Spectroscopic characterization of the isolated heme-bound PAS-B domain of neuronal PAS domain protein 2 associated with circadian rhythms

FEBS Journal

Volumn 272, Issue 16, 2005, Pages 4153-4162

  Koudo, Ryoji ^a   Kurokawa, Hirofumi ^a   Sato, Emiko ^a   Igarashi, Jotaro ^a   Uchida, Takeshi ^b   Sagami, Ikuko ^a,c   Kitagawa, Teizo ^b   Shimizu, Toru ^a  

^a TOHOKU UNIVERSITY   (Japan)

^b OKAZAKI INSTITUTE FOR INTEGRATIVE BIOSCIENCE   (Japan)

^c KYOTO PREFECTURAL UNIVERSITY   (Japan)

Author keywords

Circadian rhythms; Heme sensor protein; PAS domain; Resonance Raman spectroscopy; Transcription

Indexed keywords

ALANINE; HEMOPROTEIN; HISTIDINE; IRON COMPLEX; PROTEIN NPAS2; TRANSCRIPTION FACTOR; UNCLASSIFIED DRUG;

ABSORPTION SPECTROPHOTOMETRY; ARTICLE; BINDING KINETICS; CIRCADIAN RHYTHM; PRIORITY JOURNAL; PROTEIN BINDING; PROTEIN EXPRESSION; RAMAN SPECTROMETRY; WILD TYPE;

ANIMALS; BASE SEQUENCE; BASIC HELIX-LOOP-HELIX TRANSCRIPTION FACTORS; CHROMATOGRAPHY, GEL; CIRCADIAN RHYTHM; DNA PRIMERS; HEME; MICE; MICE, INBRED C57BL; MUTAGENESIS, SITE-DIRECTED; NERVE TISSUE PROTEINS; PROTEIN BINDING; RECOMBINANT PROTEINS; SPECTRUM ANALYSIS, RAMAN; TRANSCRIPTION FACTORS;

PHYSETER CATODON;

EID: 23844468462     PISSN: 1742464X     EISSN: None     Source Type: Journal    
DOI: 10.1111/j.1742-4658.2005.04828.x     Document Type: Article

References (34)

