Biochemical characterization of endonuclease v from the hyperthermophilic archaeon, Pyrococcus furiosus

Journal of Biochemistry

Volumn 155, Issue 5, 2014, Pages 325-333

  Kiyonari, Shinichi ^a,b   Egashira, Yuriko ^a,c   Ishino, Sonoko ^a   Ishino, Yoshizumi ^a  

^a KYUSHU UNIVERSITY   (Japan)

^b NAGOYA UNIVERSITY GRADUATE SCHOOL OF MEDICINE   (Japan)

^c SYSMEX CORPORATION   (Japan)

Author keywords

archaea; DNA repair; Endo V; hypoxanthine; Pyrococcus furiosus

Indexed keywords

ENDONUCLEASE V; INOSINE; POLYDEOXYRIBONUCLEOTIDE SYNTHASE; UNCLASSIFIED DRUG; DEOXYINOSINE; DEOXYRIBONUCLEASE (PYRIMIDINE DIMER); MAGNESIUM; RECOMBINANT PROTEIN; RNA;

ARTICLE; BACTERIAL GENOME; BIOCHEMISTRY; COMPLEX FORMATION; CONTROLLED STUDY; DNA STRAND; ENZYME ACTIVITY; ESCHERICHIA COLI; GEL MOBILITY SHIFT ASSAY; GENE PRODUCT; IN VITRO STUDY; MOLECULAR CLONING; NONHUMAN; PYROCOCCUS FURIOSUS; AMINO ACID SEQUENCE; ANALOGS AND DERIVATIVES; CHEMISTRY; ENZYME SPECIFICITY; ENZYME STABILITY; ENZYMOLOGY; GENETICS; ISOLATION AND PURIFICATION; METABOLISM; MOLECULAR GENETICS; SEQUENCE HOMOLOGY;

AMINO ACID SEQUENCE; DEOXYRIBONUCLEASE (PYRIMIDINE DIMER); ENZYME STABILITY; INOSINE; MAGNESIUM; MOLECULAR SEQUENCE DATA; PYROCOCCUS FURIOSUS; RECOMBINANT PROTEINS; RNA; SEQUENCE HOMOLOGY, AMINO ACID; SUBSTRATE SPECIFICITY;

EID: 84899793137     PISSN: 0021924X     EISSN: 17562651     Source Type: Journal    
DOI: 10.1093/jb/mvu010     Document Type: Article

References (36)

