate / chemistry*
  • Adenosine Diphosphate / metabolism
  • Catalytic Domain
  • Crystallography, X-Ray
  • Escherichia coli / genetics
  • Gene Expression
  • Humans
  • Hydrogen Bonding
  • Kinetics
  • Magnetic Resonance Spectroscopy
  • Models, Molecular
  • Pentosephosphates / chemistry
  • Pentosephosphates / metabolism
  • Phosphotransferases (Alcohol Group Acceptor) / chemistry*
  • Phosphotransferases (Alcohol Group Acceptor) / genetics
  • Phosphotransferases (Alcohol Group Acceptor) / metabolism
  • Protein Structure, Secondary
  • Protein Structure, Tertiary
  • Recombinant Proteins / chemistry
  • Recombinant Proteins / genetics
  • Recombinant Proteins / metabolism
  • Substrate Specificity
  • Xylulose / analogs & derivatives*
  • Xylulose / metabolism


  • Pentosephosphates
  • Recombinant Proteins
  • Xylulose
  • xylulose-5-phosphate
  • Adenosine Diphosphate
  • Phosphotransferases (Alcohol Group Acceptor)
  • xylulokinase

Associated data

  • PDB/4BC2
  • PDB/4BC3
  • PDB/4BC4
  • PDB/4BC5