Structure and Reaction Mechanism of l-Rhamnulose Kinase from Escherichia coli

Journal of Molecular Biology

Volumn 359, Issue 3, 2006, Pages 787-797

  Grueninger, Dirk ^a   Schulz, Georg E ^a  

^a UNIVERSITY OF FREIBURG   (Germany)

Author keywords

hexokinase hsp70 actin superfamily; in line phosphoryl transfer; induced fit; rhamnose degradation; X ray diffraction

Indexed keywords

ACTIN; ADENOSINE DIPHOSPHATE; CYSTEINE; DISULFIDE; FRUCTOSE; GLYCEROL KINASE; HEAT SHOCK PROTEIN 70; HEXOKINASE; LEVO RHAMNULOSE KINASE; PHOSPHOTRANSFERASE; UNCLASSIFIED DRUG;

AMINO ACID SEQUENCE; ARTICLE; CATALYSIS; CONFORMATIONAL TRANSITION; CRYSTAL STRUCTURE; ESCHERICHIA COLI; GENE CONTROL; INFORMATION PROCESSING; NONHUMAN; PRIORITY JOURNAL; PROTEIN BINDING; PROTEIN DETERMINATION; PROTEIN PHOSPHORYLATION; REACTION ANALYSIS; STATISTICAL ANALYSIS;

BACTERIA (MICROORGANISMS); ESCHERICHIA COLI;

EID: 33646756593     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jmb.2006.04.013     Document Type: Article

References (57)