1. Lindahl, T. (1993) Instability and decay of the primary structure of DNA. Nature 362, 709-715
2. Gates, F.T. III and Linn, S. (1977) Endonuclease V of Escherichia coli. J. Biol. Chem. 252, 1647-1653
3. Demple, B. and Linn, S. (1982) On the recognition and cleavage mechanism of Escherichia coli endodeoxyribonuclease V, a possible DNA repair enzyme. J. Biol. Chem. 257, 2848-2855
4. Yao, M., Hatahet, Z., Melamede, R.J., and Kow, Y.W. (1994) Purification and characterization of a novel deoxyinosine- specific enzyme, deoxyinosine 30 endonuclease, from Escherichia coli. J. Biol. Chem. 269, 16260-16268
5. Yao, M. and Kow, Y.W. (1994) Strand-specific cleavage of mismatch-containing DNA by deoxyinosine 30-endonuclease from Escherichia coli. J. Biol. Chem. 269, 31390-31396
6. Yao, M. and Kow, Y.W. (1996) Cleavage of insertion/ deletion mismatches, flap and pseudo-Y DNA structures by deoxyinosine 3-endonuclease from Escherichia coli. J. Biol. Chem. 271, 30672-30676
7. Guo, G. and Weiss, B. (1998) Endonuclease V (nfi) mutant of Escherichia coli K-12. J. Bacteriol. 180, 46-51
8. Schouten, K.A. and Weiss, B. (1999) Endonuclease V protects Escherichia coli against specific mutations caused by nitrous acid. Mutat. Res. 435, 245-254
9. Weiss, B. (2001) Endonuclease V of Escherichia coli prevents mutations from nitrosative deamination during nitrate/ nitrite respiration. Mutat. Res. 461, 301-309
10. Yao, M. and Kow, Y.W. (1995) Interaction of deoxyinosine 30-endonuclease from Escherichia coli with DNA containing deoxyinosine. J. Biol. Chem. 270, 28609-28616
11. Aravind, L., Walker, D.R., and Koonin, E.V. (1999) Conserved domains in DNA repair proteins and evolution of repair systems. Nucleic Acids Res. 27, 1223-1242
12. Cao, W. (2013) Endonuclease V: an unusual enzyme for repair of DNA deamination. Cell. Mol. Life. Sci. 70, 3145-3156
13. Huang, J., Lu, J., Barany, F., and Cao, W. (2001) Multiple cleavage activities of endonuclease V from Thermotoga maritima: recognition and strand nicking mechanism. Biochemistry 40, 8738-8748
14. Huang, J., Lu, J., Barany, F., and Cao, W. (2002) Mutational analysis of endonuclease V from Thermotoga maritima. Biochemistry 41, 8342-8350
15. Feng, H., Dong, L., Klutz, A. M., Aghaebrahim, N., and Cao, W. (2005) Defining amino acid residues involved in DNA-protein interactions and revelation of 3-exonuclease activity in endonuclease V. Biochemistry 44, 11486-11495
16. Feng, H., Dong, L., and Cao, W. (2006) Catalytic mechanism of endonuclease V: a catalytic and regulatory twometal model. Biochemistry 45, 10251-10259
17. Dalhus, B., Arvai, A.S., Rosnes, I., Olsen, ?E., Backe, P.H., Alseth, I., Gao, H., Cao, W., Tainer, J.A., and Bj?a? s, M. (2009) Structures of endonuclease V with DNA reveal initiation of deaminated adenine repair. Nat. Struct. Mol. Biol. 16, 138-143
18. Moe, A., Ringvoll, J., Nordstrand, L.M., Eide, L., Bj?a? s, M., Seeberg, E., Rognes, T., and Klungland, A. (2003) Incision at hypoxanthine residues in DNA by a mammalian homologue of the Escherichia coli antimutator enzyme endonuclease V. Nucleic Acids Res. 31, 3893-3900
19. Mi, R., Alford-Zappala, M., Kow, Y.W., Cunningham, R.P., and Cao, W. (2012) Human endonuclease V as a repair enzyme for DNA deamination. Mutat. Res. 735, 12-18
20. Liu, J., He, B., Qing, H., and Kow, Y.W. (2000) A deoxyinosine specific endonuclease from hyperthermophile, Archaeoglobus fulgidus: a homolog of Escherichia coli endonuclease V. Mutat. Res. 461, 169-177
21. Kanugula, S., Pauly, G.T., Moschel, R.C., and Pegg, A.E. (2005) A bifunctional DNA repair protein from Ferroplasma acidarmanus exhibits O6-alkylguanine- DNA alkyltransferase and endonuclease V activities. Proc. Natl Acad. Sci. USA 102, 3617-3622
22. Emptage, K., ONeill, R., Solovyova, A., and Connolly, B.A. (2008) Interplay between DNA polymerase and proliferating cell nuclear antigen switches off base excision repair of uracil and hypoxanthine during replication in archaea. J. Mol. Biol. 383, 762-771
23. Iwai, S. (2006) Chemical synthesis of oligonucleotides containing damaged bases for biological studies. Nucleosides Nucleotides Nucleic Acids 25, 561-582
24. Komori, K., Sakae, S., Fujikane, R., Morikawa, K., Shinagawa, H., and Ishino, Y. (2000) Biochemical characterization of the Hjc holliday junction resolvase of Pyrococcus furiosus. Nucleic Acids Res. 28, 4544-4551
25. Hosfield, D.J., Frank, G., Weng, Y., Tainer, J.A., and Shen, B. (1998) Newly discovered archaebacterial flap endonucleases show a structure-specific mechanism for DNA substrate binding and catalysis resembling human flap endonuclease-1. J. Biol. Chem. 273, 27154-27161
26. Keppetipola, N. and Shuman, S. (2005) Characterization of a thermophilic ATP-dependent DNA ligase from the euryarchaeon Pyrococcus horikoshii. J. Bacteriol. 187, 6902-6908
27. Kiyonari, S., Tahara, S., Shirai, T., Iwai, S., Ishino, S., and Ishino, Y. (2009) Biochemical properties and base excision repair complex formation of apurinic/apyrimidinic endonuclease from Pyrococcus furiosus. Nucleic Acids Res. 37, 6439-6453
28. Morita, Y., Shibutani, T., Nakanishi, N., Nishikura, K., Iwai, S., and Kuraoka, I. (2013) Human endonuclease V is a ribonuclease specific for inosine-containing RNA. Nat. Commun. 4, 2273
29. Vik, E.S., Nawaz, M. S., Andersen, P., Fladeby, C., Bj?a? s, M., Dalhus, B., and Alseth, I. (2013) Endonuclease V cleaves at inosines in RNA. Nat. Commun. 4, 2271
30. Connolly, B.A. (2009) Recognition of deaminated bases by archaeal family-B DNA polymerases. Biochem. Soc. Trans. 37, 65-68
31. Kiyonari, S., Takayama, K., Nishida, H., and Ishino, Y. (2006) Identification of a novel binding motif in Pyrococcus furiosus DNA ligase for the functional interaction with proliferating cell nuclear antigen. J. Biol. Chem. 281, 28023-28032
32. Kiyonari, S., Uchimura, M., Shirai, T., and Ishino, Y. (2008) Physical and functional interactions between uracil-DNA glycosylase and proliferating cell nuclear antigen from the euryarchaeon Pyrococcus furiosus. J. Biol. Chem. 283, 24185-24193
33. Kiyonari, S., Tahara, S., Uchimura, M., Shirai, T., Ishino, S., and Ishino, Y. (2009) Studies on the base excision repair (BER) complex in Pyrococcus furiosus. Biochem. Soc. Trans. 37, 79-82
34. Vivona, J.B. and Kelman, Z. (2003) The diverse spectrum of sliding clamp interacting proteins. FEBS Lett. 546, 167-172
35. Gray, M. W. (2013) Evolutionary origin of RNA editing. Biochemistry 51, 5235-5242
36. Agris, P.F., Vendeix, F.A., and Graham, W.D. (2007) tRNAs wobble decoding of the genome: 40 years of modification. J. Mol. Biol. 366, 1-13