Visualizing a circadian clock protein: Crystal structure of KaiC and functional insights

Molecular Cell

Volumn 15, Issue 3, 2004, Pages 375-388

  Pattanayek, Rekha ^a   Wang, Jimin ^b   Mori, Tetsuya ^a   Xu, Yao ^a   Johnson, Carl Hirschie ^a   Egli, Martin ^a  

^a VANDERBILT UNIVERSITY   (United States)

^b Bass Center for Structural Biology   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ADENOSINE TRIPHOSPHATE; PROTEIN SUBUNIT; TRANSCRIPTION FACTOR CLOCK; TRANSCRIPTION FACTOR KAIC; UNCLASSIFIED DRUG;

ARTICLE; AUTOPHOSPHORYLATION; CIRCADIAN RHYTHM; COMPLEX FORMATION; CRYSTAL STRUCTURE; MOLECULAR EVOLUTION; MUTATION; NONHUMAN; PROTEIN BINDING; PROTEIN PURIFICATION; STRUCTURE ANALYSIS; SYNECHOCOCCUS ELONGATUS;

ADENOSINE TRIPHOSPHATE; BACTERIAL PROTEINS; CIRCADIAN RHYTHM; CYANOBACTERIA; EVOLUTION, MOLECULAR; LIGHTING; MUTATION; PHOSPHORYLATION; PROTEIN STRUCTURE, TERTIARY; TIME FACTORS;

CYANOBACTERIA; SYNECHOCOCCUS; SYNECHOCOCCUS ELONGATUS;

EID: 4143103631     PISSN: 10972765     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.molcel.2004.07.013     Document Type: Article

References (48)

