Purification, Crystallization and Preliminary X-Ray Diffraction Analysis of Exodeoxyribonuclease III from Crenarchaeon Sulfolobus tokodaii Strain 7

Shuichi Miyamoto; Chieko Naoe; Masaru Tsunoda; Kazuo T. Nakamura

doi:10.4236/csta.2013.24021

Home > Journals > Chemistry & Materials Science > CSTA

CSTA> Vol.2 No.4, December 2013

Share This Article:

Open Access

Purification, Crystallization and Preliminary X-Ray Diffraction Analysis of Exodeoxyribonuclease III from Crenarchaeon Sulfolobus tokodaii Strain 7

Abstract Full-Text HTML

Download as PDF (Size:209KB) PP. 155-158

DOI: 10.4236/csta.2013.24021 3,678 Downloads 5,398 Views Citations

Author(s) Leave a comment

Shuichi Miyamoto, Chieko Naoe, Masaru Tsunoda, Kazuo T. Nakamura

Affiliation(s)

Faculty of Pharmaceutical Sciences, Sojo University, Kumamoto, Japan.
Faculty of Pharmacy, Iwaki Meisei University, Iwaki, Japan.
School of Pharmacy, Showa University, Tokyo, Japan.

ABSTRACT

Exodeoxyribonuclease III (EXOIII) acts as a 3’→5’ exonuclease and is homologous to purinic/apyrimidinic (AP) endonuclease (APE), which plays an important role in the base excision repair pathway. To structurally investigate the reaction and substrate recognition mechanisms of EXOIII, a crystallographic study of EXOIII from Sulfolobus tokodaii strain 7 was carried out. The purified enzyme was crystallized by using the hanging-drop vapor-diffusion method. The crystals belonged to space group C2, with unit-cell parameters a = 154.2, b = 47.7, c = 92.4 ?, β = 125.8° and diffracted to 1.5 ? resolution.

KEYWORDS

Crenarchaeon; Crystallization; Exodeoxyribonuclease; Sulfolobus tokodaii; X-Ray Diffraction

Conflicts of Interest

The authors declare no conflicts of interest.

Cite this paper

S. Miyamoto, C. Naoe, M. Tsunoda and K. Nakamura, "Purification, Crystallization and Preliminary X-Ray Diffraction Analysis of Exodeoxyribonuclease III from Crenarchaeon Sulfolobus tokodaii Strain 7," Crystal Structure Theory and Applications, Vol. 2 No. 4, 2013, pp. 155-158. doi: 10.4236/csta.2013.24021.

References

[1]	T. Lindahl, “Instability and Decay of the Primary Structure of DNA,” Nature, Vol. 362, No. 6422, 1993, pp. 709-715. http://dx.doi.org/10.1038/362709a0

[2]	B. Demple and L. Harrison, “Repair of Oxidative Damage to DNA: Enzymology and Biology,” Annual Review of Biochemistry, 1994, Vol. 63, 1994, pp. 915-948.

[3]	H. E. Krokan, R. Standal and G. Slupphang, “DNA Glycosylases in the Base Excision Repair of DNA,” Biochemical Journal, 1997, Vol. 325, pp. 1-16.

[4]	J. Baute and A. Depicker, “Base Excision Repair and Its Role in Maintaining Genome Stability,” Critical Reviews in Biochemistry and Molecular Biology, Vol. 43, No. 4, 2008, pp. 239-276. http://dx.doi.org/10.1080/10409230802309905

[5]	T. Lindahl and B. Nyberg, “Rate of Depurination of Native Deoxyribonucleic Acid,” Biochemistry, Vol. 11, No. 19, 1972, pp. 3610-3618. http://dx.doi.org/10.1021/bi00769a018

[6]	L. A. Loeb and B. D. Preston, “Mutagenesis by Apurinic/ Apyrimidinic Sites,” Annual Review of Genetics, Vol. 20, 1986, pp. 201-230. http://dx.doi.org/10.1146/annurev.ge.20.120186.001221

[7]	S. L. Yu, S. K. Lee, R. E. Johnson, L. Prakash and S. Prakash, “The Stalling of Transcription at Abasic Sites Is Highly Mutagenic,” Molecular and Cellular Biology, Vol. 23, No. 1, 2003, pp. 382-388. http://dx.doi.org/10.1128/MCB.23.1.382-388.2003

