Crystal Structure of the Nucleotide-binding Subunit DhaL of the Escherichia coli Dihydroxyacetone Kinase

Journal of Molecular Biology

Volumn 359, Issue 3, 2006, Pages 539-545

  Oberholzer, Anselm Erich ^a   Schneider, Philipp ^a   Baumann, Ulrich ^a   Erni, Bernhard ^a  

^a UNIVERSITY OF BERN   (Switzerland)

Author keywords

ADP; dihydroxyacetone; glycerone; phosphoenolpyruvate; phosphotransferase system

Indexed keywords

ADENOSINE DIPHOSPHATE; ADENOSINE TRIPHOSPHATE; ASPARTIC ACID; CARBOXYL GROUP; DHAL PROTEIN; DIHYDROXYACETONE; HISTIDINE; IMIDAZOLE; MAGNESIUM ION; NUCLEOTIDE BINDING PROTEIN; PHOSPHOENOLPYRUVATE; PHOSPHOTRANSFERASE; PROTEIN SUBUNIT; UNCLASSIFIED DRUG;

ARTICLE; CITROBACTER FREUNDII; CRYSTAL STRUCTURE; ESCHERICHIA COLI; HIGH ENERGY PHOSPHATE; HYDROGEN BOND; NONHUMAN; NUCLEOTIDE BINDING SITE; PRIORITY JOURNAL; PROTEIN QUATERNARY STRUCTURE;

BUTEA MONOSPERMA; CITROBACTER FREUNDII; ESCHERICHIA COLI;

EID: 33646814437     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jmb.2006.03.057     Document Type: Article

References (29)