1. Abrahams J.P., Leslie A.G.W., Lutter R., Walker J.E. Structure at 2.8 Å resolution of F1 ATPase from bovine heart mitochondria. Nature. 370:1994;621-628
2. Brünger A.T. Free R value. a novel statistical quantity for assessing the accuracy of crystal structures Nature. 355:1992;472-475
3. 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. Crystallogr. 54:1998;905-921
4. CCP4 The CCP4 (Collaborative Computational Project Number 4) suite. programs for protein crystallography Acta Crystallogr. D. Biol. Crystallogr. 50:1994;760-763
5. Ditty J.L., Williams S.B., Golden S.S. A cyanobacterial circadian timing mechanism. Annu. Rev. Genet. 37:2003;513-543
6. Dunlap J.C., Loros J.J., DeCoursey P.J. Chronobiology. Biological Timekeeping:2004;Sinauer, Sunderland, MA
7. Egelman E.H. Bacterial helicases. J. Struct. Biol. 124:1998;123-128
8. Garces R.G., Wu N., Gillon W., Pai E.F. Anabaena circadian clock proteins KaiA and KaiB reveal potential common binding site to their partner KaiC. EMBO J. 23:2004;1688-1698
9. 1-ATPase. Nature. 409:2001;637-641
10. Hayashi F., Suzuki H., Iwase R., Uzumaki T., Miyake A., Shen J.-R., Imada K., Furukawa Y., Yonekura K., Namba K., Ishiura M. ATP-induced hexameric ring structure of the cyanobacterial circadian clock protein KaiC. Genes Cells. 8:2003;287-296
11. Hayashi F., Ito H., Fujita M., Iwase R., Uzumaki T., Ishiura M. Stoichiometric interactions between cyanobacterial clock proteins KaiA and KaiC. Biochem. Biophys. Res. Commun. 316:2004;195-202
12. Holm L., Sander C. Touring protein fold space with Dali/FSSP. Nucleic Acids Res. 26:1998;316-319
13. Huang, C.C., Couch, G.S., Pettersen, E.F., and Ferrin, T.E. (1996). Chimera: an extensible molecular modeling application constructed using standard components. Pacific Symposium on Biocomputing 1, 724.
14. Ishiura M., Kutsuna S., Aoki S., Iwasaki H., Andersson C.R., Tanabe A., Golden S.S., Johnson C.H., Kondo T. Expression of a gene cluster kaiABC as a circadian feedback process in cyanobacteria. Science. 281:1998;1519-1523
15. Iwasaki H., Taniguchi Y., Kondo T., Ishiura M. Physical interactions among circadian clock proteins, KaiA, KaiB and KaiC, in Cyanobacteria. EMBO J. 18:1999;1137-1145
16. Iwasaki H., Nishiwaki T., Kitayama Y., Nakajima M., Kondo T. KaiA-stimulated KaiC phosphorylation in circadian timing loops in cyanobacteria. Proc. Natl. Acad. Sci. USA. 99:2002;15788-15793
17. Jancarik J., Kim S.-H. Sparse matrix sampling. a screening method for crystallization of proteins J. Appl. Crystallogr. 24:1991;409-411
18. Johnson C.H. Precise circadian clocks in prokaryotic cyanobacteria. Curr. Issues Mol. Biol. 6:2004;103-110
19. Jones T.A., Kjeldgaard M. Electron-density map interpretation. Meth. Enzymol. 277:1997;173-208
20. Kabsch W. Automatic processing of rotation diffraction data from crystals of initially unknown symmetry and cell constants. J. Appl. Crystallogr. 26:1993;795-800
21. Kageyama H., Kondo T., Iwasaki H. Circadian formation of clock protein complexes by KaiA, KaiB, KaiC, and SasA in cyanobacteria. J. Biol. Chem. 278:2003;2388-2395
22. Katayama M., Tsinoremas N.F., Kondo T., Golden S.S. cpmA, a gene involved in an output pathway of the cyanobacterial circadian system. J. Bacteriol. 181:1999;3516-3524
23. Kitayama Y., Iwasaki H., Nishiwaki T., Kondo T. KaiB functions as an attenuator of KaiC phosphorylation in the cyanobacterial circadian clock system. EMBO J. 22:2003;1-8
24. Kondo T., Strayer C.A., Kulkarni R.D., Taylor W., Ishiura M., Golden S.S., Johnson C.H. Circadian rhythms in prokaryotes. luciferase as a reporter of circadian gene expression in cyanobacteria Proc. Natl. Acad. Sci. USA. 90:1993;5672-5676
25. Laskey R.A., Madine M.A. A rotary pumping model for helicase function of MCM proteins at a distance from replication forks. EMBO Rep. 4:2003;26-30
26. Leipe D.D., Aravind L., Grishin N.V., Koonin E.V. The bacterial replicative helicase DnaB evolved from a RecA duplication. Genome Res. 10:2000;5-16
27. Liu Y., Tsinoremas N.F., Johnson C.H., Lebedeva N.V., Golden S.S., Ishiura M., Kondo T. Circadian orchestration of gene expression in cyanobacteria. Genes Dev. 9:1995;1469-1478
28. Min H., Liu Y., Johnson C.H., Golden S.S. Phase determination of circadian gene expression in Synechococcus elongatus PCC 7942. J. Biol. Rhythms. 19:2004;103-112
29. Mori T., Johnson C.H. Circadian programming in cyanobacteria. Sem. Cell Develop. Biol. 12:2001;271-278
30. Mori T., Saveliev S.V., Xu Y., Stafford W.F., Cox M.M., Inman R.B., Johnson C.H. Circadian clock protein KaiC forms ATP-dependent hexameric rings and binds DNA. Proc. Natl. Acad. Sci. USA. 99:2002;17203-17208
31. Nakahira Y., Katayama M., Miyashita H., Kutsuna S., Iwasaki H., Oyama T., Kondo T. Global gene repression by KaiC as a master process of prokaryotic circadian system. Proc. Natl. Acad. Sci. USA. 101:2004;881-885
32. Nicholls A., Bharadwaj R., Honig B. Grasp. graphical representation and analysis of surface properties Biophys. J. 64:1993;166-170
33. Nishiwaki T., Iwasaki H., Ishiura M., Kondo T. Nucleotide binding and autophosphorylation of the clock protein KaiC as a circadian timing process of cyanobacteria. Proc. Natl. Acad. Sci. USA. 97:2000;495-499
34. Otwinowski Z., Minor W. Processing of X-ray diffraction data collected in oscillation mode. Meth. Enzymol. 276:1997;307-326
35. Sanner M.F., Olson A.J., Spehner J.C. Reduced surface. an efficient way to compute molecular surfaces Biopolymers. 38:1996;305-320
36. Singleton M.R., Sawaya M.R., Ellenberger T., Wigley D.B. Crystal structure of T7 gene 4 helicase indicates a mechanism for sequential hydrolysis of nucleotides. Cell. 101:2000;589-600
37. Story R.M., Weber I.T., Steitz T.A. The structure of the E. coli recA protein monomer and polymer. Nature. 355:1992;318-325
38. Taniguchi Y., Yamaguchi A., Hijikata A., Iwasaki H., Kamagata K., Ishiura M., Go M., Kondo T. Two KaiA-binding domains of cyanobacterial circadian clock protein KaiC. FEBS Lett. 496:2001;86-90
39. Terwilliger T.C. Maximum likelihood density modification. Meth. Enzymol. 276:1997;530-537
40. Tong L., Rossmann M.G. Rotation function calculations with GLRF program. Acta Crystallogr. A. 46:1990;783-792
41. Toth E.A., Li Y., Sawaya M.R., Cheng Y., Ellenberger T. The crystal structure of the bifunctional primase-helicase of bacteriophage T7. Cell. 12:2003;1113-1123
42. Uzumaki T., Fujita M., Nakatsu T., Hayashi F., Shibata H., Itoh N., Kato H., Ishiura M. Role of KaiA functional domains in circadian rhythms of cyanobacteria revealed by crystal structure. Nature Struct. Mol. Biol. 11:2004;623-631
43. Vakonakis I., Sun J., Wu T., Holzenburg A., Golden S.S., LiWang A.C. NMR structure of the KaiC-interacting C-terminal domain of KaiA, a circadian clock protein. implications for the KaiA-KaiC interaction Proc. Natl. Acad. Sci. USA. 101:2004;1479-1484
44. VanLoock M.S., Yu X., Yang S., Lai A.L., Low C., Campbell M.J., Egelman E.H. ATP-mediated conformational changes in the RecA filament. Structure. 11:2003;1-20
45. Williams S.B., Vakonakis I., Golden S.S., LiWang A.C. Structure and function from the circadian clock protein KaiA of Synechococcus elongatus. a potential clock input mechanism Proc. Natl. Acad. Sci. USA. 99:2002;15357-15362
46. Xu Y., Mori T., Johnson C.H. Cyanobacterial circadian clockwork. roles of KaiA, KaiB, and the kaiBC promoter in regulating KaiC EMBO J. 22:2003;2117-2126
47. Ye S., Vakonakis I., Ioerger T.R., LiWang A.C., Sacchettini J.C. Crystal structure of circadian clock protein KaiA from Synechococcus elongatus. J. Biol. Chem. 279:2004;20511-20518
48. Yu X., Egelman E.H. The RecA hexamer is a structural homologue of ring helicases. Nat. Struct. Biol. 4:1997;101-104