A Structural Code for Discriminating between Transcription Signals Revealed by the Feast/Famine Regulatory Protein DM1 in Complex with Ligands

Structure

Volumn 15, Issue 10, 2007, Pages 1325-1338

  Okamura, Hideyasu ^a,b   Yokoyama, Katsushi ^a,b   Koike, Hideaki ^a   Yamada, Mitsugu ^a,b   Shimowasa, Ai ^a,b   Kabasawa, Mamiko ^a,b   Kawashima, Tsuyoshi ^a,b   Suzuki, Masashi ^a  

^a NATIONAL INSTITUTE OF ADVANCED INDUSTRIAL SCIENCE AND TECHNOLOGY AIST   (Japan)

^b JAPAN SCIENCE AND TECHNOLOGY AGENCY   (Japan)

Author keywords

PROTEINS

Indexed keywords

FEAST FAMINE REGULATORY PROTEIN; LYSINE; PROTEIN; TRANSCRIPTION FACTOR; UNCLASSIFIED DRUG;

ARTICLE; CRYSTAL STRUCTURE; LIGAND BINDING; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN STRUCTURE; PYROCOCCUS; SIGNAL TRANSDUCTION; TRANSCRIPTION REGULATION;

AMINO ACID SEQUENCE; ARCHAEAL PROTEINS; ARGININE; CRYSTALLOGRAPHY, X-RAY; DIMERIZATION; ISOLEUCINE; LIGANDS; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; PYROCOCCUS; SELENOMETHIONINE; TRANSCRIPTION FACTORS; TRANSCRIPTION, GENETIC;

ARCHAEA; BACTERIA (MICROORGANISMS); PYROCOCCUS;

EID: 35148829988     PISSN: 09692126     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.str.2007.07.018     Document Type: Article

References (40)

