Substrate recognition mechanism and substrate-dependent conformational changes of an ROK family glucokinase from Streptomyces griseus

Journal of Bacteriology

Volumn 194, Issue 3, 2012, Pages 607-616

  Miyazono, Ken ichi ^a   Tabei, Nobumitsu ^a   Morita, Sho ^a   Ohnishi, Yasuo ^a   Horinouchi, Sueharu ^a   Tanokura, Masaru ^a  

^a UNIVERSITY OF TOKYO   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

ADENYLYLIMIDODIPHOSPHATE; BACTERIAL PROTEIN; GLUCOKINASE; GLUCOSE; HEXOKINASE 1; PROTEIN SGGLKA; UNCLASSIFIED DRUG; ZINC ION;

ALPHA HELIX; AMINO ACID SEQUENCE; AMINO TERMINAL SEQUENCE; ARTICLE; BACTERIAL PHENOMENA AND FUNCTIONS; BINDING KINETICS; CARBON CATABOLITE REPRESSION; CARBOXY TERMINAL SEQUENCE; CONFORMATIONAL TRANSITION; CRYSTAL STRUCTURE; DIMERIZATION; ENZYME ACTIVE SITE; ENZYME ACTIVITY; ENZYME SUBSTRATE; HYDROGEN BOND; HYDROPHOBICITY; MOLECULAR RECOGNITION; NONHUMAN; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN DOMAIN; PROTEIN EXPRESSION; PROTEIN MODIFICATION; SEQUENCE ANALYSIS; STREPTOMYCES COELICOLOR; STREPTOMYCES GRISEUS; STRUCTURE ANALYSIS; ZINC FINGER MOTIF;

ADENYLYL IMIDODIPHOSPHATE; AMINO ACID MOTIFS; AMINO ACID SEQUENCE; BACTERIAL PROTEINS; BINDING SITES; GLUCOKINASE; GLUCOSE; KINETICS; MOLECULAR SEQUENCE DATA; PROTEIN BINDING; PROTEIN CONFORMATION; PROTEIN STRUCTURE, TERTIARY; SEQUENCE ALIGNMENT; STREPTOMYCES GRISEUS; SUBSTRATE SPECIFICITY;

STREPTOMYCES; STREPTOMYCES GRISEUS;

EID: 84855929228     PISSN: 00219193     EISSN: 10985530     Source Type: Journal    
DOI: 10.1128/JB.06173-11     Document Type: Article

References (57)