1. Hogenesch JB, Gu YZ, Jain S & Brandfield CA (1998) The basic-helix-loop-helix-PAS orphan MOPs forms transcriptionally active complexes with circadian and hypoxia factors. Proc Natl Acad Sci USA 95, 5474-5479.
2. Rutter J, Reick M, Wu LC & McKnight SL (2001) Regulation of Clock and NPAS2 DNA Binding by the Redox State of NAD Cofactors. Science 293, 510-514.
3. Reppert SM & Weaver DR (2002) Coordination of circadian timing in mammals. Nature 418, 935-941.
4. Isojima Y, Okumura N & Nagai K (2003) Molecular mechanism of mammalian circadian clock. J Biochem (Tokyo) 134, 777-784.
5. Green CB & Menaker M (2003) Clock on the brain. Science 301, 319-320.
6. Van Gelder RN, Herzog ED, Schwartz WJ & Taghert PH (2003) Circadian rhythms: in the loop at last. Science 300, 1534-1535.
7. Schibler U (2003) Liver regeneration clocks on. Science 302, 234-235.
8. Oishi K, Miyazaki K, Kadota K, Kikuno R, Nagase T, Atsumi G, Ohkura N, Azama T, Mesaki M, Yokimasa S, et al. (2003) Genome-wide expression analysis of mouse liver reveals CLOCK-regulated circadian output genes. J Biol Chem 278, 41519-41527.
9. Hirayama J, Namura H, Ishikawa T, Kobayashi Y & Todo T (2003) Functional and structural analyses of cryptochrome: vertebrate Cry regions responsible for interaction with the Clock:BMAL heterodimer and its nuclear locations. J Biol Chem 278, 35620-35628.
10. Brandstaetter R (2004) Circadian lessons from peripheral clocks: is the time of the mammalian pacemaker up? Proc Natl Acad Sci USA 101, 5699-5700.
11. Reick M, Garcia JA, Dudley C & McKnight SL (2001) NPAS2: an analog of Clock operative in the mammalian forebrain. Science 293, 506-509.
12. Dudley CA, Erbal-Sieler C, Estill SJ, Reick M, Franken P, Pitts S & McKnight SL (2003) Altered patterns of sleep and behavioral adaptability in NPAS2-deficient mice. Science 301, 379-383.
13. McNamara P, Seo SP, Rudic RD, Sehgal A, Chakravarti D & FitzGerald GA (2001) Regulation of CLOCK and MOP4 by nuclear hormone receptors in the vasculature: a humoral mechanism to reset a peripheral clock. Cell 105, 877-889.
14. Dioum EM, Rutter J, Tuckerman JR, Gonzalez G, Gilles-Gonzalez MA & McKnight SL (2002) NPAS2: a gas-responsive transcription factor. Science 298, 2385-2339.
15. Kaasik K & Lee CC (2004) Reciprocal regulation of haem biosynthesis and the circadian clock in mammals. Nature 430, 467-471.
16. Klatt P, Schmidt K, Werner ER & Mayer B (1996) Determination of nitric oxide synthase cofactors: heme, FAD, FMN, and tetrahydrobiopterin. Methods Enzymol 268, 358-365.
17. Hargrove MS, Barrick D & Olson JS (1996) The association rate constant for heme binding to globin is independent of protein structure. Biochemistry 35, 11293-11299.
18. Hagrove MS, Singleton EW, Quillin ML, Qrtiz LA, Phillips GN, Jr Mathews AJ & Olson JS (1994) His64 (E7)-Tyr apomyoglobin as a reagent for measuring rates of hemin dissociation. J Biol Chem 269, 4207-4214.
19. Mathews FS (2001) b-Type cytochrome electron carriers: cytochromes 6562 and b5, and Flavocytochrome b2. In Handbook of Metalloproteins (Messer-Schmidt A, Huber R, Poulos T & Wieghardt K, eds), vol. 1, pp. 159-171. John Wiley & Sons, Chichester.
20. Antonini E & Brunori M (1971) Hemoglobin and Myoglobin in Their Reactions with Ligands. Elsevier/North-Holland Biomedical Press, Amsterdam.
21. Sato E, Sagami I, Uchida T, Sato A, Kitagawa T, Igarashi J & Shimizu T (2004) SOUL in mouse eye is a new hexameric heme-bound protein with characteristic optical absorption, resonance Raman spectral, and heme-binding properties. Biochemistry 43, 14189-14198.
22. Jain R & Chan MK (2003) Mechanisms of ligand discrimination by heme proteins. J Biol Inorg Chem 8, 1-11.
23. Kurokawa H, Lee DS, Watanabe M, Sagami I, Mikami B, Raman CS & Shimizu T (2004) A redox-controlled molecular switch revealed by the crystal structure of a bacterial heme PAS sensor. J Biol Chem 279, 20189-20193.
24. Harper SM, Neil LC & Gardner KH (2003) Structural basis of a phototropin light switch. Science 301, 1541-1544.
25. Crosson S & Moffat K (2001) Structure of flavin-binding plant photoreceptor domain: insights into light-mediated signal transduction. Proc Natl Acad Sci USA 98, 2995-3000.
26. Vreede J, van der Horst MA, Hellingwerf KJ, Crielaard W & and van Aalten DMF (2003) PAS domains: common structural and common flexibility. J Biol Chem 278, 18434-18439.
27. Yildiz O, Doi M, Yujnovsky I, Cardone L, Berndt A, Henning S, Schulze S, Urbanke C, Sassone-Corsi P & Wolf E (2005) Crystal structure and interactions of the PAS repeat region of the Drosophila clock protein, PERIOD. Mol Cell 17, 69-82.
28. Erbel PJA, Card PB, Karakuzu O, Bruick RK & Gardner KH (2003) Structural basis for PAS domain heterodimerization in the basic-helix-loop- helix-PAS transcription factor hypoxia-inducible factor. Proc Natl Acad Sci USA 100, 15504-15509.
29. Amezcua CA, Harper SM, Rutter J & Gardner KH (2002) Structure and interactions of PAS kinase N-terminal PAS domain: model for intramolecular kinase regulation. Structure 10, 1349-1361.
30. 15N chemical shift assignment of the N-terminal PAS domain of mNPAS2. J Biomol NMR 21, 383-384.
31. Uchida T, Sato E, Sato A, Sagami I, Shimizu T & Kitagawa T (2005) CO-dependent activity controlling mechanism of heme-containing CO-sensor protein, NPAS2. J Biol Chem 280, 21358-21368.
32. Park H, Suquet C, Satterlee JD & Kang CH (2004) Insights into signal transduction involving PAS domain oxygen-sensing heme proteins from the X-ray crystal structure of Escherichia coli Dos heme domain (Ec DosH). Biochemistry 43, 2738-2746.
33. Key J & Moffat K (2005) Crystal structures of deoxy and CO-bound bjFixLH reveal details of ligand recognition and signaling. Biochemistry 44, 4627-4635.
34. Yoshimura T, Sagami I, Sasakura Y & Shimizu T (2003) Relationships between heme incorporation, tetramer formation, and catalysis of a heme-regulated phosphodiesterase from Escherichia coli: a study of deletion and site-directed mutants. J Biol Chem 278, 53105-53111.