1. McNeil M., Darvill A.G., Fry S.C., and Albersheim P. Structure and function of the primary cell walls of plants. Annu. Rev. Biochem. 53 (1984) 625-663
2. Moralejo P., Egan S.M., Hidalgo E., and Aguilar J. Sequencing and characterization of a gene cluster encoding the enzymes for l-rhamnose metabolism in Escherichia coli. J. Bacteriol. 175 (1993) 5585-5594
3. Bork P., Sander C., and Valencia A. An ATPase domain common to prokaryotic cell cycle proteins, sugar kinases, actin, and hsp70 heat shock proteins. Proc. Natl Acad. Sci. USA 89 (1992) 7290-7294
4. Anderson C.M., Stenkamp R.E., and Steitz T.A. Sequencing a protein by X-ray crystallography. II. Refinement of yeast hexokinase B co-ordinates and sequence at 2.1 Å resolution. J. Mol. Biol. 123 (1978) 15-33
5. Flaherty K.M., DeLuca-Flaherty C., and McKay D.B. Three-dimensional structure of the ATPase fragment of a 70k heat-shock cognate protein. Nature 346 (1990) 623-628
6. Kabsch W., Mannherz H.G., Suck D., Pai E.F., and Holmes K.C. Atomic structure of the actin: DNase I complex. Nature 347 (1990) 37-44
7. Hurley J.H., Faber H.R., Worthylake D., Meadow N.D., Roseman S., Pettigrew D.W., and Remington S.J. Structure of the regulatory complex of Escherichia coli IIIGlc with glycerol kinase. Science 259 (1993) 673-677
8. van den Ent F., and Löwe J. Crystal structure of the cell division protein FtsA from Thermotoga maritima. EMBO J. 19 (2000) 5300-5307
9. Buss K.A., Cooper D.R., Ingram-Smith C., Ferry J.G., Sanders D.A., and Hasson M.S. Urkinase: structure of acetate kinase, a member of the ASKHA superfamily of phosphotransferases. J. Bacteriol. 183 (2001) 680-686
10. Locher K.P., Hans M., Yeh A.P., Schmid B., Buckel W., and Rees D.C. Crystal structure of the Acidaminococcus fermentans 2-hydroxyglutaryl-CoA dehydrase component A. J. Mol. Biol. 307 (2001) 297-308
11. van den Ent F., Moller-Jensen J., Amos L.A., Gerdes K., and Löwe J. F-actin-like filaments formed by plasmid segregation protein ParM. EMBO J. 21 (2002) 6935-6943
12. Diao J., Cooper D.R., Sanders D.A., and Hasson M.S. Crystallization of butyrate kinase 2 from Thermotoga maritima mediated by vapor diffusion of acetic acid. Accession code 1SAZ. Acta Crystallog. sect. D 59 (2003) 1100-1102
13. Mukai T., Kawai S., Mori S., Mikami B., and Murata K. Crystal structure of bacterial inorganic polyphosphate/ATP-glucomannokinase. J. Biol. Chem. 279 (2004) 50591-50600
14. Simanshu D.H., Savithri H.S., and Murthy M.R.N. Crystal structures of ADP and AMPPNP-bound propionate kinase (TdcD) from Salmonella typhimurium: comparison with members of acetate and sugar kinase/heat shock cognate 70/actin superfamily. J. Mol. Biol. 352 (2005) 876-892
15. Bennett Jr. W.S., and Steitz T.A. Glucose-induced conformational change in yeast hexokinase. Proc. Natl Acad. Sci. USA 75 (1978) 4848-4852
16. Dreusicke D., and Schulz G.E. The glycine-rich loop of adenylate kinase forms a giant anion hole. FEBS Letters 208 (1986) 301-304
17. 18O]triphosphate and the mechanistic consequences for the reactions catalyzed by glycerol kinase, hexokinase, pyruvate kinase, and acetate kinase. Biochemistry 18 (1979) 3927-3933
18. Todhunter J.A., and Purich D.L. Evidence for the formation of a gamma-phosphorylated glutamyl residue in the Escherichia coli acetate kinase reaction. Biochem. Biophys. Res. Commun. 60 (1974) 273-280
19. Spector L.B. Acetate kinase: a triple-displacement enzyme. Proc. Natl Acad. Sci. USA 77 (1980) 2626-2630
20. Gorrell A., Lawrence S.H., and Ferry J.G. Structural and kinetic analyses of arginine residues in the active site of the acetate kinase from Methanosarcina thermophila. J. Biol. Chem. 280 (2005) 10731-10742
21. Korndörfer I.P., Fessner W.D., and Matthews B.W. The structure of rhamnose isomerase from Escherichia coli and its relation with xylose isomerase illustrates a change between inter and intra-subunit complementation during evolution. J. Mol. Biol. 300 (2000) 917-933
22. Kroemer M., Merkel I., and Schulz G.E. Structure and catalytic mechanism of l-rhamnulose-1-phosphate aldolase. Biochemistry 42 (2003) 10560-10568
23. Kanehisa M. The KEGG database. Novartis Found. Symp. 247 (2002) 91-101
24. Derewenda Z.S. Rational protein crystallization by mutational surface engineering. Structure 12 (2004) 529-535
25. Pautsch A., Vogt J., Model K., Siebold C., and Schulz G.E. Strategy for membrane protein crystallization exemplified with OmpA and OmpX. Proteins: Struct. Funct. Genet. 34 (1999) 167-172
26. Rost B., Yachdav G., and Liu J. The PredictProtein server. Nucl. Acids Res. 32 (2004) W321-W326
27. Doublie S. Preparation of selenomethionyl proteins for phase determination. Methods Enzymol. 276 (1997) 523-530