[8]	P. W. Doetsch and R. P. Cunningham, “The Enzymology of Apurinic/Apyrimidinic Endonucleases,” Mutation Research, Vol. 236, No. 2-3, 1990, pp. 173-201. http://dx.doi.org/10.1016/0921-8777(90)90004-O

[9]	G. Barzilay and I. D. Hickson, “Structure and Function of Apurinic/Apyrimidinic Endonucleases,” Bioessays, Vol. 17, No. 8, 1995, pp. 713-719. http://dx.doi.org/10.1002/bies.950170808

[10]	J. P. Erzberger, D. Barsky, O. D. Scharer, M. E. Colvin and D. M. Wilson III, “Elements in Abasic Site Recognition by the Major Human and Escherichia coli Apurinic/ Apyrimidinic Endonucleases,” Nucleic Acids Research, Vol. 26, No. 11, 1998, pp. 2771-2778. http://dx.doi.org/10.1093/nar/26.11.2771

[11]	D. Lu, J. Silhan, J. T. MacDonald, E. P. Carpenter, K. Jensen, C. M. Tang, G. S. Baldwin and P. S. Freemont, “Structural Basis for the Recognition and Cleavage of Abasic DNA in Neisseria meningitidis,” Proceedings of the National Academy of Sciences of the United States of America, Vol. 109, No. 42, 2012, pp. 16852-16857. http://dx.doi.org/10.1073/pnas.1206563109

[12]	C. D. Mol, C.-F. Kuo, M. M. Thayer, R. P. Cunningham and J. A. Tainer, “Structure and Function of the Multifunctional DNA-Repair Enzyme Exonuclease III,” Nature, Vol. 374, No. 6520, 1995, pp. 381-386. http://dx.doi.org/10.1038/374381a0

[13]	M. A. Gorman, S. Morera, D. G. Rothwell, E. de La Fortelle, C. D. Mol, J. A. Tainer, I. D. Hickson and P. S. Freemont, “The Crystal Structure of the Human DNA Repair Endonuclease HAP1 Suggests the Recognition of Extra-Helical Deoxyribose at DNA Abasic Sites,” EMBO Journal, Vol. 16, No. 21, 1997, pp. 6548-6558. http://dx.doi.org/10.1093/emboj/16.21.6548

[14]	Y. Kawarabayasi, Y. Hino, H. Horikawa, K. Jin-no, M. Takahashi, M. Sekine, S. Baba, A. Ankai, H. Kosugi, A. Hosoyama, S. Fukui, Y. Nagai, K. Nishijima, R. Otsuka, H. Nakazawa, M. Takamiya, Y. Kato, T. Yoshizawa, T. Tanaka, Y. Kudoh, J. Yamazaki, N. Kushida, A. Oguchi, K. Aoki, S. Masuda, M. Yanagii, M. Nishimura, A. Yamagishi, T. Oshima and H. Kikuchi, “Complete Genome Sequence of an Aerobic Thermoacidophilic Crenarchaeon, Sulfolobus tokodaii Strain 7,” DNA Research, Vol. 8, No. 4, 2001, pp. 123-140. http://dx.doi.org/10.1093/dnares/8.4.123

[15]	Z. Otwinowski and W. Minor, “Processing of X-Ray Diffraction Data Collected in Oscillation Mode,” Methods in Enzymology, Vol. 276, 1997, pp. 307-326. http://dx.doi.org/10.1016/S0076-6879(97)76066-X

[16]	B. W. Matthews, “Solvent Content of Protein Crystals,” Journal of Molecular Biology, Vol. 33, No. 2, 1968, pp. 491-497. http://dx.doi.org/10.1016/0022-2836(68)90205-2

[17]	A. Vagin, and A. Teplyakov, “MOLREP: An Automated Program for Molecular Replacement,” Journal of Applied Crystallography, Vol. 30, Part 10, 1997, pp. 1022-1025. http://dx.doi.org/10.1107/S0021889897006766

[18]	Collaborative Computational Project, Number 4, “The CCP4 Suite: Programs for Protein Crystallography,” Acta Crystallographica Section D, Vol. 50, Part 5, 1994, pp. 760-763. http://dx.doi.org/10.1107/S0907444994003112