1. Agapay R.C., Savvides S.N., Van Driessche G., Devreese B., Van Beeumen J., Jongejan J.A., and Hagen W.R. Expression, purification, crystallization and preliminary crystallographic analysis of a stand-alone RAM domain with hydrolytic activity from the hyperthermophile Pyrococcus furiosus. Acta Crystallogr. Sect. F Struct. Biol. Cryst. Commun. 61 (2005) 914-916
2. Barlow D.J., and Thornton J.M. Ion-pairs in proteins. J. Mol. Biol. 168 (1983) 867-885
3. Brinkman A.B., Bell S.D., Lebbink R.J., de Vos W.M., and van der Oost J. The Sulfolobus solfataricus Lrp-like protein LysM regulates lysine biosynthesis in response to lysine availability. J. Biol. Chem. 277 (2002) 29537-29549
4. Brünger A.T. X-PLORE v3.1 Manual (1992), Yale University, New Haven, CT
5. Brünger A.T., Adams P.D., Clore G.M., DeLano W.L., Gros P., Grosse-Kunstleve R.W., Jiang J.S., Kuszewski J., Nilges M., Pannu N.S., et al. Crystallography and NMR system: a new software suite for macromolecular structure determination. Acta Crystallogr. D Biol. Crystallog. 54 (1998) 905-921
6. Calvo J.M., and Matthews R.G. The leucine-responsive regulatory protein, a global regulator of metabolism in Escherichia coli. Microbiol. Rev. 58 (1994) 466-490
7. CCP4 (Collaborative Computational Project, Number 4). The CCP4 suite: programs for protein crystallography. Acta Crystallogr. D Biol. Crystallogr. 50 (1994) 760-763
8. Chen S., and Calvo J.M. Leucine-induced dissociation of Escherichia coli Lrp hexadecamers to octamers. J. Mol. Biol. 319 (2002) 1031-1042
9. Chu B. Laser Light Scattering (1974), Academic Press, New York
10. de los Rios S., and Perona J.J. Structure of the Escherichia coli leucine-responsive regulatory protein Lrp reveals a novel octameric assembly. J. Mol. Biol. 366 (2007) 1589-1602
11. Engh R.A., and Huber R. Accurate bond and angle parameters for X-ray protein structure refinement. Acta Crystallogr. A 47 (1991) 392-400
12. González J.M., Masuchi Y., Robb F.T., Ammerman J.W., Maeder D.L., Yanagibayashi M., Tamaoka J., and Kato C. Pyrococcus horikoshii sp. nov., a hyperthermophilic archaeon isolated from a hydrothermal vent at the Okinawa Trough. Extremophiles 2 (1998) 123-130
13. Inoue H., Inagaki K., Eriguchi S., Tamura T., Esaki N., Soda K., and Tanaka H. Molecular characterization of the mde operon involved in L-methionine catabolism of Pseudomonas putida. J. Bacteriol. 179 (1997) 3956-3962
14. Jafri S., Evoy S., Cho K., Craighead H.G., and Winans S.C. An Lrp-type transcriptional regulator from Agrobacterium tumefaciens condenses more than 100 nucleotides of DNA into globular nucleoprotein complexes. J. Mol. Biol. 288 (1999) 811-824
15. Jones T.A., Zou J.Y., Cowan S.W., and Kjeldgaard M. Improved methods for building protein models in electron density maps and the location of errors in these models. Acta Crystallogr. A 47 (1991) 110-119
16. Koike H., Sakuma M., Mikami A., Amano N., and Suzuki M. A possible disk to cylinder transition of assemblies of feast/famine regulatory proteins, FFRPs. Proc. Jpn. Acad. 79B (2003) 63-69
17. Koike H., Ishijima S.A., Clowney L., and Suzuki M. The archaeal feast/famine regulatory protein: potential roles of its assembly forms for regulating transcription. Proc. Natl. Acad. Sci. USA 101 (2004) 2840-2845
18. Kölling R., and Lother H. AsnC: an autogenously regulated activator of asparagine synthase A transcription in Escherichia coli. J. Bacteriol. 164 (1985) 310-315
19. Koradi R., Billeter M., and Wüthrich K. MOLMOL: a program for display and analysis of macromolecular structures. J. Mol. Graph. 14 (1996) 51-55
20. Kudo N., Allen M.D., Koike H., Katsuya Y., and Suzuki M. Crystallization and secondary-structure determination of a protein of the Lrp/AsnC family from a hyperthermophilic archaeon. Acta Crystallogr. D Biol. Crystallogr. 57 (2001) 469-471
21. Leonard P.M., Smits S.H.J., Sedelnikova S.E., Brinkman A.B., de Vos W.M., van der Oost J., Rice D.W., and Rafferty J.B. Crystal structure of the Lrp-like transcriptional regulator from the archaeon Pyrococcus furiosus. EMBO J. 20 (2001) 990-997
22. Madhusudhan K.T., Luo J., and Sokatch J.R. In vitro transcriptional studies of the bkd operon of Pseudomonas putida: L-branched-chain amino acids and D-leucine are the inducers. J. Bacteriol. 181 (1999) 2889-2894
23. Marasco R., Varcamonti M., La Cara F., Ricca E., de Felice M., and Sacco M. In vivo footprinting analysis of Lrp binding to the ilvIH promoter region of Escherichia coli. J. Bacteriol. 176 (1994) 5197-5201
24. McDonald I.K., and Thornton J.M. Satisfying hydrogen bonding potential in proteins. J. Mol. Biol. 238 (1994) 777-793
25. McRee D.E. XtalView/Xfit: a versatile program for manipulating atomic coordinate and electron density. J. Struct. Biol. 125 (1999) 156-165
26. Nakano N., Okazaki N., Satoh S., Takio K., Kuramitsu S., Shinkai A., and Yokoyama S. Structure of the stand-alone RAM domain protein from Thermus thermophilus HB8. Acta Crystallogr. Sect. F Struct. Biol. Cryst. Commun. 62 (2006) 855-860
27. Peekhaus N., Tolner B., Poolman B., and Krämer R. The glutamate uptake regulatory protein (Grp) of Zymomonas mobilis and its relation to the global regulator Lrp of Escherichia coli. J. Bacteriol. 177 (1995) 5140-5147
28. Perrakis A., Sixma T.K., Wilson K.S., and Lamzin V.S. wARP: improvement and extension of crystallographic phases by weighted averaging multiple-refined dummy atomic models. Acta Crystallogr. D Biol. Crystallogr. 53 (1997) 448-455
29. Platko J.V., and Calvo J.M. Mutations affecting the ability of Escherichia coli Lrp to bind DNA, activate transcription, or respond to leucine. J. Bacteriol. 175 (1993) 1110-1117
30. Ren J., Sainsbury S., Combs S.E., Capper R.G., Jordan P.W., Berrow N.S., Stammers D.K., Saunders N.J., and Owens R.J. The structure and transcriptional analysis of a global regulator from Neisseria meningitides. J. Biol. Chem. 282 (2007) 14655-14664
31. Saiki R.K., Gelfand D.H., Stoffel S., Scharf S.J., Higuchi R., Horn G.T., Mullis K., and Erlich H.A. Primer-directed enzymatic amplification of DNA with a thermostable DNA polymerase. Science 239 (1988) 487-491
32. Sakuma M., Nakamura M., Koike H., and Suzuki M. Light scattering from assemblies of an archaeal feast/famine regulatory protein, DM1 (pot1216151). Proc. Jpn. Acad. 81B (2005) 110-116
33. Sali A., and Blundell T.L. Comparative protein modelling by satisfaction of spatial restraints. J. Mol. Biol. 234 (1993) 779-815
34. Suzuki M. Structure and function of the feast/famine regulatory proteins, FFRPs. Proc. Jpn. Acad. 79B (2003) 274-289
35. Suzuki M., Amano N., and Koike H. The DNA-binding domain of feast/famine regulatory protein, FFRP. Proc. Jpn. Acad. 79B (2003) 92-98
36. Thaw P., Sedelnikova S.E., Muranova T., Wiese S., Ayora S., Alonso J.C., Brinkman A.B., Akerboom J., van der Oost J., and Rafferty J.B. Structural insight into gene transcriptional regulation and effecter binding by the Lrp/AsnC family. Nucleic Acids Res. 34 (2006) 1439-1449
37. Woese C.R., Kandler O., and Wheelis M.L. Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya. Proc. Natl. Acad. Sci. USA 87 (1990) 4576-4579
38. Yokoyama K., and Suzuki M. Orthologous and paralogous FFRPs in E. coli and related proteobacteria. Proc. Jpn. Acad. 81B (2005) 129-139
39. Yokoyama K., Ebihara S., Kikuchi T., and Suzuki M. Binding of the feast/famine regulatory protein (FFRP) FL11 (pot0434017) to DNA in the "promoter to coding" region of gene fl11. Proc. Jpn. Acad. 81B (2005) 64-75
40. Yokoyama K., Ishijima S.A., Clowney L., Koike H., Aramaki H., Tanaka C., Makino K., and Suzuki M. Feast/famine regulatory proteins (FFRPs): Escherichia coli Lrp, AsnC and related archaeal transcription factors. FEMS Microbiol. Rev. 30 (2006) 89-108