1UOD

Crystal structure of the dihydroxyacetone kinase from E. coli in complex with dihydroxyacetone-phosphate

Summary for 1UOD

• Entry DOI: 10.2210/pdb1uod/pdb
• Related: 1OI2 1OI3 1UOE
• Descriptor: DIHYDROXYACETONE KINASE, GLYCERALDEHYDE-3-PHOSPHATE, SULFATE ION, ... (4 entities in total)
• Functional Keywords: transferase, kinase
• Biological source: ESCHERICHIA COLI
• Total number of polymer chains: 2
• Total formula weight: 79597.46

Authors

Siebold, C.,Garcia-Alles, L.F.,Luthi-Nyffeler, T.,Flukiger-Bruhwiler, K.,Burgi, H.-B.,Baumann, U.,Erni, B. (deposition date: 2003-09-16, release date: 2004-09-24, Last modification date: 2024-11-13)

Primary citation

Garcia-Alles, L.F.,Siebold, C.,Luthi-Nyffeler, T.,Flukiger-Bruhwiler, K.,Schneider, P.,Burgi, H.-B.,Baumann, U.,Erni, B.
Phosphoenolpyruvate- and ATP-Dependent Dihydroxyacetone Kinases: Covalent Substrate-Binding and Kinetic Mechanism
Biochemistry, 43:13037-, 2004

PubMed Abstract: Dihydroxyacetone (Dha) kinases are a sequence-conserved family of enzymes, which utilize two different phosphoryldonors, ATP in animals, plants, and some bacteria, and a multiphosphoprotein of the phosphoenolpyruvate carbohydrate phosphotransferase system (PTS) in most bacteria. Here, we compare the PTS-dependent kinase of Escherichia coli and the ATP-dependent kinase of Citrobacter freundii. They display 30% sequence identity. The binding constants of the E. coli kinase for eleven short-chain carbonyl compounds were determined by acetone precipitation of the enzyme-substrate complexes. They are 3.4 microM for Dha, 780 microM for Dha-phosphate (DhaP), 50 microM for D,L-glyceraldehyde (GA), and 90 microM for D,L-glyceraldehyde-3-phosphate. The k(cat) for Dha of the PTS-dependent kinase is 290 min(-1), and that of the ATP-dependent kinase is 1050 min(-1). The Km for Dha of both kinases is <6 microM. The X-ray structures of the enzyme-GA and the enzyme-DhaP complex show that substrates as well as products are bound in hemiaminal linkage to an active-site histidine. Quantum-mechanical calculations offer no indication for activation of the reacting hydroxyl group by the formation of the hemiaminal. However, the formation of the hemiaminal bond allows selection for short-chain carbonyl compounds and discrimination against structurally similar polyols. The Dha kinase remains fully active in the presence of 2 M glycerol, and phosphorylates trace impurities of carbonyl compounds present in glycerol.

PubMed: 15476397
DOI: 10.1021/BI048575M

Experimental method

X-RAY DIFFRACTION (1.9 Å)