1. Aleshin AE, et al. 2000. Crystal structures of mutant monomeric hexokinase I reveal multiple ADP binding sites and conformational changes relevant to allosteric regulation. J. Mol. Biol. 296:1001-1015.
2. Anderson CM, Stenkamp RE, Steitz TA. 1978. Sequencing a protein by x-ray crystallography. II. Refinement of yeast hexokinase B co-ordinates and sequence at 2.1 A resolution. J. Mol. Biol. 123:15-33.
3. Angell S, Lewis C, Buttner M, Bibb M. 1994. Glucose repression in Streptomyces coelicolor A3(2): a likely regulatory role for glucose kinase. Mol. Gen. Genet. 244:135-143.
4. Angell S, Schwarz E, Bibb M. 1992. The glucose kinase gene of Streptomyces coelicolor A3(2): its nucleotide sequence, transcriptional analysis and role in glucose repression. Mol. Microbiol. 6:2833-2844.
5. Arora KK, Filburn CR, Pedersen PL. 1993. Structure/function relationships in hexokinase. Site-directed mutational analyses and characterization of overexpressed fragments implicate different functions for the Nand C-terminal halves of the enzyme. J. Biol. Chem. 268:18259-18266.
6. Brückner R, Titgemeyer F. 2002. Carbon catabolite repression in bacteria: choice of the carbon source and autoregulatory limitation of sugar utilization. FEMS Microbiol. Lett. 209:141-148.
7. Chater KF. 1993. Genetics of differentiation in Streptomyces. Annu. Rev. Microbiol. 47:685-713.
8. Claessen D, de Jong W, Dijkhuizen L, and Wösten H. 2006. Regulation of Streptomyces development: reach for the sky! Trends Microbiol. 14:313-319.
9. Conejo MS, Thompson SM, Miller BG. 2010. Evolutionary bases of carbohydrate recognition and substrate discrimination in the ROK protein family. J. Mol. Evol. 70:545-556.
10. Demain A. 2000. Small bugs, big business: the economic power of the microbe. Biotechnol. Adv. 18:499-514.
11. Gouet P, Courcelle E, Stuart DI, Metoz F. 1999. ESPript: analysis of multiple sequence alignments in PostScript. Bioinformatics 15:305-308.
12. Görke B, Stülke J. 2008. Carbon catabolite repression in bacteria: many ways to make the most out of nutrients. Nat. Rev. Microbiol. 6:613- 624.
13. Hansen T, Reichstein B, Schmid R, Schönheit P. 2002. The first archaeal ATP-dependent glucokinase, from the hyperthermophilic crenarchaeon Aeropyrum pernix, represents a monomeric, extremely thermophilic ROK glucokinase with broad hexose specificity. J. Bacteriol. 184:5955-5965.
14. Hayward S, Berendsen HJ. 1998. Systematic analysis of domain motions in proteins from conformational change: new results on citrate synthase and T4 lysozyme. Proteins 30:144-154.
15. Hijikata A, Yura K, Noguti T, Go M. 2011. Revisiting gap locations in amino acid sequence alignments and a proposal for a method to improve them by introducing solvent accessibility. Proteins 79:1868-1877.
16. Holm L, Park J. 2000. DaliLite workbench for protein structure comparison. Bioinformatics 16:566-567.
17. Holmes KC, Sander C, Valencia A. 1993. A new ATP-binding fold in actin, hexokinase and Hsc70. Trends Cell Biol. 3:53-59.
18. Horinouchi S. 2002. A microbial hormone, A-factor, as a master switch for morphological differentiation and secondary metabolism in Streptomyces griseus. Front. Biosci. 7:d2045-2057.
19. Imriskova I, et al. 2005. Biochemical characterization of the glucose kinase from Streptomyces coelicolor compared to Streptomyces peucetius var. caesius. Res. Microbiol. 156:361-366.
20. Ingram C, Westpheling J. 1995. The glucose kinase gene of Streptomyces coelicolor is not required for glucose repression of the chi63 promoter. J. Bacteriol. 177:3587-3588.
21. Ito S, et al. 2003. Crystal structure of an ADP-dependent glucokinase from Pyrococcus furiosus: implications for a sugar-induced conformational change in ADP-dependent kinase. J. Mol. Biol. 331:871- 883.
22. Ito S, et al. 2001. Structural basis for the ADP-specificity of a novel glucokinase from a hyperthermophilic archaeon. Structure 9:205-214.
23. Kabsch W. 1993. Automatic processing of rotation diffraction data from crystals of initially unknown symmetry and cell constants. J. Appl. Cryst. 26:795- 800.
24. Kamata K, Mitsuya M, Nishimura T, Eiki J, Nagata Y. 2004. Structural basis for allosteric regulation of the monomeric allosteric enzyme human glucokinase. Structure 12:429-438.
25. Krissinel E, Henrick K. 2007. Inference of macromolecular assemblies from crystalline state. J. Mol. Biol. 372:774-797.
26. Kwakman J, Postma P. 1994. Glucose kinase has a regulatory role in carbon catabolite repression in Streptomyces coelicolor. J. Bacteriol. 176:2694-2698.
27. Larion M, Moore LB, Thompson SM, Miller BG. 2007. Divergent evolution of function in theROKsugar kinase superfamily: role of enzyme loops in substrate specificity. Biochemistry 46:13564-13572.
28. Lovell SC, et al. 2003. Structure validation by Calpha geometry: phi, psi and Cbeta deviation. Proteins 50:437- 450.