1. Erni B., Siebold C., Christen S., Srinivas A., Oberholzer A., and Baumann U. Small substrate, big surprise: fold, function and phylogeny of dihydroxyacetone kinases. Cell. Mol. Life Sci. (2006) In the press
2. Gutknecht R., Beutler R., Garcia Alles L.F., Baumann U., and Erni B. The dihydroxyacetone kinase of Escherichia coli utilizes a phosphoprotein instead of ATP as phosphoryldonor. EMBO J. 20 (2001) 2480-2486
3. Erni B., Zanolari B., and Kocher H.P. The mannose permease of Escherichia coli consists of three different proteins: amino acid sequence and function in sugar transport, sugar phosphorylation, and penetration of phage lambda DNA. J. Biol. Chem. 262 (1987) 5238-5247
4. Nunn R.S., Markovic-Housley Z., Génovésio-Taverne J.C., Flükiger K., Rizkallah P.J., Jansonius J.N., et al. Structure of the IIA domain of the mannose transporter from Escherichia coli at 1.7 Å resolution. J. Mol. Biol. 259 (1996) 502-511
5. Luers G.H., Advani R., Wenzel T., and Subramani S. The Pichia pastoris dihydroxyacetone kinase is a PTS1-containing, but cytosolic, protein that is essential for growth on methanol. Yeast 14 (1998) 759-771
6. Waites M.J., and Quayle J.R. The interrelation transketolase and dihydroxyacetone synthase activities in the methylotrophic yeast Candida boidinii. J. Gen. Microbiol. 124 (1981) 309-316
7. Forage R.G., and Lin E.C. DHA system mediating aerobic and anaerobic dissimilation of glycerol in Klebsiella pneumoniae NCIB 418. J. Bacteriol. 151 (1982) 591-599
8. Jin R.Z., and Lin E.C.C. An inducible phosphoenolpyruvate: dihydroxyacetone phosphotransferase system in Escherichia coli. J. Gen. Microbiol. 130 (1984) 83-88
9. Molin M., Norbeck J., and Blomberg A. Dihydroxyacetone kinases in Saccharomyces cerevisiae are involved in detoxification of dihydroxyacetone. J. Biol. Chem. 278 (2003) 1415-1423
10. Taguchi T., Murase S., and Miwa I. Glyceraldehyde metabolism in human erythrocytes in comparison with that of glucose and dihydroxyacetone. Cell. Biochem. Funct. 20 (2002) 223-226
11. Antinozzi P.A., Ishihara H., Newgard C.B., and Wollheim C.B. Mitochondrial metabolism sets the maximal limit of fuel-stimulated insulin secretion in a model pancreatic beta cell: a survey of four fuel secretagogues. J. Biol. Chem. 277 (2002) 11746-11755
12. Feron V.J., Til H.P., de Vrijer F., Woutersen R.A., Cassee F.R., and van Bladeren P.J. Aldehydes: occurrence, carcinogenic potential, mechanism of action and risk assessment. Mutat. Res. 259 (1991) 363-385
13. Petersen A.B., Wulf H.C., Gniadecki R., and Gajkowska B. Dihydroxyacetone, the active browning ingredient in sunless tanning lotions, induces DNA damage, cell-cycle block and apoptosis in cultured HaCaT keratinocytes. Mutat. Res. 560 (2004) 173-186
14. Tessier F.J., Monnier V.M., Sayre L.A., and Kornfield J.A. Triosidines: novel Maillard reaction products and crosslinks from the reaction of triose sugars with lysine and arginine residues. Biochem. J. 369 (2003) 705-719
15. Siebold C., Arnold I., Garcia-Alles L.F., Baumann U., and Erni B. Crystal structure of the Citrobacter freundii dihydroxyacetone kinase reveals an eight-stranded alpha-helical barrel ATP-binding domain. J. Biol. Chem. 278 (2003) 48236-48244
16. Cheek S., Ginalski K., Zhang H., and Grishin N.V. A comprehensive update of the sequence and structure classification of kinases. BMC Struct. Biol. 5 (2005) 6
17. Vetter I.R., and Wittinghofer A. Nucleoside triphosphate-binding proteins: different scaffolds to achieve phosphoryl transfer. Quart. Rev. Biophys. 32 (1999) 1-56
18. Garcia-Alles L.F., Siebold C., Nyffeler T.L., Flukiger-Bruhwiler K., Schneider P., Burgi H.B., et al. Phosphoenolpyruvate- and ATP-dependent dihydroxyacetone kinases: covalent substrate-binding and kinetic mechanism. Biochemistry 43 (2004) 13037-13045
19. Siebold C., Garcia-Alles L.F., Erni B., and Baumann U. A novel mechanism of covalent substrate binding in the X-ray structure of the DhaK subunit of the Escherichia coli dihydroxyacetone kinase. Proc. Natl Acad. Sci. USA 100 (2003) 8188-8192
20. Bachler C., Flukiger-Bruhwiler K., Schneider P., Bahler P., and Erni B. From ATP as substrate to ADP as coenzyme: functional evolution of the nucleotide binding subunit of dihydroxyacetone kinases. J. Biol. Chem. 280 (2005) 18321-18325
21. Bachler C., Schneider P., Bahler P., Lustig A., and Erni B. Escherichia coli dihydroxyacetone kinase controls gene expression by binding to transcription factor DhaR. EMBO J. 24 (2005) 283-293
22. Kleywegt G.J., and Jones T.A. Phi/psi-chology: Ramachandran revisited. Structure 4 (1996) 1395-1400
23. Vondrasek J., Bendova L., Klusak V., and Hobza P. Unexpectedly strong energy stabilization inside the hydrophobic core of small protein rubredoxin mediated by aromatic residues: correlated ab initio quantum chemical calculations. J. Am. Chem. Soc. 127 (2005) 2615-2619
24. Kabsch W. Automatic indexing of rotation diffraction patterns. J. Appl. Crystallog. 21 (1988) 67-72
25. Kabsch W. Automatic processing of rotation diffraction data from crystals of initially unknown symmetry and cell constants. J. Appl. Crystallog. 26 (1993) 795-800
26. Storoni L.C., McCoy A.J., and Read R.J. Likelihood-enhanced fast rotation functions. Acta Crystallog. sect. D 60 (2004) 432-438
27. Brunger A.T., Adams P.D., Clore G.M., DeLano W.L., Gros P.R.W., Jiang J.S., et al. Crystallography & NMR system: A new software suite for macromolecular structure determination. Acta Crystallog. sect. D 54 (1998) 905-921
28. Jones T.A., Zou J.Y., and Cowan S.W. Improved methods for binding protein models in electron density maps and the location of errors in these models. Acta Crystallog. sect. A 47 (1991) 110-119
29. Murshudov G.N., Vagin A.A., and Dodson E.J. Refinement of macromolecular structures by the maximum-likelihood method. Acta Crystallog. sect. D 53 (1997) 240-255