28. Yeh J.I., Charrier V., Paulo J., Hou L., Darbon E., Claiborne A., et al. Structures of enterococcal glycerol kinase in the absence and presence of glycerol: correlation of conformation to substrate binding and a mechanism of activation by phosphorylation. Biochemistry 43 (2004) 362-373
29. Ormö M., Bystrom C.E., and Remington S.J. Crystal structure of a complex of Escherichia coli glycerol kinase and an allosteric effector fructose-1,6-bisphosphate. Biochemistry 37 (1998) 16565-16572
30. Holmes K.C., Popp D., Gebhard W., and Kabsch W. Atomic model of the actin filament. Nature 347 (1990) 44-49
31. Britton M.E., and Kapoor M. The oligomeric state, complex formation, and chaperoning activity of Hsp70 and Hsp80 of Neurospora crassa. Biochem. Biol. Cell 80 (2002) 797-809
32. Altschul S.F., Madden T.L., Schäffer A.A., Zhang J., Zhang Z., Miller W., and Lipman D.J. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucl. Acids Res. 25 (1997) 3389-3402
33. Holm L., and Sander C. Protein structure comparison by alignment of distance matrices. J. Mol. Biol. 233 (1993) 123-138
34. Fessner W.-D., Badia J., Eyrisch O., Schneider A., and Sinerius G. Enzymatic syntheses of rare ketose 1-phosphates. Tetrahedron Letters 33 (1992) 5231-5234
35. Badia J., Gimenez R., Baldoma L., Barnes E., Fessner W.-D., and Aguilar J. l-Lyxose metabolism employs the l-rhamnose pathway in mutant cells of Escherichia coli adapted to grow on l-lyxose. J. Bacteriol. 173 (1991) 5144-5150
36. Singh-Wissmann K., Ingram-Smith C., Miles R.D., and Ferry J.G. Identification of essential glutamates in the acetate kinase from Methanosarcina thermophila. J. Bacteriol. 180 (1998) 1129-1134
37. Bystrom C.E., Pettigrew D.W., Branchaud B.P., O'Brien P., and Remington S.J. Crystal structures of Escherichia coli glycerol kinase variant S58W in complex with nonhydrolyzable ATP analogues reveal a putative active conformation of the enzyme as a result of domain motion. Biochemistry 38 (1999) 3508-3518
38. Page R., Lindberg U., and Schutt C.E. Domain motions in actin. J. Mol. Biol. 280 (1998) 463-474
39. Jiang J., Prasad K., Lafer E.M., and Sousa R. Structural basis of interdomain communication in the hsc70 chaperone. Mol. Cell 20 (2005) 513-524
40. Vonrhein C., Schlauderer G.J., and Schulz G.E. Movie of the structural changes during a catalytic cycle of nucleoside monophosphate kinases. Structure 3 (1995) 483-490
41. Schulz G.E. Binding of nucleotides by proteins. Curr. Opin. Struct. Biol. 2 (1992) 61-67
42. 5A, showing the pathway of phosphoryl transfer. Protein Sci. 4 (1995) 1262-1271
43. Matte A., Tari L.W., and Delbaere L.T.J. How do kinases transfer phosphoryl groups?. Structure 6 (1998) 413-419
44. Anderson C.M., Stenkamp R.E., McDonald R.C., and Steitz T.A. A refined model of the sugar binding site of yeast hexokinase B. J. Mol. Biol. 123 (1978) 207-219
45. Kuser P.R., Krauchenco S., Antunes O.A.C., and Polikarpov I. The high resolution crystal structure of yeast hexokinase PII with the correct primary sequence provides new insights into its mechanism of action. J. Biol. Chem. 275 (2000) 20814-20821
46. Kabsch W. Automatic processing of rotation diffraction data from crystals of initially unknown symmetry and cell constants. J. Appl. Crystallog. 26 (1993) 795-800
47. Schneider T.R., and Sheldrick G.M. Substructure solution with SHELXD. Acta Crystallog. sect. D 58 (2002) 1772-1779
48. de la Fortelle E., and Bricogne G. Maximum likelihood heavy-atom parameter refinement for multiple isomorphous replacement and multivavelength anomalous diffraction methods. Methods Enzymol. 276 (1997) 472-494
49. Perrakis A., Sixma T.K., Wilson K.S., and Lamzin V.S. wARP: improvement and extension of crystallographic phases by weighted averaging of multiple refined dummy atomic models. Acta Crystallog. sect. D 53 (1997) 448-455
50. Emsley P., and Cowtan K. Coot: model-building tools for molecular graphics. Acta Crystallog. sect. D 60 (2004) 2126-2132
51. 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
52. Schüttelkopf A.W., and van Aalten D.M.F. PRODRG: a tool for high throughput crystallography of protein-ligand complexes. Acta Crystallog. sect. D 60 (2004) 1355-1363
53. Read R.J. Pushing the boundaries of molecular replacement with maximum likelihood. Acta Crystallog. sect. D 57 (2001) 1373-1382
54. Vagin A., and Teplyakov A. MOLREP: an automated program for molecular replacement. J. Appl. Crystallog. 30 (1997) 1022-1025
55. Brünger A.T., Adams P.D., Clore G.M., DeLano W.L., Grosse-Kunstleve R.W., and Jiang J.S. Crystallography & NMR system: a new software suite for macromolecular structure determination. Acta Crystallog. sect. D 54 (1998) 905-921
56. Kleywegt G.J., and Jones T.A. Where freedom is given, liberties are taken. Structure 3 (1995) 535-540
57. Fenn T.D., Ringe D., and Petsko G.A. POVscript+: a program for model and data visualization using persistence of vision ray-tracing. J. Appl. Crystallog. 36 (2003) 944-947