29. Lunin V, et al. 2004. Crystal structures of Escherichia coli ATPdependent glucokinase and its complex with glucose. J. Bacteriol. 186:6915-6927.
30. Mahr K, et al. 2000. Glucose kinase of Streptomyces coelicolor A3(2): large-scale purification and biochemical analysis. Antonie Van Leeuwenhoek 78:253-261.
31. Marina A, Waldburger CD, Hendrickson WA. 2005. Structure of the entire cytoplasmic portion of a sensor histidine-kinase protein. EMBO J. 24:4247- 4259.
32. Mathews II, Erion MD, Ealick SE. 1998. Structure of human adenosine kinase at 1.5 A resolution. Biochemistry 37:15607-15620.
33. McRee DE. 1999. XtalView/Xfit-a versatile program for manipulating atomic coordinates and electron density. J. Struct. Biol. 125:156-165.
34. Mesak L, Mesak F, Dahl M. 2004. Bacillus subtilis GlcK activity requires cysteines within a motif that discriminates microbial glucokinases into two lineages. BMC Microbiol. 4:6.
35. Meyer D, Schneider-Fresenius C, Horlacher R, Peist R, Boos W. 1997. Molecular characterization of glucokinase from Escherichia coli K-12. J. Bacteriol. 179:1298-1306.
36. Miyazono K, et al. 2011. Purification, crystallization and preliminary X-ray analysis of glucokinase from Streptomyces griseus in complex with glucose. Acta Crystallogr. Sect. F Struct. Biol. Cryst. Commun. 67:914-916.
37. Murshudov GN, Vagin AA, Dodson EJ. 1997. Refinement of macromolecular structures by the maximum-likelihood method. Acta Crystallogr. D Biol. Crystallogr. 53:240-255.
38. Nam T, et al. 2008. Analyses of Mlc-IIBGlc interaction and a plausible molecular mechanism of Mlc inactivation by membrane sequestration. Proc. Natl. Acad. Sci. U. S. A. 105:3751-3756.
39. Parche S, Nothaft H, Kamionka A, Titgemeyer F. 2000. Sugar uptake and utilisation in Streptomyces coelicolor: a PTS view to the genome. Antonie Van Leeuwenhoek 78:243-251.
40. Plumbridge J. 2002. Regulation of gene expression in the PTS in Escherichia coli: the role and interactions of Mlc. Curr. Opin. Microbiol. 5:187-193.
41. Ramos I, et al. 2004. Glucose kinase alone cannot be responsible for carbon source regulation in Streptomyces peucetius var. caesius. Res. Microbiol. 155:267-274.
42. Ronimus R, Morgan H. 2004. Cloning and biochemical characterization of a novel mouse ADP-dependent glucokinase. Biochem. Biophys. Res. Commun. 315:652- 658.
43. Ruiz B, et al. 2010. Production of microbial secondary metabolites: regulation by the carbon source. Crit. Rev. Microbiol. 36:146-167.
44. Sakuraba H, et al. 2002. ADP-dependent glucokinase/phosphofructokinase, a novel bifunctional enzyme from the hyperthermophilic archaeon Methanococcus jannaschii. J. Biol. Chem. 277:12495-12498.
45. Sánchez S, et al. 2010. Carbon source regulation of antibiotic production. J. Antibiot. (Tokyo) 63:442- 459.
46. Schiefner A, et al. 2005. The crystal structure of Mlc, a global regulator of sugar metabolism in Escherichia coli. J. Biol. Chem. 280:29073-29079.
47. Sigrell JA, Cameron AD, Mowbray SL. 1999. Induced fit on sugar binding activates ribokinase. J. Mol. Biol. 290:1009-1018.
48. Storer AC, Cornish-Bowden A. 1976. Kinetics of rat liver glucokinase. Co-operative interactions with glucose at physiologically significant concentrations. Biochem. J. 159:7-14.
49. Suzuki Y, Shimizu T, Morii H, Tanokura M. 1997. Hydrolysis of AMPPNP by the motor domain of ncd, a kinesin-related protein. FEBS Lett. 409:29-32.
50. Titgemeyer F, Reizer J, Reizer A, Saier MJ. 1994. Evolutionary relationships between sugar kinases and transcriptional repressors in bacteria. Microbiology 140:2349-2354.
51. Titgemeyer F, et al. 1995. Identification and characterization of phosphoenolpyruvate:fructose phosphotransferase systems in three Streptomyces species. Microbiology 141:51-58.
52. Tong Y, Tempel W, Nedyalkova L, Mackenzie F, Park HW. 2009. Crystal structure of the N-acetylmannosamine kinase domain of GNE. PLoS One 4:e7165.
53. Tsuge H, et al. 2002. Crystal structure of the ADP-dependent glucokinase from Pyrococcus horikoshii at 2.0-A resolution: a large conformational change in ADP-dependent glucokinase. Protein Sci. 11:2456-2463.
54. Vagin A, Teplyakov A. 1997. MOLREP: an Automated Program for Molecular Replacement. J. Appl. Cryst. 30:1022-1025.
55. van Wezel GP, et al. 2007. A new piece of an old jigsaw: glucose kinase is activated posttranslationally in a glucose transport-dependent manner in streptomyces coelicolor A3(2). J. Mol. Microbiol. Biotechnol. 12:67-74.
56. van Wezel GP, et al. 2005. GlcP constitutes the major glucose uptake system of Streptomyces coelicolor A3(2). Mol. Microbiol. 55:624-636.
57. Zeng C, Aleshin AE, Hardie JB, Harrison RW, Fromm HJ. 1996. ATP-binding site of human brain hexokinase as studied by molecular modeling and site-directed mutagenesis. Biochemistry 35:13157-13164.